phd.bib

@incollection{achaz2014,
  title = {The {{Reproducibility}} of {{Adaptation}} in the {{Light}} of {{Experimental Evolution}} with {{Whole Genome Sequencing}}},
  booktitle = {Ecological {{Genomics}}},
  author = {Achaz, Guillaume and {Rodriguez-Verdugo}, Alejandra and Gaut, Brandon S. and Tenaillon, Olivier},
  editor = {Landry, Christian R. and {Aubin-Horth}, Nadia},
  year = {2014},
  volume = {781},
  pages = {211--231},
  publisher = {{Springer Netherlands}},
  address = {{Dordrecht}},
  doi = {10.1007/978-94-007-7347-9_11},
  isbn = {978-94-007-7346-2 978-94-007-7347-9},
  langid = {english}
}

@misc{adami1994,
  title = {Evolutionary {{Learning}} in the {{2D Artificial Life System}} "{{Avida}}"},
  author = {Adami, Chris and Brown, C Titus},
  year = {1994},
  publisher = {{ijk}},
  doi = {12345},
  abstract = {We present a new tierra-inspired arti cial life system with local interactions and two-dimensional geometry, based on an update mechanism akin to that of 2D cellular automata. We nd that the spatial geometry is conducive to the development of diversity and thus improves adaptive capabilities. We also demonstrate the adaptive strength of the system by breeding cells with simple computational abilities, and study the dependence of this adaptability on mutation rate and population size.},
  langid = {english},
  note = {\url{https://arxiv.org/abs/adap-org/9405003}}
}

@article{adami2006,
  title = {Digital Genetics: Unravelling the Genetic Basis of Evolution},
  shorttitle = {Digital Genetics},
  author = {Adami, Christoph},
  year = {2006},
  month = feb,
  journal = {Nature Reviews Genetics},
  volume = {7},
  number = {2},
  pages = {109--118},
  issn = {1471-0056, 1471-0064},
  doi = {10.1038/nrg1771},
  abstract = {Digital genetics, or the genetics of digital organisms, is a new field of research that has become possible as a result of the remarkable power of evolution experiments that use computers. Self-replicating strands of computer code that inhabit specially prepared computers can mutate, evolve and adapt to their environment. Digital organisms make it easy to conduct repeatable, controlled experiments, which have a perfect genetic `fossil record'. This allows researchers to address fundamental questions about the genetic basis of the evolution of complexity, genome organization, robustness and evolvability, and to test the consequences of mutations, including their interaction and recombination, on the fate of populations and lineages.},
  langid = {english}
}

@article{baba2006,
  title = {Construction of {{{\emph{Escherichia}}}}{\emph{ Coli}} {{K}}-12 In-frame, Single-gene Knockout Mutants: The {{Keio}} Collection},
  shorttitle = {Construction of {{{\emph{Escherichia}}}}{\emph{ Coli}} {{K}}-12 In-frame, Single-gene Knockout Mutants},
  author = {Baba, Tomoya and Ara, Takeshi and Hasegawa, Miki and Takai, Yuki and Okumura, Yoshiko and Baba, Miki and Datsenko, Kirill A and Tomita, Masaru and Wanner, Barry L and Mori, Hirotada},
  year = {2006},
  month = jan,
  journal = {Molecular Systems Biology},
  volume = {2},
  number = {1},
  issn = {1744-4292, 1744-4292},
  doi = {10.1038/msb4100050},
  langid = {english}
}

@article{batut2013,
  title = {In Silico Experimental Evolution: A Tool to Test Evolutionary Scenarios},
  shorttitle = {In Silico Experimental Evolution},
  author = {Batut, B{\'e}r{\'e}nice and Parsons, David P and Fischer, Stephan and Beslon, Guillaume and Knibbe, Carole},
  year = {2013},
  journal = {BMC Bioinformatics},
  volume = {14},
  number = {Suppl 15},
  pages = {S11},
  issn = {1471-2105},
  doi = {10.1186/1471-2105-14-S15-S11},
  abstract = {Comparative genomics has revealed that some species have exceptional genomes, compared to their closest relatives. For instance, some species have undergone a strong reduction of their genome with a drastic reduction of their genic repertoire. Deciphering the causes of these atypical trajectories can be very difficult because of the many phenomena that are intertwined during their evolution (e.g. changes of population size, environment structure and dynamics, selection strength, mutation rates...). Here we propose a methodology based on synthetic experiments to test the individual effect of these phenomena on a population of simulated organisms. We developed an evolutionary model - aevol - in which evolutionary conditions can be changed one at a time to test their effects on genome size and organization (e.g. coding ratio). To illustrate the proposed approach, we used aevol to test the effects of a strong reduction in the selection strength on a population of (simulated) bacteria. Our results show that this reduction of selection strength leads to a genome reduction of \textasciitilde 35\% with a slight loss of coding sequences (\textasciitilde 15\% of the genes are lost - mainly those for which the contribution to fitness is the lowest). More surprisingly, under a low selection strength, genomes undergo a strong reduction of the noncoding compartment (\textasciitilde 55\% of the noncoding sequences being lost). These results are consistent with what is observed in reduced Prochlorococcus strains (marine cyanobacteria) when compared to close relatives.},
  langid = {english}
}

@incollection{beslon2021,
  title = {Of {{Evolution}}, {{Systems}} and {{Complexity}}},
  booktitle = {Evolutionary {{Systems Biology}}: {{Advances}}, {{Questions}}, and {{Opportunities}}},
  author = {Beslon, Guillaume and Liard, Vincent and Parsons, David P. and {Rouzaud-Cornabas}, Jonathan},
  editor = {Crombach, Anton},
  year = {2021},
  pages = {1--18},
  publisher = {{Springer International Publishing}},
  address = {{Cham}},
  doi = {10.1007/978-3-030-71737-7_1},
  abstract = {The question of complexity in biological systems is recurrent in evolutionary biology and is central in complex systems science for obvious reasons. But this question is surprisingly overlooked by evolutionary systems biology. This comes unexpected given the roots of systems biology in complex systems science but also given that a proper understanding of the origin and evolution of complexity would provide clues for a better understanding of extant biological systems. In this chapter, we will explore the links between evolutionary systems biology and biological systems complexity, in terms of concepts, tools and results. In particular, we will show how complex models can be used to explore this question and show that complexity can spontaneously accumulate even in simple conditions owing to a ``complexity ratchet'' fuelled by sign epistasis.},
  isbn = {978-3-030-71737-7}
}

@article{blattner1997,
  title = {The {{Complete Genome Sequence}} of {{Escherichia}} Coli {{K-12}}},
  author = {Blattner, F. R.},
  year = {1997},
  month = sep,
  journal = {Science},
  volume = {277},
  number = {5331},
  pages = {1453--1462},
  issn = {00368075, 10959203},
  doi = {10.1126/science.277.5331.1453},
  langid = {english}
}

@article{brackley2016,
  title = {Stochastic {{Model}} of {{Supercoiling-Dependent Transcription}}},
  author = {Brackley, C. A. and Johnson, J. and Bentivoglio, A. and Corless, S. and Gilbert, N. and Gonnella, G. and Marenduzzo, D.},
  year = {2016},
  month = jun,
  journal = {Physical Review Letters},
  volume = {117},
  number = {1},
  pages = {018101},
  issn = {0031-9007, 1079-7114},
  doi = {10.1103/PhysRevLett.117.018101},
  langid = {english}
}

@article{brinza2013,
  title = {Genomic Analysis of the Regulatory Elements and Links with Intrinsic {{DNA}} Structural Properties in the Shrunken Genome of {{Buchnera}}},
  author = {Brinza, Lilia and Calevro, Federica and Charles, Hubert},
  year = {2013},
  journal = {BMC Genomics},
  volume = {14},
  number = {1},
  pages = {73},
  issn = {1471-2164},
  doi = {10.1186/1471-2164-14-73},
  abstract = {Background: Buchnera aphidicola is an obligate symbiotic bacterium, associated with most of the aphididae, whose genome has drastically shrunk during intracellular evolution. Gene regulation in Buchnera has been a matter of controversy in recent years as the combination of genomic information with the experimental results has been contradictory, refuting or arguing in favour of a functional and responsive transcription regulation in Buchnera. The goal of this study was to describe the gene transcription regulation capabilities of Buchnera based on the inventory of cis- and trans-regulators encoded in the genomes of five strains from different aphids (Acyrthosiphon pisum, Schizaphis graminum, Baizongia pistacea, Cinara cedri and Cinara tujafilina), as well as on the characterisation of some intrinsic structural properties of the DNA molecule in these bacteria. Results: Interaction graph analysis shows that gene neighbourhoods are conserved between E. coli and Buchnera in structures called transcriptons, interactons and metabolons, indicating that selective pressures have acted on the evolution of transcriptional, protein-protein interaction and metabolic networks in Buchnera. The transcriptional regulatory network in Buchnera is composed of a few general DNA-topological regulators (Nucleoid Associated Proteins and topoisomerases), with the quasi-absence of any specific ones (except for multifunctional enzymes with a known gene expression regulatory role in Escherichia coli, such as AlaS, PepA and BolA, and the uncharacterized hypothetical regulators YchA and YrbA). The relative positioning of regulatory genes along the chromosome of Buchnera seems to have conserved its ancestral state, despite the genome erosion. Sigma-70 promoters with canonical thermodynamic sequence profiles were detected upstream of about 94\% of the CDS of Buchnera in the different aphids. Based on Stress-Induced Duplex Destabilization (SIDD) measurements, unstable {$\sigma$}70 promoters were found specifically associated with the regulator and transporter genes. Conclusions: This genomic analysis provides supporting evidence of a selection of functional regulatory structures and it has enabled us to propose hypotheses concerning possible links between these regulatory elements and the DNA-topology (i.e., supercoiling, curvature, flexibility and base-pair stability) in the regulation of gene expression in the shrunken genome of Buchnera.},
  langid = {english}
}

@article{cameron2012,
  title = {A {{Fundamental Regulatory Mechanism Operating}} through {{OmpR}} and {{DNA Topology Controls Expression}} of {{Salmonella Pathogenicity Islands SPI-1}} and {{SPI-2}}},
  author = {Cameron, Andrew D. S. and Dorman, Charles J.},
  editor = {Casades{\'u}s, Josep},
  year = {2012},
  month = mar,
  journal = {PLoS Genetics},
  volume = {8},
  number = {3},
  pages = {e1002615},
  issn = {1553-7404},
  doi = {10.1371/journal.pgen.1002615},
  abstract = {DNA topology has fundamental control over the ability of transcription factors to access their target DNA sites at gene promoters. However, the influence of DNA topology on protein\textendash DNA and protein\textendash protein interactions is poorly understood. For example, relaxation of DNA supercoiling strongly induces the well-studied pathogenicity gene ssrA (also called spiR) in Salmonella enterica, but neither the mechanism nor the proteins involved are known. We have found that relaxation of DNA supercoiling induces expression of the Salmonella pathogenicity island (SPI)-2 regulator ssrA as well as the SPI-1 regulator hilC through a mechanism that requires the two-component regulator OmpR-EnvZ. Additionally, the ompR promoter is autoregulated in the same fashion. Conversely, the SPI-1 regulator hilD is induced by DNA relaxation but is repressed by OmpR. Relaxation of DNA supercoiling caused an increase in OmpR binding to DNA and a concomitant decrease in binding by the nucleoid-associated protein FIS. The reciprocal occupancy of DNA by OmpR and FIS was not due to antagonism between these transcription factors, but was instead a more intrinsic response to altered DNA topology. Surprisingly, DNA relaxation had no detectable effect on the binding of the global repressor H-NS. These results reveal the underlying molecular mechanism that primes SPI genes for rapid induction at the onset of host invasion. Additionally, our results reveal novel features of the archetypal two-component regulator OmpR. OmpR binding to relaxed DNA appears to generate a locally supercoiled state, which may assist promoter activation by relocating supercoiling stress-induced destabilization of DNA strands. Much has been made of the mechanisms that have evolved to regulate horizontally-acquired genes such as SPIs, but parallels among the ssrA, hilC, and ompR promoters illustrate that a fundamental form of regulation based on DNA topology coordinates the expression of these genes regardless of their origins.},
  langid = {english}
}

@article{cameron2013,
  title = {Transmission of an {{Oxygen Availability Signal}} at the {{Salmonella}} Enterica {{Serovar Typhimurium}} Fis {{Promoter}}},
  author = {Cameron, Andrew D. S. and Kr{\"o}ger, Carsten and Quinn, Heather J. and Scally, Isobel K. and Daly, Anne J. and Kary, Stefani C. and Dorman, Charles J.},
  editor = {Hayes, Finbarr},
  year = {2013},
  month = dec,
  journal = {PLoS ONE},
  volume = {8},
  number = {12},
  pages = {e84382},
  issn = {1932-6203},
  doi = {10.1371/journal.pone.0084382},
  abstract = {The nucleoid-associated protein FIS is a global regulator of gene expression and chromosome structure in Escherichia coli and Salmonella enterica. Despite the importance of FIS for infection and intracellular invasion, very little is known about the regulation of S. enterica fis expression. Under standard laboratory growth conditions, fis is highly expressed during rapid growth but is then silenced as growth slows. However, if cells are cultured in nonaerated conditions, fis expression is sustained during stationary phase. This led us to test whether the redox-sensing transcription factors ArcA and FNR regulate S. enterica fis. Deletion of FNR had no detectable effect, whereas deletion of ArcA had the unexpected effect of further elevating fis expression in stationary phase. ArcA required RpoS for induction of fis expression, suggesting that ArcA indirectly affects fis expression. Other putative regulators were found to play diverse roles: FIS acted directly as an auto-repressor (as expected), whereas CRP had little direct effect on fis expression. Deleting regions of the fis promoter led to the discovery of a novel anaerobically-induced transcription start site (Pfis-2) upstream of the primary transcription start site (Pfis-1). Promoter truncation also revealed that the shortest functional fis promoter was incapable of sustained expression. Moreover, fis expression was observed to correlate directly with DNA supercoiling in non-aerated conditions. Thus, the full-length S. enterica fis promoter region may act as a topological switch that is sensitive to stress-induced duplex destabilisation and upregulates expression in non-aerated conditions.},
  langid = {english}
}

@article{crick1958,
  title = {On Protein Synthesis},
  author = {Crick, F. H.},
  year = {1958},
  journal = {Symposia of the Society for Experimental Biology},
  volume = {12},
  pages = {138--163},
  issn = {0081-1386},
  langid = {english},
  pmid = {13580867}
}

@article{crombach2008,
  title = {Evolution of {{Evolvability}} in {{Gene Regulatory Networks}}},
  author = {Crombach, Anton and Hogeweg, Paulien},
  editor = {Sauro, Herbert M.},
  year = {2008},
  month = jul,
  journal = {PLoS Computational Biology},
  volume = {4},
  number = {7},
  pages = {e1000112},
  issn = {1553-7358},
  doi = {10.1371/journal.pcbi.1000112},
  abstract = {Gene regulatory networks are perhaps the most important organizational level in the cell where signals from the cell state and the outside environment are integrated in terms of activation and inhibition of genes. For the last decade, the study of such networks has been fueled by large-scale experiments and renewed attention from the theoretical field. Different models have been proposed to, for instance, investigate expression dynamics, explain the network topology we observe in bacteria and yeast, and for the analysis of evolvability and robustness of such networks. Yet how these gene regulatory networks evolve and become evolvable remains an open question. An individual-oriented evolutionary model is used to shed light on this matter. Each individual has a genome from which its gene regulatory network is derived. Mutations, such as gene duplications and deletions, alter the genome, while the resulting network determines the gene expression pattern and hence fitness. With this protocol we let a population of individuals evolve under Darwinian selection in an environment that changes through time.},
  langid = {english}
}

@article{crozat2005,
  title = {Long-{{Term Experimental Evolution}} in {{Escherichia}} Coli . {{XII}}. {{DNA Topology}} as a {{Key Target}} of {{Selection}}},
  author = {Crozat, Estelle and Philippe, Nad{\`e}ge and Lenski, Richard E. and Geiselmann, Johannes and Schneider, Dominique},
  year = {2005},
  month = feb,
  journal = {Genetics},
  volume = {169},
  number = {2},
  pages = {523--532},
  issn = {0016-6731, 1943-2631},
  doi = {10.1534/genetics.104.035717},
  abstract = {The genetic bases of adaptation are being investigated in 12 populations of Escherichia coli, founded from a common ancestor and serially propagated for 20,000 generations, during which time they achieved substantial fitness gains. Each day, populations alternated between active growth and nutrient exhaustion. DNA supercoiling in bacteria is influenced by nutritional state, and DNA topology helps coordinate the overall pattern of gene expression in response to environmental changes. We therefore examined whether the genetic controls over supercoiling might have changed during the evolution experiment. Parallel changes in topology occurred in most populations, with the level of DNA supercoiling increasing, usually in the first 2000 generations. Two mutations in the topA and fis genes that control supercoiling were discovered in a population that served as the focus for further investigation. Moving the mutations, alone and in combination, into the ancestral background had an additive effect on supercoiling, and together they reproduced the net change in DNA topology observed in this population. Moreover, both mutations were beneficial in competition experiments. Clonal interference involving other beneficial DNA topology mutations was also detected. These findings define a new class of fitness-enhancing mutations and indicate that the control of DNA supercoiling can be a key target of selection in evolving bacterial populations.},
  langid = {english}
}

@article{crozat2010,
  title = {Parallel {{Genetic}} and {{Phenotypic Evolution}} of {{DNA Superhelicity}} in {{Experimental Populations}} of {{Escherichia}} Coli},
  author = {Crozat, E. and Winkworth, C. and Gaffe, J. and Hallin, P. F. and Riley, M. A. and Lenski, R. E. and Schneider, D.},
  year = {2010},
  month = sep,
  journal = {Molecular Biology and Evolution},
  volume = {27},
  number = {9},
  pages = {2113--2128},
  issn = {0737-4038, 1537-1719},
  doi = {10.1093/molbev/msq099},
  abstract = {DNA supercoiling is the master function that interconnects chromosome structure and global gene transcription. This function has recently been shown to be under strong selection in Escherichia coli. During the evolution of 12 initially identical populations propagated in a defined environment for 20,000 generations, parallel increases in DNA supercoiling were observed in ten populations. The genetic changes associated with the increased supercoiling were examined in one population, and beneficial mutations in the genes topA (encoding topoisomerase I) and fis (encoding a histone-like protein) were identified. To elucidate the molecular basis and impact of these changes, we quantified the level of genetic, phenotypic, and molecular parallelism linked to DNA supercoiling in all 12 evolving populations. First, sequence determination of DNA topology-related loci revealed strong genetic parallelism, with mutations concentrated in three genes (topA, fis, and dusB), although the populations had different alleles at each locus. Statistical analyses of these polymorphisms implied the action of positive selection and, moreover, suggested that fis and dusB, which belong to the same operon, have related functions. Indeed, we demonstrated that DusB regulates the expression of fis by both experimental and phylogenetic analyses. Second, molecular analyses of five mutations in fis and dusB affecting the transcription, translation, and protein activity of Fis also revealed strong parallelism in the resulting phenotypic effects. Third, artificially increasing DNA supercoiling in one of the two populations that lacked DNA topology changes led to a significant fitness increase. The high levels of molecular and genetic parallelism, targeting a small subset of the many genes involved in DNA supercoiling, indicate that changes in DNA superhelicity have been important in the evolution of these populations. Surprisingly, however, most of the evolved alleles we tested had either no detectable or slightly deleterious effects on fitness, despite these signatures of positive selection.},
  langid = {english}
}

@article{dages2020,
  title = {Fis Protein Forms {{DNA}} Topological Barriers to Confine Transcription-coupled {{DNA}} Supercoiling in {{Escherichia}}~Coli},
  author = {Dages, Samantha and Zhi, Xiaoduo and Leng, Fenfei},
  year = {2020},
  journal = {FEBS Letters},
  pages = {8},
  langid = {english}
}

@book{darwin1859,
  title = {On the {{Origin}} of {{Species}} by {{Means}} of {{Natural Selection}}, or the {{Preservation}} of {{Favoured Races}} in the {{Struggle}} for {{Life}}},
  author = {Darwin, Charles},
  year = {1859},
  publisher = {{John Murray}}
}

@book{darwin1868,
  title = {The {{Variation}} of {{Animals}} and {{Plants}} under {{Domestication}}},
  author = {Darwin, Charles},
  year = {1868},
  publisher = {{John Murray}}
}

@article{davilalopez2010,
  title = {Analysis of {{Gene Order Conservation}} in {{Eukaryotes Identifies Transcriptionally}} and {{Functionally Linked Genes}}},
  author = {D{\'a}vila L{\'o}pez, Marcela and Mart{\'i}nez Guerra, Juan Jos{\'e} and Samuelsson, Tore},
  editor = {DeSalle, Robert},
  year = {2010},
  month = may,
  journal = {PLoS ONE},
  volume = {5},
  number = {5},
  pages = {e10654},
  issn = {1932-6203},
  doi = {10.1371/journal.pone.0010654},
  abstract = {The order of genes in eukaryotes is not entirely random. Studies of gene order conservation are important to understand genome evolution and to reveal mechanisms why certain neighboring genes are more difficult to separate during evolution. Here, genome-wide gene order information was compiled for 64 species, representing a wide variety of eukaryotic phyla. This information is presented in a browser where gene order may be displayed and compared between species. Factors related to non-random gene order in eukaryotes were examined by considering pairs of neighboring genes. The evolutionary conservation of gene pairs was studied with respect to relative transcriptional direction, intergenic distance and functional relationship as inferred by gene ontology. The results show that among gene pairs that are conserved the divergently and co-directionally transcribed genes are much more common than those that are convergently transcribed. Furthermore, highly conserved pairs, in particular those of fungi, are characterized by a short intergenic distance. Finally, gene pairs of metazoa and fungi that are evolutionary conserved and that are divergently transcribed are much more likely to be related by function as compared to poorly conserved gene pairs. One example is the ribosomal protein gene pair L13/S16, which is unusual as it occurs both in fungi and alveolates. A specific functional relationship between these two proteins is also suggested by the fact that they are part of the same operon in both eubacteria and archaea. In conclusion, factors associated with non-random gene order in eukaryotes include relative gene orientation, intergenic distance and functional relationships. It seems likely that certain pairs of genes are conserved because the genes involved have a transcriptional and/or functional relationship. The results also indicate that studies of gene order conservation aid in identifying genes that are related in terms of transcriptional control.},
  langid = {english}
}

@article{delacampa2017,
  title = {The {{Transcriptome}} of {{Streptococcus}} Pneumoniae {{Induced}} by {{Local}} and {{Global Changes}} in {{Supercoiling}}},
  author = {{de la Campa}, Adela G. and Ferr{\'a}ndiz, Mar{\'i}a J. and {Mart{\'i}n-Galiano}, Antonio J. and Garc{\'i}a, Mar{\'i}a T. and {Tirado-V{\'e}lez}, Jose M.},
  year = {2017},
  month = jul,
  journal = {Frontiers in Microbiology},
  volume = {8},
  pages = {1447},
  issn = {1664-302X},
  doi = {10.3389/fmicb.2017.01447},
  abstract = {The bacterial chromosome is compacted in a manner optimal for DNA transactions to occur. The degree of compaction results from the level of DNA-supercoiling and the presence of nucleoid-binding proteins. DNA-supercoiling is homeostatically maintained by the opposing activities of relaxing DNA topoisomerases and negative supercoil-inducing DNA gyrase. DNA-supercoiling acts as a general cis regulator of transcription, which can be superimposed upon other types of more specific trans regulatory mechanism. Transcriptomic studies on the human pathogen Streptococcus pneumoniae, which has a relatively small genome ({$\sim$}2 Mb) and few nucleoid-binding proteins, have been performed under conditions of local and global changes in supercoiling. The response to local changes induced by fluoroquinolone antibiotics, which target DNA gyrase subunit A and/or topoisomerase IV, involves an increase in oxygen radicals which reduces cell viability, while the induction of global supercoiling changes by novobiocin (a DNA gyrase subunit B inhibitor), or by seconeolitsine (a topoisomerase I inhibitor), has revealed the existence of topological domains that specifically respond to such changes. The control of DNA-supercoiling in S. pneumoniae occurs mainly via the regulation of topoisomerase gene transcription: relaxation triggers the up-regulation of gyrase and the down-regulation of topoisomerases I and IV, while hypernegative supercoiling down-regulates the expression of topoisomerase I. Relaxation affects 13\% of the genome, with the majority of the genes affected located in 15 domains. Hypernegative supercoiling affects 10\% of the genome, with one quarter of the genes affected located in 12 domains. However, all the above domains overlap, suggesting that the chromosome is organized into topological domains with fixed locations. Based on its response to relaxation, the pneumococcal chromosome can be said to be organized into five types of domain: up-regulated, down-regulated, position-conserved non-regulated, position-variable non-regulated, and AT-rich. The AT content is higher in the up-regulated than in the down-regulated domains. Genes within the different domains share structural and functional characteristics. It would seem that a topology-driven selection pressure has defined the chromosomal location of the metabolism, virulence and competence genes, which suggests the existence of topological rules that aim to improve bacterial fitness.},
  langid = {english}
}

@incollection{dicosmo2020,
  title = {Archiving and {{Referencing Source Code}} with {{Software Heritage}}},
  booktitle = {Mathematical {{Software}} \textendash{} {{ICMS}} 2020},
  author = {Di Cosmo, Roberto},
  editor = {Bigatti, Anna Maria and Carette, Jacques and Davenport, James H. and Joswig, Michael and {de Wolff}, Timo},
  year = {2020},
  volume = {12097},
  pages = {362--373},
  publisher = {{Springer International Publishing}},
  address = {{Cham}},
  doi = {10.1007/978-3-030-52200-1_36},
  abstract = {Software, and software source code in particular, is widely used in modern research. It must be properly archived, referenced, described and cited in order to build a stable and long lasting corpus of scientific knowledge. In this article we show how the Software Heritage universal source code archive provides a means to fully address the first two concerns, by archiving seamlessly all publicly available software source code, and by providing intrinsic persistent identifiers that allow to reference it at various granularities in a way that is at the same time convenient and effective.},
  isbn = {978-3-030-52199-8 978-3-030-52200-1},
  langid = {english}
}

@article{dorman2016,
  title = {{{DNA}} Supercoiling Is a Fundamental Regulatory Principle in the Control of Bacterial Gene Expression},
  author = {Dorman, Charles J. and Dorman, Matthew J.},
  year = {2016},
  month = sep,
  journal = {Biophysical Reviews},
  volume = {8},
  number = {3},
  pages = {209--220},
  issn = {1867-2450, 1867-2469},
  doi = {10.1007/s12551-016-0205-y},
  langid = {english}
}

@article{dorman2019,
  title = {{{DNA}} Supercoiling and Transcription in Bacteria: A Two-Way Street},
  shorttitle = {{{DNA}} Supercoiling and Transcription in Bacteria},
  author = {Dorman, Charles J.},
  year = {2019},
  month = dec,
  journal = {BMC Molecular and Cell Biology},
  volume = {20},
  number = {1},
  pages = {26},
  issn = {2661-8850},
  doi = {10.1186/s12860-019-0211-6},
  abstract = {Background: The processes of DNA supercoiling and transcription are interdependent because the movement of a transcription elongation complex simultaneously induces under- and overwinding of the DNA duplex and because the initiation, elongation and termination steps of transcription are all sensitive to the topological state of the DNA. Results: Policing of the local and global supercoiling of DNA by topoisomerases helps to sustain the major DNAbased transactions by eliminating barriers to the movement of transcription complexes and replisomes. Recent data from whole-genome and single-molecule studies have provided new insights into how interactions between transcription and the supercoiling of DNA influence the architecture of the chromosome and how they create cellto-cell diversity at the level of gene expression through transcription bursting. Conclusions: These insights into fundamental molecular processes reveal mechanisms by which bacteria can prevail in unpredictable and often hostile environments by becoming unpredictable themselves.},
  langid = {english}
}

@article{drlica1991,
  title = {Control of Bacterial {{DNA}} Supercoiling},
  author = {Drlica, Karl},
  year = {1991},
  month = oct,
  journal = {Molecular Microbiology},
  volume = {6},
  number = {4},
  pages = {9},
  doi = {10.1111/j.1365-2958.1992.tb01486.x},
  abstract = {Two DNA topojsomerases control the level of negative supercoiling in bacterial celts. DNA gyrase introduces supercoils, and DNA topoisomerase I prevents supercoiling from reaching unacceptably high levels. Perturbations of supercoiling are corrected by the substrate preferences of these topoisomerases with respectto DNA topology and by changes in expression of the genes encoding the enzymes. However, supercoiling changes when the growth environment is altered in ways that also affect cellular energetics. The ratio of [ATP] to [ADP], to which gyrase is sensitive, may be involved in the response of supercoiling to growth conditions. Inside cells, supercoiling is partitioned into two components, superhelical tension and restrained supercoils. Shifts in superhelical tension elicited by nicking or by salt shock do not rapidly change the level of restrained supercoiling. However, a steady-state change in supercoiling caused by mutation of topA does alter both tension and restrained supercoils. This communication between the two compartments may play a role in the control of supercoiling.},
  langid = {english}
}

@article{duprey2021,
  title = {The Regulation of {{DNA}} Supercoiling across Evolution},
  shorttitle = {The Regulation Of},
  author = {Duprey, Alexandre and Groisman, Eduardo A.},
  year = {2021},
  month = aug,
  journal = {Protein Science},
  pages = {pro.4171},
  issn = {0961-8368, 1469-896X},
  doi = {10.1002/pro.4171},
  abstract = {DNA supercoiling controls a variety of cellular processes, including transcription, recombination, chromosome replication, and segregation, across all domains of life. As a physical property, DNA supercoiling alters the double helix structure by under- or over-winding it. Intriguingly, the evolution of DNA supercoiling reveals both similarities and differences in its properties and regulation across the three domains of life. Whereas all organisms exhibit local, constrained DNA supercoiling, only bacteria and archaea exhibit unconstrained global supercoiling. DNA supercoiling emerges naturally from certain cellular processes and can also be changed by enzymes called topoisomerases. While structurally and mechanistically distinct, topoisomerases that dissipate excessive supercoils exist in all domains of life. By contrast, topoisomerases that introduce positive or negative supercoils exist only in bacteria and archaea. The abundance of topoisomerases is also transcriptionally and post-transcriptionally regulated in domainspecific ways. Nucleoid-associated proteins, metabolites, and physicochemical factors influence DNA supercoiling by acting on the DNA itself or by impacting the activity of topoisomerases. Overall, the unique strategies that organisms have evolved to regulate DNA supercoiling hold significant therapeutic potential, such as bactericidal agents that target bacteria-specific processes or anticancer drugs that hinder abnormal DNA replication by acting on eukaryotic topoisomerases specialized in this process. The investigation of DNA supercoiling therefore reveals general principles, conserved mechanisms, and kingdom-specific variations relevant to a wide range of biological questions.},
  langid = {english}
}

@article{elhanafi2000,
  title = {Activation and Silencing of Leu-500 Promoter by Transcription-Induced {{DNA}} Supercoiling in the {{Salmonella}} Chromosome: {{Transcription-dependent}} Modulation of Leu-500 Promoter in {{topA}} Mutants},
  shorttitle = {Activation and Silencing of Leu-500 Promoter by Transcription-Induced {{DNA}} Supercoiling in the {{Salmonella}} Chromosome},
  author = {El Hanafi, Driss and Bossi, Lionello},
  year = {2000},
  month = aug,
  journal = {Molecular Microbiology},
  volume = {37},
  number = {3},
  pages = {583--594},
  issn = {0950382X, 13652958},
  doi = {10.1046/j.1365-2958.2000.02015.x},
  abstract = {The notion that transcription can generate supercoils in the DNA template largely stems from work with small circular plasmids. In the present work, we tested this model in the bacterial chromosome using a supercoiling-sensitive promoter as a functional sensor of superhelicity changes. The leu-500 promoter of Salmonella typhimurium is a mutant and inactive variant of the leucine operon promoter that regains activity if negative DNA supercoiling rises above normal levels, typically as a result of mutations affecting DNA topoisomerase I (topA mutants). Activation of the leu-500 promoter was analysed in topA mutant cells harbouring transcriptionally inducible tet or cat gene cassettes inserted in the region upstream from the leu operon. Some insertions inhibited leu-500 promoter activation in the absence of inducer. This effect is dramatic in the interval between 1.7 kb and 0.6 kb from the leu operon, suggesting that the insertions physically interfere with the mechanism responsible for activation. Superimposed on these effects, transcription of the inserted gene stimulated or inhibited leu-500 promoter activity depending on whether this gene was oriented divergently from the leu operon or in the same direction respectively. Interestingly, transcription-mediated inhibition of leu-500 promoter was observed with inserts as far as 5 kb from the leu operon, and it could be relieved by the introduction of a strong gyrase site between the inserted element and the leu-500 promoter. These results are consistent with the idea that transcriptionally generated positive and negative supercoils can diffuse along chromosomal DNA and, depending on their topological sign, elicit opposite responses from the leu-500 promoter.},
  langid = {english}
}

@article{elhoudaigui2019,
  title = {Bacterial Genome Architecture Shapes Global Transcriptional Regulation by {{DNA}} Supercoiling},
  author = {El~Houdaigui, Bilal and Forquet, Rapha{\"e}l and Hindr{\'e}, Thomas and Schneider, Dominique and Nasser, William and Reverchon, Sylvie and Meyer, Sam},
  year = {2019},
  month = jun,
  journal = {Nucleic Acids Research},
  volume = {47},
  number = {11},
  pages = {5648--5657},
  issn = {0305-1048, 1362-4962},
  doi = {10.1093/nar/gkz300},
  abstract = {DNA supercoiling acts as a global transcriptional regulator in bacteria, that plays an important role in adapting their expression programme to environmental changes, but for which no quantitative or even qualitative regulatory model is available. Here, we focus on spatial supercoiling heterogeneities caused by the transcription process itself, which strongly contribute to this regulation mode. We propose a new mechanistic modeling of the transcriptionsupercoiling dynamical coupling along a genome, which allows simulating and quantitatively reproducing in vitro and in vivo transcription assays, and highlights the role of genes' local orientation in their supercoiling sensitivity. Consistently with predictions, we show that chromosomal relaxation artificially induced by gyrase inhibitors selectively activates convergent genes in several enterobacteria, while conversely, an increase in DNA supercoiling naturally selected in a long-term evolution experiment with Escherichia coli favours divergent genes. Simulations show that these global expression responses to changes in DNA supercoiling result from fundamental mechanical constraints imposed by transcription, independently from more specific regulation of each promoter. These constraints underpin a significant and predictable contribution to the complex rules by which bacteria use DNA supercoiling as a global but fine-tuned transcriptional regulator.},
  langid = {english}
}

@article{elhoudaigui2020,
  title = {{{TwisTranscripT}}: Stochastic Simulation of the Transcription-Supercoiling Coupling},
  shorttitle = {{{TwisTranscripT}}},
  author = {El Houdaigui, Bilal and Meyer, Sam},
  editor = {Luigi Martelli, Pier},
  year = {2020},
  month = jun,
  journal = {Bioinformatics},
  volume = {36},
  number = {12},
  pages = {3899--3901},
  issn = {1367-4803, 1460-2059},
  doi = {10.1093/bioinformatics/btaa221},
  abstract = {Abstract                            Summary               Transcription and DNA supercoiling are involved in a complex, dynamical and non-linear coupling that results from the basal interaction between DNA and RNA polymerase. We present the first software to simulate this coupling, applicable to a wide range of bacterial organisms. TwisTranscripT allows quantifying its contribution in global transcriptional regulation, and provides a mechanistic basis for the widely observed, evolutionarily conserved and currently unexplained co-regulation of adjacent operons that might play an important role in genome evolution.                                         Availability and implementation               TwisTranscripT is freely available at https://github.com/sammeyer2017/TwisTranscripT. It is implemented in Python3 and supported on MacOS X, Linux and Windows.},
  langid = {english}
}

@book{felsenstein2019,
  title = {Theoretical {{Evolutionary Genetics}}},
  author = {Felsenstein, Joe},
  year = {2019},
  note = {\url{https://evolution.genetics.washington.edu/pgbook/pgbook.html}}
}

@article{ferrandiz2010,
  title = {The Genome of {{Streptococcus}} Pneumoniae Is Organized in Topology-Reacting Gene Clusters},
  author = {Ferrandiz, M.-J. and {Martin-Galiano}, A. J. and Schvartzman, J. B. and {de la Campa}, A. G.},
  year = {2010},
  month = jun,
  journal = {Nucleic Acids Research},
  volume = {38},
  number = {11},
  pages = {3570--3581},
  issn = {0305-1048, 1362-4962},
  doi = {10.1093/nar/gkq106},
  abstract = {The transcriptional response of Streptococcus pneumoniae was examined after exposure to the GyrB-inhibitor novobiocin. Topoisomer distributions of an internal plasmid confirmed DNA relaxation and recovery of the native level of supercoiling at low novobiocin concentrations. This was due to the up-regulation of DNA gyrase and the downregulation of topoisomerases I and IV. In addition, {$>$}13\% of the genome exhibited relaxation-dependent transcription. The majority of the responsive genes ({$>$}68\%) fell into 15 physical clusters (14.6\textendash 85.6 kb) that underwent coordinated regulation, independently of operon organization. These genomic clusters correlated with AT content and codon composition, showing the chromosome to be organized into topology-reacting gene clusters that respond to DNA supercoiling. In particular, down-regulated clusters were flanked by 11\textendash 40 kb AT-rich zones that might have a putative structural function. This is the first case where genes responding to changes in the level of supercoiling in a coordinated manner were found organized as functional clusters. Such an organization revealed DNA supercoiling as a general feature that controls gene expression superimposed on other kinds of more specific regulatory mechanisms.},
  langid = {english}
}

@article{forquet2021,
  title = {Role of the {{Discriminator Sequence}} in the {{Supercoiling Sensitivity}} of {{Bacterial Promoters}}},
  author = {Forquet, Rapha{\"e}l and Pineau, Ma{\"i}wenn and Nasser, William and Reverchon, Sylvie and Meyer, Sam},
  editor = {Oliveira, Pedro H.},
  year = {2021},
  month = aug,
  journal = {mSystems},
  volume = {6},
  number = {4},
  issn = {2379-5077},
  doi = {10.1128/mSystems.00978-21},
  abstract = {DNA supercoiling acts as a global transcriptional regulator that contributes to the rapid transcriptional response of bacteria to many environmental changes. Although a large fraction of promoters from phylogenetically distant species respond to superhelical variations, the sequence or structural determinants of this behavior remain elusive. Here, we focus on the sequence of the ``discriminator'' element that was shown to modulate this response in several promoters. We develop a quantitative thermodynamic model of this regulatory effect, focusing on open complex formation during transcription initiation independently from promoter-specific regulatory proteins. We analyze previous and new expression data and show that the model predictions quantitatively match the in vitro and in vivo supercoiling response of selected promoters with mutated discriminator sequences. We then test the universality of this mechanism by a statistical analysis of promoter sequences from transcriptomes of phylogenetically distant bacteria under conditions of supercoiling variations (i) by gyrase inhibitors, (ii) by environmental stresses, or (iii) inherited in the longest-running evolution experiment. In all cases, we identify a robust and significant sequence signature in the discriminator region, suggesting that supercoiling-modulated promoter opening underpins a ubiquitous regulatory mechanism in the prokaryotic kingdom based on the fundamental mechanical properties of DNA and its basal interaction with RNA polymerase.},
  langid = {english}
}

@article{forquet2022,
  title = {Quantitative Contribution of the Spacer Length in the Supercoiling-Sensitivity of Bacterial Promoters},
  author = {Forquet, Rapha{\"e}l and Nasser, William and Reverchon, Sylvie and Meyer, Sam},
  year = {2022},
  month = jul,
  journal = {Nucleic Acids Research},
  volume = {50},
  number = {13},
  pages = {7287--7297},
  issn = {0305-1048, 1362-4962},
  doi = {10.1093/nar/gkac579},
  abstract = {DNA supercoiling acts as a global transcriptional regulator in bacteria, but the promoter sequence or structural determinants controlling its effect remain unclear. It was previously proposed to modulate the torsional angle between the -10 and -35 hexamers, and thereby regulate the formation of the closedcomplex depending on the length of the `spacer' between them. Here, we develop a thermodynamic model of this notion based on DNA elasticity, providing quantitative and parameter-free predictions of the relative activation of promoters containing a short versus long spacer when the DNA supercoiling level is varied. The model is tested through an analysis of in vitro and in vivo expression assays of mutant promoters with variable spacer lengths, confirming its accuracy for spacers ranging from 15 to 19 nucleotides, except those of 16 nucleotides where other regulatory mechanisms likely overcome the effect of this specific step. An analysis at the whole-genome scale in Escherichia coli then demonstrates a significant effect of the spacer length on the genomic expression after transient or inheritable superhelical variations, validating the model's predictions. Altogether, this study shows an example of mechanical constraints associated to promoter binding by RNA Polymerase underpinning a basal and global regulatory mechanism.},
  langid = {english}
}

@article{gardner2000,
  title = {Construction of a Genetic Toggle Switch in {{Escherichia}} Coli},
  author = {Gardner, Timothy S. and Cantor, Charles R. and Collins, James J.},
  year = {2000},
  month = jan,
  journal = {Nature},
  volume = {403},
  number = {6767},
  pages = {339--342},
  issn = {0028-0836, 1476-4687},
  doi = {10.1038/35002131},
  langid = {english}
}

@article{gaubert2020,
  title = {Understanding and Monitoring the Evolution of the {{Covid-19}} Epidemic from Medical Emergency Calls: The Example of the {{Paris}} Area},
  shorttitle = {Understanding and Monitoring the Evolution of the {{Covid-19}} Epidemic from Medical Emergency Calls},
  author = {Gaubert, St{\'e}phane and Akian, Marianne and Allamigeon, Xavier and Boyet, Marin and Colin, Baptiste and Grohens, Th{\'e}otime and Massouli{\'e}, Laurent and Parsons, David P. and Adnet, Fr{\'e}d{\'e}ric and Chanzy, {\'E}rick and Goix, Laurent and Lapostolle, Fr{\'e}d{\'e}ric and Lecarpentier, {\'E}ric and Leroy, Christophe and Loeb, Thomas and Marx, Jean-S{\'e}bastien and T{\'e}lion, Caroline and Tr{\'e}luyer, Laurent and Carli, Pierre},
  year = {2020},
  month = nov,
  journal = {Comptes Rendus. Math\'ematique},
  volume = {358},
  number = {7},
  pages = {843--875},
  issn = {1778-3569},
  doi = {10.5802/crmath.99},
  langid = {english}
}

@article{giovannoni2005,
  title = {Genome {{Streamlining}} in a {{Cosmopolitan Oceanic Bacterium}}},
  author = {Giovannoni, Stephen J. and Tripp, H. James and Givan, Scott and Podar, Mircea and Vergin, Kevin L. and Baptista, Damon and Bibbs, Lisa and Eads, Jonathan and Richardson, Toby H. and Noordewier, Michiel and Rapp{\'e}, Michael S. and Short, Jay M. and Carrington, James C. and Mathur, Eric J.},
  year = {2005},
  month = aug,
  journal = {Science},
  volume = {309},
  number = {5738},
  pages = {1242--1245},
  issn = {0036-8075, 1095-9203},
  doi = {10.1126/science.1114057},
  abstract = {The SAR11 clade consists of very small, heterotrophic marine {$\alpha$}-proteobacteria that are found throughout the oceans, where they account for about 25\% of all microbial cells.               Pelagibacter ubique               , the first cultured member of this clade, has the smallest genome and encodes the smallest number of predicted open reading frames known for a free-living microorganism. In contrast to parasitic bacteria and archaea with small genomes,               P. ubique               has complete biosynthetic pathways for all 20 amino acids and all but a few cofactors.               P. ubique               has no pseudogenes, introns, transposons, extrachromosomal elements, or inteins; few paralogs; and the shortest intergenic spacers yet observed for any cell.},
  langid = {english}
}

@article{glass2006,
  title = {Essential Genes of a Minimal Bacterium},
  author = {Glass, John I. and {Assad-Garcia}, Nacyra and Alperovich, Nina and Yooseph, Shibu and Lewis, Matthew R. and Maruf, Mahir and Hutchison, Clyde A. and Smith, Hamilton O. and Venter, J. Craig},
  year = {2006},
  month = jan,
  journal = {Proceedings of the National Academy of Sciences},
  volume = {103},
  number = {2},
  pages = {425--430},
  issn = {0027-8424, 1091-6490},
  doi = {10.1073/pnas.0510013103},
  abstract = {Mycoplasma genitalium               has the smallest genome of any organism that can be grown in pure culture. It has a minimal metabolism and little genomic redundancy. Consequently, its genome is expected to be a close approximation to the minimal set of genes needed to sustain bacterial life. Using global transposon mutagenesis, we isolated and characterized gene disruption mutants for 100 different nonessential protein-coding genes. None of the 43 RNA-coding genes were disrupted. Herein, we identify 382 of the 482               M. genitalium               protein-coding genes as essential, plus five sets of disrupted genes that encode proteins with potentially redundant essential functions, such as phosphate transport. Genes encoding proteins of unknown function constitute 28\% of the essential protein-coding genes set. Disruption of some genes accelerated               M. genitalium               growth.},
  langid = {english}
}

@article{good2017,
  title = {The Dynamics of Molecular Evolution over 60,000 Generations},
  author = {Good, Benjamin H. and McDonald, Michael J. and Barrick, Jeffrey E. and Lenski, Richard E. and Desai, Michael M.},
  year = {2017},
  month = nov,
  journal = {Nature},
  volume = {551},
  number = {7678},
  pages = {45--50},
  issn = {0028-0836, 1476-4687},
  doi = {10.1038/nature24287},
  langid = {english}
}

@inproceedings{grohens2021,
  title = {A {{Genome-Wide Evolutionary Simulation}} of the {{Transcription-Supercoiling Coupling}}},
  booktitle = {The 2021 {{Conference}} on {{Artificial Life}}},
  author = {Grohens, Th{\'e}otime and Meyer, Sam and Beslon, Guillaume},
  year = {2021},
  publisher = {{MIT Press}},
  abstract = {DNA supercoiling (SC), the level of under- or overwinding of the DNA polymer around itself, is widely recognized as an ancestral regulation mechanism of gene expression in bacteria. Higher negative SC levels facilitate the opening of the DNA double helix at gene promoters, and increase the associated expression levels. Different levels of SC have been measured in bacteria exposed to different environments, leading to the hypothesis that SC variation can be an environmental response. Moreover, DNA transcription has been shown to generate local variations in the SC level, and therefore to impact the transcription of neighboring genes.},
  langid = {english}
}

@article{grohens2022a,
  title = {A {{Genome-Wide Evolutionary Simulation}} of the {{Transcription-Supercoiling Coupling}}},
  author = {Grohens, Th{\'e}otime and Meyer, Sam and Beslon, Guillaume},
  year = {2022},
  month = aug,
  journal = {Artificial Life},
  pages = {1--18},
  issn = {1064-5462, 1530-9185},
  doi = {10.1162/artl_a_00373},
  abstract = {Abstract             DNA supercoiling, the level of under- or overwinding of the DNA polymer around itself, is widely recognized as an ancestral regulation mechanism of gene expression in bacteria. Higher levels of negative supercoiling facilitate the opening of the DNA double helix at gene promoters and thereby increase gene transcription rates. Different levels of supercoiling have been measured in bacteria exposed to different environments, leading to the hypothesis that variations in supercoiling could be a response to changes in the environment. Moreover, DNA transcription has been shown to generate local variations in the supercoiling level and, therefore, to impact the transcription rate of neighboring genes. In this work, we study the coupled dynamics of DNA supercoiling and transcription at the genome scale. We implement a genome-wide model of gene expression based on the transcription-supercoiling coupling. We show that, in this model, a simple change in global DNA supercoiling is sufficient to trigger differentiated responses in gene expression levels via the transcription-supercoiling coupling. Then, studying our model in the light of evolution, we demonstrate that this non-linear response to different environments, mediated by the transcription-supercoiling coupling, can serve as the basis for the evolution of specialized phenotypes.},
  langid = {english}
}

@misc{grohens2022b,
  type = {Preprint},
  title = {Emergence of {{Supercoiling-Mediated Regulatory Networks}} through {{Bacterial Chromosome Rearrangements}}},
  author = {Grohens, Th{\'e}otime and Meyer, Sam and Beslon, Guillaume},
  year = {2022},
  month = sep,
  publisher = {{Systems Biology}},
  doi = {10.1101/2022.09.23.509185},
  abstract = {DNA supercoiling, the level of twist and writhe of the DNA molecule around itself, plays a major role in the regulation of gene expression in bacteria by modulating promoter activity. The level of supercoiling is a dynamic property of the chromosome, and it changes in response to external and internal stimuli including many environmental perturbations but also, importantly, in response to gene transcription. As transcription itself depends on the level of supercoiling, the interplay between these two factors results in a coupling between the transcription rates, and expression levels, of neighboring genes.},
  langid = {english},
  note = {\url{https://www.biorxiv.org/content/10.1101/2022.09.23.509185v1}}
}

@article{herault2014,
  title = {Role of the {{LysR-type}} Transcriptional Regulator {{PecT}} and {{DNA}} Supercoiling in the Thermoregulation of {\emph{Pel}} Genes, the Major Virulence Factors in {{{\emph{Dickeya}}}}{\emph{ Dadantii}}: {{{\emph{Dickeya}}}}{\emph{ Dadantii}} {{PecT}} Protein and Virulence Thermoregulation},
  shorttitle = {Role of the {{LysR-type}} Transcriptional Regulator {{PecT}} and {{DNA}} Supercoiling in the Thermoregulation of {\emph{Pel}} Genes, the Major Virulence Factors in {{{\emph{Dickeya}}}}{\emph{ Dadantii}}},
  author = {H{\'e}rault, Elodie and Reverchon, Sylvie and Nasser, William},
  year = {2014},
  month = mar,
  journal = {Environmental Microbiology},
  volume = {16},
  number = {3},
  pages = {734--745},
  issn = {14622912},
  doi = {10.1111/1462-2920.12198},
  langid = {english}
}

@article{hindre2012,
  title = {New Insights into Bacterial Adaptation through in Vivo and in Silico Experimental Evolution},
  author = {Hindr{\'e}, Thomas and Knibbe, Carole and Beslon, Guillaume and Schneider, Dominique},
  year = {2012},
  month = may,
  journal = {Nature Reviews Microbiology},
  volume = {10},
  number = {5},
  pages = {352--365},
  issn = {1740-1526, 1740-1534},
  doi = {10.1038/nrmicro2750},
  abstract = {Microbiology research has recently undergone major developments that have led to great progress towards obtaining an integrated view of microbial cell function. Microbial genetics, high-throughput technologies and systems biology have all provided an improved understanding of the structure and function of bacterial genomes and cellular networks. However, integrated evolutionary perspectives are needed to relate the dynamics of adaptive changes to the phenotypic and genotypic landscapes of living organisms. Here, we review evolution experiments, carried out both in vivo with microorganisms and in silico with artificial organisms, that have provided insights into bacterial adaptation and emphasize the potential of bacterial regulatory networks to evolve.},
  langid = {english}
}

@article{hsieh1991,
  title = {Bacterial {{DNA}} Supercoiling and [{{ATP}}]/[{{ADP}}] Ratio: Changes Associated with Salt Shock.},
  shorttitle = {Bacterial {{DNA}} Supercoiling and [{{ATP}}]/[{{ADP}}] Ratio},
  author = {Hsieh, L S and {Rouviere-Yaniv}, J and Drlica, K},
  year = {1991},
  journal = {Journal of Bacteriology},
  volume = {173},
  number = {12},
  pages = {3914--3917},
  issn = {0021-9193, 1098-5530},
  doi = {10.1128/JB.173.12.3914-3917.1991},
  langid = {english}
}

@article{hunter2007,
  title = {Matplotlib: {{A 2D Graphics Environment}}},
  shorttitle = {Matplotlib},
  author = {Hunter, John D.},
  year = {2007},
  journal = {Computing in Science \& Engineering},
  volume = {9},
  number = {3},
  pages = {90--95},
  issn = {1521-9615},
  doi = {10.1109/MCSE.2007.55},
  langid = {english}
}

@misc{johnstone2022,
  title = {Supercoiling-Mediated Feedback Rapidly Couples and Tunes Transcription},
  author = {Johnstone, Christopher P. and Galloway, Kate E.},
  year = {2022},
  month = apr,
  institution = {{Synthetic Biology}},
  doi = {10.1101/2022.04.20.488937},
  abstract = {Transcription induces a wave of DNA supercoiling, altering the binding affinity of RNA polymerases and reshaping the biochemical landscape of gene regulation. As supercoiling rapidly diffuses, transcription dynamically reshapes the regulation of proximal genes, forming a complex feedback loop. The resulting intergene coupling may provide a mechanism to control transcriptional variance in engineered gene networks and explain the behavior of co-localized native circuits. However, a theoretical framework is needed for integrating both biophysical and biochemical transcriptional regulation to investigate the role of supercoiling-mediated feedback within multi-gene systems. Here, we model transcriptional regulation under the influence of supercoiling-mediated polymerase dynamics, allowing us to identify patterns of expression that result from physical intergene coupling and explore integration of this biophysical model with a set of canonical biochemical gene regulatory systems. We find that gene syntax\textemdash the relative ordering and orientation of genes\textemdash defines the expression profiles, variance, burst dynamics, and intergene correlation of two-gene systems. By applying our model to both a synthetic toggle switch and the endogenous zebrafish segmentation network, we find that supercoiling can enhance or weaken conventional biochemical regulatory strategies such as mRNA- and protein-mediated feedback loops. Together, our results suggest that supercoiling couples behavior between neighboring genes, representing a novel regulatory mechanism. Integrating biophysical regulation into the analysis and design of gene regulation provides a framework for enhanced understanding of native networks and engineering of synthetic gene circuits.},
  langid = {english},
  note = {\url{https://www.biorxiv.org/content/10.1101/2022.04.20.488937v1}}
}

@article{junier2016,
  title = {Conserved {{Units}} of {{Co-Expression}} in {{Bacterial Genomes}}: {{An Evolutionary Insight}} into {{Transcriptional Regulation}}},
  shorttitle = {Conserved {{Units}} of {{Co-Expression}} in {{Bacterial Genomes}}},
  author = {Junier, Ivan and Rivoire, Olivier},
  editor = {{Moreno-Hagelsieb}, Gabriel},
  year = {2016},
  month = may,
  journal = {PLOS ONE},
  volume = {11},
  number = {5},
  pages = {e0155740},
  issn = {1932-6203},
  doi = {10.1371/journal.pone.0155740},
  langid = {english}
}

@article{klein2021,
  title = {The Bacterial Promoter Spacer Modulates Promoter Strength and Timing by Length, {{TG-motifs}} and {{DNA}} Supercoiling Sensitivity},
  author = {Klein, Carlo A. and Teufel, Marc and Weile, Carl J. and Sobetzko, Patrick},
  year = {2021},
  month = dec,
  journal = {Scientific Reports},
  volume = {11},
  number = {1},
  pages = {24399},
  issn = {2045-2322},
  doi = {10.1038/s41598-021-03817-4},
  abstract = {Abstract             Transcription, the first step to gene expression, is a central coordination process in all living matter. Besides a plethora of regulatory mechanisms, the promoter architecture sets the foundation of expression strength, timing and the potential for further regulatory modulation. In this study, we investigate the effects of promoter spacer length and sequence composition on strength and supercoiling sensitivity in bacteria. Combining transcriptomics data analysis and standardized synthetic promoter libraries, we exclude effects of specific promoter sequence contexts. Analysis of promoter activity shows a strong variance with spacer length and spacer sequence composition. A detailed study of the spacer sequence composition under selective conditions reveals an extension to the -10 region that enhances RNAP binding but damps promoter activity. Using physiological changes in DNA supercoiling levels, we link promoter supercoiling sensitivity to overall spacer GC-content. Time-resolved promoter activity screens, only possible with a novel mild treatment approach, reveal strong promoter timing potentials solely based on DNA supercoiling sensitivity in the absence of regulatory sites or alternative sigma factors.},
  langid = {english}
}

@incollection{knibbe2005,
  title = {Self-Adaptation of {{Genome Size}} in {{Artificial Organisms}}},
  booktitle = {Advances in {{Artificial Life}}},
  author = {Knibbe, C. and Beslon, G. and Lefort, V. and Chaudier, F. and Fayard, J. -M.},
  editor = {Hutchison, David and Kanade, Takeo and Kittler, Josef and Kleinberg, Jon M. and Mattern, Friedemann and Mitchell, John C. and Naor, Moni and Nierstrasz, Oscar and Pandu Rangan, C. and Steffen, Bernhard and Sudan, Madhu and Terzopoulos, Demetri and Tygar, Dough and Vardi, Moshe Y. and Weikum, Gerhard and Capcarr{\`e}re, Mathieu S. and Freitas, Alex A. and Bentley, Peter J. and Johnson, Colin G. and Timmis, Jon},
  year = {2005},
  volume = {3630},
  pages = {423--432},
  publisher = {{Springer Berlin Heidelberg}},
  address = {{Berlin, Heidelberg}},
  doi = {10.1007/11553090_43},
  abstract = {In this paper we investigate the evolutionary pressures influencing genome size in artificial organisms. These were designed with three organisation levels (genome, proteome, phenotype) and are submitted to local mutations as well as rearrangements of the genomic structure. Experiments with various per-locus mutation rates show that the genome size always stabilises, although the fitness computation does not penalise genome length. The equilibrium value is closely dependent on the mutational pressure, resulting in a constant genome-wide mutation rate and a constant average impact of rearrangements. Genome size therefore selfadapts to the variation intensity, reflecting a balance between at least two pressures: evolving more and more complex functions with more and more genes, and preserving genome robustness by keeping it small.},
  isbn = {978-3-540-28848-0 978-3-540-31816-3},
  langid = {english}
}

@article{kouzine2013,
  title = {Transcription-Dependent Dynamic Supercoiling Is a Short-Range Genomic Force},
  author = {Kouzine, Fedor and Gupta, Ashutosh and Baranello, Laura and Wojtowicz, Damian and {Ben-Aissa}, Khadija and Liu, Juhong and Przytycka, Teresa M and Levens, David},
  year = {2013},
  month = mar,
  journal = {Nature Structural \& Molecular Biology},
  volume = {20},
  number = {3},
  pages = {396--403},
  issn = {1545-9993, 1545-9985},
  doi = {10.1038/nsmb.2517},
  langid = {english}
}

@article{krogh2018,
  title = {Impact of {{Chromosomal Architecture}} on the {{Function}} and {{Evolution}} of {{Bacterial Genomes}}},
  author = {Krogh, Th{\o}ger J. and {M{\o}ller-Jensen}, Jakob and Kaleta, Christoph},
  year = {2018},
  month = aug,
  journal = {Frontiers in Microbiology},
  volume = {9},
  pages = {2019},
  issn = {1664-302X},
  doi = {10.3389/fmicb.2018.02019},
  abstract = {The bacterial nucleoid is highly condensed and forms compartment-like structures within the cell. Much attention has been devoted to investigating the dynamic topology and organization of the nucleoid. In contrast, the specific nucleoid organization, and the relationship between nucleoid structure and function is often neglected with regard to importance for adaption to changing environments and horizontal gene acquisition. In this review, we focus on the structure-function relationship in the bacterial nucleoid. We provide an overview of the fundamental properties that shape the chromosome as a structured yet dynamic macromolecule. These fundamental properties are then considered in the context of the living cell, with focus on how the informational flow affects the nucleoid structure, which in turn impacts on the genetic output. Subsequently, the dynamic living nucleoid will be discussed in the context of evolution. We will address how the acquisition of foreign DNA impacts nucleoid structure, and conversely, how nucleoid structure constrains the successful and sustainable chromosomal integration of novel DNA. Finally, we will discuss current challenges and directions of research in understanding the role of chromosomal architecture in bacterial survival and adaptation.},
  langid = {english}
}

@article{kuo2009,
  title = {The Consequences of Genetic Drift for Bacterial Genome Complexity},
  author = {Kuo, Chih-Horng and Moran, Nancy A. and Ochman, Howard},
  year = {2009},
  month = aug,
  journal = {Genome Research},
  volume = {19},
  number = {8},
  pages = {1450--1454},
  issn = {1088-9051},
  doi = {10.1101/gr.091785.109},
  abstract = {Genetic drift, which is particularly effective within small populations, can shape the size and complexity of genomes by affecting the fixation of deleterious mutations. In Bacteria, assessing the contribution of genetic drift to genome evolution is problematic because the usual methods, based on intraspecific polymorphisms, can be thwarted by difficulties in delineating species' boundaries. The increased availability of sequenced bacterial genomes allows application of an alternative estimator of drift, the genome-wide ratio of replacement to silent substitutions in protein-coding sequences. This ratio, which reflects the action of purifying selection across the entire genome, shows a strong inverse relationship with genome size, indicating that drift promotes genome reduction in bacteria.},
  langid = {english}
}

@article{lal2016,
  title = {Genome Scale Patterns of Supercoiling in a Bacterial Chromosome},
  author = {Lal, Avantika and Dhar, Amlanjyoti and Trostel, Andrei and Kouzine, Fedor and Seshasayee, Aswin S. N. and Adhya, Sankar},
  year = {2016},
  month = apr,
  journal = {Nature Communications},
  volume = {7},
  number = {1},
  pages = {11055},
  issn = {2041-1723},
  doi = {10.1038/ncomms11055},
  langid = {english}
}

@inproceedings{lam2015,
  title = {Numba: A {{LLVM-based Python JIT}} Compiler},
  shorttitle = {Numba},
  booktitle = {Proceedings of the {{Second Workshop}} on the {{LLVM Compiler Infrastructure}} in {{HPC}} - {{LLVM}} '15},
  author = {Lam, Siu Kwan and Pitrou, Antoine and Seibert, Stanley},
  year = {2015},
  pages = {1--6},
  publisher = {{ACM Press}},
  address = {{Austin, Texas}},
  doi = {10.1145/2833157.2833162},
  abstract = {Dynamic, interpreted languages, like Python, are attractive for domain-experts and scientists experimenting with new ideas. However, the performance of the interpreter is often a barrier when scaling to larger data sets. This paper presents a just-in-time compiler for Python that focuses in scientific and array-oriented computing. Starting with the simple syntax of Python, Numba compiles a subset of the language into efficient machine code that is comparable in performance to a traditional compiled language. In addition, we share our experience in building a JIT compiler using LLVM[1].},
  isbn = {978-1-4503-4005-2},
  langid = {english}
}

@article{lenski1991,
  title = {Long-{{Term Experimental Evolution}} in {{Escherichia}} Coli. {{I}}. {{Adaptation}} and {{Divergence During}} 2,000 {{Generations}}},
  author = {Lenski, Richard E. and Rose, Michael R. and Simpson, Suzanne C. and Tadler, Scott C.},
  year = {1991},
  journal = {The American Naturalist},
  volume = {138},
  number = {6},
  pages = {1315--1341},
  abstract = {We assess thedegreeto whichadaptationto a uniformenvironmenatmongindependentlyevolvingasexual populationsis associated withincreasingdivergenceof those populations. In addition,we are concernedwiththe patternof adaptationitself,particularlywhether therateof increase in mean fitnesstendsto declinewiththenumberofgenerationsof selection in a constantenvironmentT. he correspondencebetween the rate of increase in mean fitness and the within-populationgenetic variance of fitness,as expected fromFisher's fundamental theorem,is also addressed. Twelve Escherichlia coli populationswere foundedfroma single clonal ancestor and allowed to evolve for2,000 generations.Mean fitnessincreased by about 37\%. However, the rateof increase in mean fitnesswas slowerin latergenerations.There was no statisticallysignificanwt ithin-populatiogneneticvarianceoffitness,buttherewas significant between-populationvariance. Althoughtheestimatedgeneticvariationin fitnesswithinpopulations was not statisticallysignificanti,t was consistentin magnitudewiththeoreticalexpectations. Similarly,the varianceof mean fitnessbetweenpopulationswas consistentwitha model thatincorporatedstochasticvariationin thetimingand orderof substitutionast a finitenumber of nonepistaticloci, coupled withsubstitutionadl elays and interferencbeetween substitutions arisingfromclonality.These results,takenas a whole, are consistentwiththeoreticalexpectations thatdo not invoke divergencedue to multiplefitnesspeaks in a Wrightianevolutionary landscape.},
  langid = {english}
}

@article{lepage2019,
  title = {A Polymer Model of Bacterial Supercoiled {{DNA}} Including Structural Transitions of the Double Helix},
  author = {Lepage, Thibaut and Junier, Ivan},
  year = {2019},
  month = aug,
  journal = {Physica A: Statistical Mechanics and its Applications},
  volume = {527},
  pages = {121196},
  issn = {03784371},
  doi = {10.1016/j.physa.2019.121196},
  abstract = {DNA supercoiling, the under or overwinding of DNA, is a key physical mechanism both participating to compaction of bacterial genomes and making genomic sequences adopt various structural forms. DNA supercoiling may lead to the formation of braided superstructures (plectonemes), or it may locally destabilize canonical B-DNA to generate denaturation bubbles, left-handed Z-DNA and other functional alternative forms. Prediction of the relative fraction of these structures has been limited because of a lack of predictive polymer models that can capture the multiscale properties of long DNA molecules. In this work, we address this issue by extending the self-avoiding rodlike chain model of DNA so that every site of the chain is allocated with an additional structural degree of freedom reflecting variations of DNA forms. Efficient simulations of the model reveal its relevancy to capture multiscale properties of long chains (here up to 21 kb) as reported in magnetic tweezers experiments. Well-controlled approximations further lead to accurate analytical estimations of thermodynamic properties in the high force regime, providing, in combination with experiments, a simple, yet powerful framework to infer physical parameters describing alternative forms. In this regard, using simulated data, we find that extension curves at forces above 2 pN may lead, alone, to erroneous parameter estimations as a consequence of an underdetermination problem. We thus revisit published data in light of these findings and discuss the relevancy of previously proposed sets of parameters for both denatured and left-handed DNA forms. Altogether, our work paves the way for a scalable quantitative model of bacterial DNA. \textcopyright{} 2019 Elsevier B.V. All rights reserved.},
  langid = {english}
}

@article{levy2004,
  title = {Antibacterial Resistance Worldwide: Causes, Challenges and Responses},
  shorttitle = {Antibacterial Resistance Worldwide},
  author = {Levy, Stuart B and Marshall, Bonnie},
  year = {2004},
  month = dec,
  journal = {Nature Medicine},
  volume = {10},
  number = {S12},
  pages = {S122-S129},
  issn = {1078-8956, 1546-170X},
  doi = {10.1038/nm1145},
  langid = {english}
}

@phdthesis{liard2020,
  type = {Th\`eses},
  title = {Origine \'Evolutive de La Complexit\'e Des Syst\`emes Biologiques : {{Une}} \'Etude Par \'Evolution Exp\'erimentale in Silico},
  author = {Liard, Vincent},
  year = {2020},
  month = oct,
  number = {2020LYSEI085},
  hal_id = {tel-03177236},
  hal_version = {v1},
  pdf = {https://tel.archives-ouvertes.fr/tel-03177236/file/these.pdf},
  school = {Universit\'e de Lyon}
}

@article{liu1987,
  title = {Supercoiling of the {{DNA}} Template during Transcription.},
  author = {Liu, L. F. and Wang, J. C.},
  year = {1987},
  month = oct,
  journal = {Proceedings of the National Academy of Sciences},
  volume = {84},
  number = {20},
  pages = {7024--7027},
  issn = {0027-8424, 1091-6490},
  doi = {10.1073/pnas.84.20.7024},
  abstract = {Transcription of a right-handed double-helical DNA requires a relative rotation of the RNA polymerase and its nascent RNA around the DNA. We describe conditions under which the resistance to the rotational motion of the transcription ensemble around the DNA can be large. In such cases, the advancing polymerase generates positive supercoils in the DNA template ahead of it and negative supercoils behind it. Mutual annihilation of the positively and negatively supercoiled regions may be prevented by anchoring points on the DNA to a large structure, or, in the case of an unanchored plasmid, by the presence of two oppositely oriented transcription units. In prokaryotes, DNA topoisomerase I preferentially removes negative supercoils and DNA gyrase (topoisomerase II) removes positive ones. Our model thus provides an explanation for the experimentally observed high degree of negative or positive supercoiling of intracellular pBR322 DNA when DNA topoisomerase I or gyrase is respectively inhibited. We discuss the implications of our model in terms of supercoiling regulation, DNA conformational transitions, and gene regulation in both prokaryotes and eukaryotes.},
  langid = {english}
}

@article{ma2016,
  title = {{{DNA}} Supercoiling during Transcription},
  author = {Ma, Jie and Wang, Michelle D.},
  year = {2016},
  month = nov,
  journal = {Biophysical Reviews},
  volume = {8},
  number = {S1},
  pages = {75--87},
  issn = {1867-2450, 1867-2469},
  doi = {10.1007/s12551-016-0215-9},
  abstract = {The twin-supercoiled-domain model describes how transcription can drive DNA supercoiling, and how DNA supercoiling, in turn, plays an important role in regulating gene transcription. In vivo and in vitro experiments have disclosed many details of the complex interactions in this relationship, and, recently, new insights have been gained with the help of genome-wide DNA supercoiling mapping techniques and single-molecule methods. This review summarizes the general mechanisms of the interplay between DNA supercoiling and transcription, considers the biological implications, and focuses on recent important discoveries and technical advances in this field. We highlight the significant impact of DNA supercoiling in transcription, but also more broadly in all processes operating on DNA.},
  langid = {english}
}

@article{marshall2000,
  title = {{{DNA}} Topology and Adaptation of {{Salmonella Typhimurium}} to an Intracellular Environment},
  author = {Marshall, David G and Bowe, Frances and Hale, Christine and Dougan, Gordon and Dorman, Charles J},
  year = {2000},
  journal = {Phil. Trans. R. Soc. Lond. B},
  pages = {10},
  langid = {english}
}

@article{martisb.2019,
  title = {{{DNA Supercoiling}}: An {{Ancestral Regulator}} of {{Gene Expression}} in {{Pathogenic Bacteria}}?},
  shorttitle = {{{DNA Supercoiling}}},
  author = {Martis B., Shiny and Forquet, Rapha{\"e}l and Reverchon, Sylvie and Nasser, William and Meyer, Sam},
  year = {2019},
  journal = {Computational and Structural Biotechnology Journal},
  volume = {17},
  pages = {1047--1055},
  issn = {20010370},
  doi = {10.1016/j.csbj.2019.07.013},
  abstract = {DNA supercoiling acts as a global and ancestral regulator of bacterial gene expression. In this review, we advocate that it plays a pivotal role in host-pathogen interactions by transducing environmental signals to the bacterial chromosome and coordinating its transcriptional response. We present available evidence that DNA supercoiling is modulated by environmental stress conditions relevant to the infection process according to ancestral mechanisms, in zoopathogens as well as phytopathogens. We review the results of transcriptomics studies obtained in widely distant bacterial species, showing that such structural transitions of the chromosome are associated to a complex transcriptional response affecting a large fraction of the genome. Mechanisms and computational models of the transcriptional regulation by DNA supercoiling are then discussed, involving both basal interactions of RNA Polymerase with promoter DNA, and more specific interactions with regulatory proteins. A final part is specifically focused on the regulation of virulence genes within pathogenicity islands of several pathogenic bacterial species.},
  langid = {english}
}

@article{menzel1987,
  title = {Modulation of Transcription by {{DNA}} Supercoiling: A Deletion Analysis of the {{Escherichia}} Coli {{gyrA}} and {{gyrB}} Promoters.},
  shorttitle = {Modulation of Transcription by {{DNA}} Supercoiling},
  author = {Menzel, R and Gellert, M},
  year = {1987},
  month = jun,
  journal = {Proceedings of the National Academy of Sciences},
  volume = {84},
  number = {12},
  pages = {4185--4189},
  issn = {0027-8424, 1091-6490},
  doi = {10.1073/pnas.84.12.4185},
  abstract = {Expression of the genes determining the subunits of Escherichia coli DNA gyrase (gyrA and gyrB) is known to be induced by relaxation of the template DNA. In this paper we report a deletion analysis of the gyrA and gyrB promoter regions. We find that a DNA sequence 20 base pairs long that includes the -10 consensus region, the transcription start point, and the first few transcribed bases is responsible for the property of induction by DNA relaxation. We propose a model for relaxation-stimulated transcription in which promoter clearance is the rate-limiting step.},
  langid = {english}
}

@article{meyer2014,
  title = {Torsion-{{Mediated Interaction}} between {{Adjacent Genes}}},
  author = {Meyer, Sam and Beslon, Guillaume},
  editor = {Morozov, Alexandre V.},
  year = {2014},
  month = sep,
  journal = {PLoS Computational Biology},
  volume = {10},
  number = {9},
  pages = {e1003785},
  issn = {1553-7358},
  doi = {10.1371/journal.pcbi.1003785},
  abstract = {DNA torsional stress is generated by virtually all biomolecular processes involving the double helix, in particular transcription where a significant level of stress propagates over several kilobases. If another promoter is located in this range, this stress may strongly modify its opening properties, and hence facilitate or hinder its transcription. This mechanism implies that transcribed genes distant of a few kilobases are not independent, but coupled by torsional stress, an effect for which we propose the first quantitative and systematic model. In contrast to previously proposed mechanisms of transcriptional interference, the suggested coupling is not mediated by the transcription machineries, but results from the universal mechanical features of the double-helix. The model shows that the effect likely affects prokaryotes as well as eukaryotes, but with different consequences owing to their different basal levels of torsion. It also depends crucially on the relative orientation of the genes, enhancing the expression of eukaryotic divergent pairs while reducing that of prokaryotic convergent ones. To test the in vivo influence of the torsional coupling, we analyze the expression of isolated gene pairs in the Drosophila melanogaster genome. Their orientation and distance dependence is fully consistent with the model, suggesting that torsional gene coupling may constitute a widespread mechanism of (co)regulation in eukaryotes.},
  langid = {english}
}

@article{meyer2018,
  title = {Chromosomal Organization of Transcription: In a Nutshell},
  shorttitle = {Chromosomal Organization of Transcription},
  author = {Meyer, Sam and Reverchon, Sylvie and Nasser, William and Muskhelishvili, Georgi},
  year = {2018},
  month = jun,
  journal = {Current Genetics},
  volume = {64},
  number = {3},
  pages = {555--565},
  issn = {0172-8083, 1432-0983},
  doi = {10.1007/s00294-017-0785-5},
  abstract = {Early studies of transcriptional regulation focused on individual gene promoters defined specific transcription factors as central agents of genetic control. However, recent genome-wide data propelled a different view by linking spatially organized gene expression patterns to chromosomal dynamics. Therefore, the major problem in contemporary molecular genetics concerned with transcriptional gene regulation is to establish a unifying model that reconciles these two views. This problem, situated at the interface of polymer physics and network theory, requires development of an integrative methodology. In this review, we discuss recent achievements in classical model organism E. coli and provide some novel insights gained from studies of a bacterial plant pathogen, D. dadantii. We consider DNA topology and the basal transcription machinery as key actors of regulation, in which activation of functionally relevant genes is coupled to and coordinated with the establishment of extended chromosomal domains of coherent transcription. We argue that the spatial organization of genome plays a fundamental role in its own regulation.},
  langid = {english}
}

@article{muskhelishvili2019,
  title = {Coherent {{Domains}} of {{Transcription Coordinate Gene Expression During Bacterial Growth}} and {{Adaptation}}},
  author = {Muskhelishvili, Georgi and Forquet, Rapha{\"e}l and Reverchon, Sylvie and Meyer, Sam and Nasser, William},
  year = {2019},
  month = dec,
  journal = {Microorganisms},
  volume = {7},
  number = {12},
  pages = {694},
  issn = {2076-2607},
  doi = {10.3390/microorganisms7120694},
  abstract = {Recent studies strongly suggest that in bacteria, both the genomic pattern of DNA thermodynamic stability and the order of genes along the chromosomal origin-to-terminus axis are highly conserved and that this spatial organization plays a crucial role in coordinating genomic transcription. In this article, we explore the relationship between genomic sequence organization and transcription in the commensal bacterium Escherichia coli and the plant pathogen Dickeya. We argue that, while in E. coli the gradient of DNA thermodynamic stability and gene order along the origin-to-terminus axis represent major organizational features orchestrating temporal gene expression, the genomic sequence organization of Dickeya is more complex, demonstrating extended chromosomal domains of thermodynamically distinct DNA sequences eliciting specific transcriptional responses to various kinds of stress encountered during pathogenic growth. This feature of the Dickeya genome is likely an adaptation to the pathogenic lifestyle utilizing differences in genomic sequence organization for the selective expression of virulence traits. We propose that the coupling of DNA thermodynamic stability and genetic function provides a common organizational principle for the coordinated expression of genes during both normal and pathogenic bacterial growth.},
  langid = {english}
}

@article{nelson1999,
  title = {Evidence for Lateral Gene Transfer between {{Archaea}} and {{Bacteria}} from Genome Sequence of {{Thermotoga}} Maritima},
  author = {Nelson, Karen E. and Clayton, Rebecca A. and Gill, Steven R. and Gwinn, Michelle L. and Dodson, Robert J. and Haft, Daniel H. and Hickey, Erin K. and Peterson, Jeremy D. and Nelson, William C. and Ketchum, Karen A. and McDonald, Lisa and Utterback, Teresa R. and Malek, Joel A. and Linher, Katja D. and Garrett, Mina M. and Stewart, Ashley M. and Cotton, Matthew D. and Pratt, Matthew S. and Phillips, Cheryl A. and Richardson, Delwood and Heidelberg, John and Sutton, Granger G. and Fleischmann, Robert D. and Eisen, Jonathan A. and White, Owen and Salzberg, Steven L. and Smith, Hamilton O. and Venter, J. Craig and Fraser, Claire M.},
  year = {1999},
  month = may,
  journal = {Nature},
  volume = {399},
  number = {6734},
  pages = {323--329},
  issn = {0028-0836, 1476-4687},
  doi = {10.1038/20601},
  langid = {english}
}

@article{nelson2004,
  title = {The Regulatory Content of Intergenic {{DNA}} Shapes Genome Architecture},
  author = {Nelson, Craig E and Hersh, Bradley M and Carroll, Sean B},
  year = {2004},
  journal = {Genome Biology},
  pages = {15},
  abstract = {Background: Factors affecting the organization and spacing of functionally unrelated genes in metazoan genomes are not well understood. Because of the vast size of a typical metazoan genome compared to known regulatory and protein-coding regions, functional DNA is generally considered to have a negligible impact on gene spacing and genome organization. In particular, it has been impossible to estimate the global impact, if any, of regulatory elements on genome architecture. Results: To investigate this, we examined the relationship between regulatory complexity and gene spacing in Caenorhabditis elegans and Drosophila melanogaster. We found that gene density directly reflects local regulatory complexity, such that the amount of noncoding DNA between a gene and its nearest neighbors correlates positively with that gene's regulatory complexity. Genes with complex functions are flanked by significantly more noncoding DNA than genes with simple or housekeeping functions. Genes of low regulatory complexity are associated with approximately the same amount of noncoding DNA in D. melanogaster and C. elegans, while loci of high regulatory complexity are significantly larger in the more complex animal. Complex genes in C. elegans have larger 5' than 3' noncoding intervals, whereas those in D. melanogaster have roughly equivalent 5' and 3' noncoding intervals. Conclusions: Intergenic distance, and hence genome architecture, is highly nonrandom. Rather, it is shaped by regulatory information contained in noncoding DNA. Our findings suggest that in compact genomes, the species-specific loss of nonfunctional DNA reveals a landscape of regulatory information by leaving a profile of functional DNA in its wake.},
  langid = {english}
}

@article{ofria2004,
  title = {Avida: {{A Software Platform}} for {{Research}} in {{Computational Evolutionary Biology}}},
  shorttitle = {Avida},
  author = {Ofria, Charles and Wilke, Claus O.},
  year = {2004},
  month = mar,
  journal = {Artificial Life},
  volume = {10},
  number = {2},
  pages = {191--229},
  issn = {1064-5462, 1530-9185},
  doi = {10.1162/106454604773563612},
  abstract = {Avida is a software platform for experiments with self-replicating and evolving computer programs. It provides detailed control over experimental settings and protocols, a large array of measurement tools, and sophisticated methods to analyze and post-process experimental data. We explain the general principles on which Avida is built, as well as its main components and their interactions. We also explain how experiments are set up, carried out, and analyzed.},
  langid = {english}
}

@article{peter2004,
  title = {Genomic Transcriptional Response to Loss of Chromosomal Supercoiling in {{Escherichia}} Coli},
  author = {Peter, Brian J and Arsuaga, Javier and Breier, Adam M and Khodursky, Arkady B and Brown, Patrick O and Cozzarelli, Nicholas R},
  year = {2004},
  journal = {Genome Biology},
  pages = {16},
  abstract = {Background: The chromosome of Escherichia coli is maintained in a negatively supercoiled state, and supercoiling levels are affected by growth phase and a variety of environmental stimuli. In turn, supercoiling influences local DNA structure and can affect gene expression. We used microarrays representing nearly the entire genome of Escherichia coli MG1655 to examine the dynamics of chromosome structure. Results: We measured the transcriptional response to a loss of supercoiling caused either by genetic impairment of a topoisomerase or addition of specific topoisomerase inhibitors during logphase growth and identified genes whose changes are statistically significant. Transcription of 7\% of the genome (306 genes) was rapidly and reproducibly affected by changes in the level of supercoiling; the expression of 106 genes increased upon chromosome relaxation and the expression of 200 decreased. These changes are most likely to be direct effects, as the kinetics of their induction or repression closely follow the kinetics of DNA relaxation in the cells. Unexpectedly, the genes induced by relaxation have a significantly enriched AT content in both upstream and coding regions. Conclusions: The 306 supercoiling-sensitive genes are functionally diverse and widely dispersed throughout the chromosome. We propose that supercoiling acts as a second messenger that transmits information about the environment to many regulatory networks in the cell.},
  langid = {english}
}

@article{pineau2022a,
  title = {What Is a Supercoiling-Sensitive Gene? {{Insights}} from Topoisomerase {{I}} Inhibition in the {{Gram-negative}} Bacterium {{{\emph{Dickeya}}}}{\emph{ Dadantii}}},
  shorttitle = {What Is a Supercoiling-Sensitive Gene?},
  author = {Pineau, Ma{\"i}wenn and Martis~B., Shiny and Forquet, Rapha{\"e}l and Baude, Jessica and Villard, Camille and Grand, Lucie and Popowycz, Florence and Soul{\`e}re, Laurent and Hommais, Florence and Nasser, William and Reverchon, Sylvie and Meyer, Sam},
  year = {2022},
  month = sep,
  journal = {Nucleic Acids Research},
  volume = {50},
  number = {16},
  pages = {9149--9161},
  issn = {0305-1048, 1362-4962},
  doi = {10.1093/nar/gkac679},
  abstract = {DNA supercoiling is an essential mechanism of bacterial chromosome compaction, whose level is mainly regulated by topoisomerase I and DNA gyrase. Inhibiting either of these enzymes with antibiotics leads to global supercoiling modifications and subsequent changes in global gene expression. In previous studies, genes responding to DNA relaxation induced by DNA gyrase inhibition were categorised as `supercoiling-sensitive'. Here, we studied the opposite variation of DNA supercoiling in the phytopathogen Dickeya dadantii using the non-marketed antibiotic seconeolitsine. We showed that the drug is active against topoisomerase I from this species, and analysed the first transcriptomic response of a Gramnegative bacterium to topoisomerase I inhibition. We find that the responding genes essentially differ from those observed after DNA relaxation, and further depend on the growth phase. We characterised these genes at the functional level, and also detected distinct patterns in terms of expression level, spatial and orientational organisation along the chromosome. Altogether, these results highlight that the supercoiling-sensitivity is a complex feature, which depends on the action of specific topoisomerases, on the physiological conditions, and on their genomic context. Based on previous in vitro expression data of several promoters, we propose a qualitative model of SC-dependent regulation that accounts for many of the contrasting transcriptomic features observed after DNA gyrase or topoisomerase I inhibition.},
  langid = {english}
}

@article{postow2004,
  title = {Topological Domain Structure of the {{Escherichia}} Coli Chromosome},
  author = {Postow, L. and Hardy, Christine D. and Arsuaga, Javier and Cozzarelli, Nicholas R},
  year = {2004},
  month = jul,
  journal = {Genes \& Development},
  volume = {18},
  number = {14},
  pages = {1766--1779},
  issn = {0890-9369},
  doi = {10.1101/gad.1207504},
  langid = {english}
}

@article{rhee1999,
  title = {Transcriptional Coupling between the Divergent Promoters of a Prototypic {{LysR-type}} Regulatory System, the {{ilvYC}} Operon of {{Escherichia}} Coli},
  author = {Rhee, K. Y. and Opel, M. and Ito, E. and Hung, S.-p. and Arfin, S. M. and Hatfield, G. W.},
  year = {1999},
  month = dec,
  journal = {Proceedings of the National Academy of Sciences},
  volume = {96},
  number = {25},
  pages = {14294--14299},
  issn = {0027-8424, 1091-6490},
  doi = {10.1073/pnas.96.25.14294},
  langid = {english}
}

@article{rutten2019,
  title = {Adapting the Engine to the Fuel: Mutator Populations Can Reduce the Mutational Load by Reorganizing Their Genome Structure},
  shorttitle = {Adapting the Engine to the Fuel},
  author = {Rutten, Jacob Pieter and Hogeweg, Paulien and Beslon, Guillaume},
  year = {2019},
  month = dec,
  journal = {BMC Evolutionary Biology},
  volume = {19},
  number = {1},
  pages = {191},
  issn = {1471-2148},
  doi = {10.1186/s12862-019-1507-z},
  abstract = {Background: Mutators are common in bacterial populations, both in natural isolates and in the lab. The fate of these lineages, which mutation rate is increased up to 100\texttimes, has long been studied using population genetics models, showing that they can spread in a population following an environmental change. However in stable conditions, they suffer from the increased mutational load, hence being overcome by non-mutators. However, these results don't take into account the fact that an elevated mutation rate can impact the genetic structure, hence changing the sensitivity of the population to mutations. Here we used Aevol, an in silico experimental evolution platform in which genomic structures are free to evolve, in order to study the fate of mutator populations evolving for a long time in constant conditions. Results: Starting from wild-types that were pre-evolved for 300,000 generations, we let 100 mutator populations (point mutation rate \texttimes 100) evolve for 100,000 further generations in constant conditions. As expected all populations initially undergo a fitness loss. However, after that the mutator populations started to recover. Most populations ultimately recovered their ancestors fitness, and a significant fraction became even fitter than the non-mutator control clones that evolved in parallel. By analyzing the genomes of the mutators, we show that the fitness recovery is due to two mechanisms: i. an increase in robustness through compaction of the coding part of the mutator genomes, ii. an increase of the selection coefficient that decreases the mean-fitness of the population. Strikingly the latter is due to the accumulation of non-coding sequences in the mutators genomes. Conclusion: Our results show that the mutational burden that is classically thought to be associated with mutator phenotype is escapable. On the long run mutators adapted their genomes and reshaped the distribution of mutation effects. Therewith the lineage is able to recover fitness even though the population still suffers the elevated mutation rate. Overall these results change our view of mutator dynamics: by being able to reduce the deleterious effect of the elevated mutation rate, mutator populations may be able to last for a very long time; A situation commonly observed in nature.},
  langid = {english}
}

@article{schneiker2007,
  title = {Complete Genome Sequence of the Myxobacterium {{Sorangium}} Cellulosum},
  author = {Schneiker, Susanne and Perlova, Olena and Kaiser, Olaf and Gerth, Klaus and Alici, Aysel and Altmeyer, Matthias O and Bartels, Daniela and Bekel, Thomas and Beyer, Stefan and Bode, Edna and Bode, Helge B and Bolten, Christoph J and Choudhuri, Jomuna V and Doss, Sabrina and Elnakady, Yasser A and Frank, Bettina and Gaigalat, Lars and Goesmann, Alexander and Groeger, Carolin and Gross, Frank and Jelsbak, Lars and Jelsbak, Lotte and Kalinowski, J{\"o}rn and Kegler, Carsten and Knauber, Tina and Konietzny, Sebastian and Kopp, Maren and Krause, Lutz and Krug, Daniel and Linke, Bukhard and Mahmud, Taifo and {Martinez-Arias}, Rosa and McHardy, Alice C and Merai, Michelle and Meyer, Folker and Mormann, Sascha and {Mu{\~n}oz-Dorado}, Jose and Perez, Juana and Pradella, Silke and Rachid, Shwan and Raddatz, G{\"u}nter and Rosenau, Frank and R{\"u}ckert, Christian and Sasse, Florenz and Scharfe, Maren and Schuster, Stephan C and Suen, Garret and {Treuner-Lange}, Anke and Velicer, Gregory J and Vorh{\"o}lter, Frank-J{\"o}rg and Weissman, Kira J and Welch, Roy D and Wenzel, Silke C and Whitworth, David E and Wilhelm, Susanne and Wittmann, Christoph and Bl{\"o}cker, Helmut and P{\"u}hler, Alfred and M{\"u}ller, Rolf},
  year = {2007},
  month = nov,
  journal = {Nature Biotechnology},
  volume = {25},
  number = {11},
  pages = {1281--1289},
  issn = {1087-0156, 1546-1696},
  doi = {10.1038/nbt1354},
  langid = {english}
}

@article{sevier2017,
  title = {Mechanical {{Properties}} of {{Transcription}}},
  author = {Sevier, Stuart A. and Levine, Herbert},
  year = {2017},
  month = jun,
  journal = {Physical Review Letters},
  volume = {118},
  number = {26},
  pages = {268101},
  issn = {0031-9007, 1079-7114},
  doi = {10.1103/PhysRevLett.118.268101},
  langid = {english}
}

@article{sevier2018,
  title = {Properties of Gene Expression and Chromatin Structure with Mechanically Regulated Elongation},
  author = {Sevier, Stuart A and Levine, Herbert},
  year = {2018},
  month = jul,
  journal = {Nucleic Acids Research},
  volume = {46},
  number = {12},
  pages = {5924--5934},
  issn = {0305-1048, 1362-4962},
  doi = {10.1093/nar/gky382},
  abstract = {In recent years, physical elements of transcription have emerged as central in our understanding of gene expression. Recent work has been done introducing a simple description of the basic physical elements of transcription where RNA elongation, RNA polymerase (RNAP) rotation and DNA supercoiling are coupled (1). Here we generalize this framework to accommodate the behavior of many RNAPs operating on multiple genes on a shared piece of DNA. The resulting framework is combined with wellestablished stochastic processes of transcription resulting in a model which characterizes the impact of the mechanical properties of transcription on gene expression and DNA structure. Transcriptional bursting readily emerges as a common phenomenon with origins in the geometric nature of the genetic system and results in the bounding of gene expression statistics. Properties of a multiple gene system are examined with special attention paid to the role that genome composition (gene orientation, size and intergenic distance) plays in the ability of genes to transcribe. The role of transcription in shaping DNA structure is examined and the possibility of transcription driven domain formation is discussed.},
  langid = {english}
}

@misc{sevier2021,
  title = {Collective Polymerase Dynamics Emerge from {{DNA}} Supercoiling during Transcription},
  author = {Sevier, Stuart A. and Hormoz, Sahand},
  year = {2021},
  month = nov,
  institution = {{Biophysics}},
  doi = {10.1101/2021.11.24.469850},
  abstract = {All biological processes ultimately come from physical interactions. The mechanical properties of DNA play a critical role in transcription. RNA polymerase can over or under twist DNA (referred to as DNA supercoiling) when it moves along a gene resulting in mechanical stresses in DNA that impact its own motion and that of other polymerases. For example, when enough supercoiling accumulates, an isolated polymerase halts and transcription stops. DNA supercoiling can also mediate non-local interactions between polymerases that shape gene expression fluctuations. Here, we construct a comprehensive model of transcription that captures how RNA polymerase motion changes the degree of DNA supercoiling which in turn feeds back into the rate at which polymerases are recruited and move along the DNA. Surprisingly, our model predicts that a group of three or more polymerases move together at a constant velocity and sustain their motion (forming what we call a polymeton) whereas one or two polymerases would have halted. We further show that accounting for the impact of DNA supercoiling on both RNA polymerase recruitment and velocity recapitulates empirical observations of gene expression fluctuations. Finally, we propose a mechanical toggle switch whereby interactions between genes are mediated by DNA twisting as opposed to proteins. Understanding the mechanical regulation of gene expression provides new insights into how endogenous genes can interact and informs the design of new forms of engineered interactions.           PACS numbers:},
  langid = {english},
  note = {\url{https://www.biorxiv.org/content/10.1101/2021.11.24.469850v3}}
}

@article{sobetzko2016,
  title = {Transcription-Coupled {{DNA}} Supercoiling Dictates the Chromosomal Arrangement of Bacterial Genes},
  author = {Sobetzko, Patrick},
  year = {2016},
  month = feb,
  journal = {Nucleic Acids Research},
  volume = {44},
  number = {4},
  pages = {1514--1524},
  issn = {0305-1048, 1362-4962},
  doi = {10.1093/nar/gkw007},
  abstract = {Over the recent decade, the central importance of DNA supercoiling in chromosome organization and global gene regulation of bacteria became more and more visible. With a regulon comprising more than 2000 genes in Escherichia coli, DNA supercoiling is among the most influential regulators of gene expression found in bacteria so far. However, the mechanism creating thousands of diverse temporal gene expression patterns coordinated by DNA supercoiling remains unclear. In this study we show that a specific chromosomal arrangement of genes modulates the local levels of DNA supercoiling at gene promoters via transcription-coupled DNA supercoiling (TCDS) in the model organism E. coli. Our findings provide a consistent explanation for the strong positive coupling of temporal gene expression patterns of neighboring genes. Using comparative genomics we are furthermore able to provide evidence that TCDS is a driving force for the evolution of chromosomal gene arrangement patterns in other Enterobacteriaceae. With the currently available data of promoter supercoiling sensitivity we prove that the same principle is applicable also for the evolutionary distant gram-positive pathogenic bacterium Streptococcus pneumoniae. Moreover, our findings are fully consistent with recent investigations concerning the regulatory impact of TCDS on gene pairs in eukaryots underpinning the broad applicability of our analysis.},
  langid = {english}
}

@article{thomas1997,
  title = {Intragenic Duplication and Divergence in the Spectrin Superfamily of Proteins},
  author = {Thomas, G. H. and Newbern, E. C. and Korte, C. C. and Bales, M. A. and Muse, S. V. and Clark, A. G. and Kiehart, D. P.},
  year = {1997},
  month = dec,
  journal = {Molecular Biology and Evolution},
  volume = {14},
  number = {12},
  pages = {1285--1295},
  issn = {0737-4038, 1537-1719},
  doi = {10.1093/oxfordjournals.molbev.a025738},
  langid = {english}
}

@article{tobe1995,
  title = {Thermoregulation of {{virB}} Transcription in {{Shigella}} Flexneri by Sensing of Changes in Local {{DNA}} Superhelicity},
  author = {Tobe, T and Yoshikawa, M and Sasakawa, C},
  year = {1995},
  month = feb,
  journal = {Journal of Bacteriology},
  volume = {177},
  number = {4},
  pages = {1094--1097},
  issn = {0021-9193, 1098-5530},
  doi = {10.1128/jb.177.4.1094-1097.1995},
  abstract = {Transcription of the virB gene, a transcriptional regulator of invasion genes on the large plasmid of Shigella flexneri, is strictly regulated by growth temperature; when bacteria are grown at 37 degrees C, virB transcription is highly activated, while at 30 degrees C the level of virB transcription decreases to less than 5\% of that at 37 degrees C. Transcription from the virB promoter is activated by VirF, which is encoded on the same plasmid, in a DNA superhelicity-dependent manner (T. Tobe, M. Yoshikawa, T. Mizuno, and C. Sasakawa, J. Bacteriol. 175:6142-6149, 1993). Here we provide evidence supporting the involvement of negative superhelicity in the thermoregulation of virB transcription. A local negatively supercoiled domain in the virB promoter region was created by activating a divergent transcription from the T7 RNA polymerase-dependent promoter, phi 10, which was placed upstream of the virB promoter in the opposite orientation. Transcription from the virB promoter was activated even at 30 degrees C by induction of divergent transcription. Levels of virB transcription correlated with levels of expressed T7 RNA polymerase. Transcriptional activation of virB by the system depended completely upon VirF function. The level of virB transcription achieved by introducing a negatively supercoiled domain was enough to give rise to expression of invasion capacity at 30 degrees C. These results indicated that the repression of virB transcription at 30 degrees C was caused by a reduction in negative superhelicity around the virB promoter region at 30 degrees C.},
  langid = {english}
}

@article{toh2006,
  title = {Massive Genome Erosion and Functional Adaptations Provide Insights into the Symbiotic Lifestyle of {{{\emph{Sodalis}}}}{\emph{ Glossinidius}} in the Tsetse Host},
  author = {Toh, Hidehiro and Weiss, Brian L. and Perkin, Sarah A.H. and Yamashita, Atsushi and Oshima, Kenshiro and Hattori, Masahira and Aksoy, Serap},
  year = {2006},
  month = feb,
  journal = {Genome Research},
  volume = {16},
  number = {2},
  pages = {149--156},
  issn = {1088-9051},
  doi = {10.1101/gr.4106106},
  abstract = {Sodalis glossinidius               is a maternally transmitted endosymbiont of tsetse flies (               Glossina               spp.), an insect of medical and veterinary significance. Analysis of the complete sequence of               Sodalis               ' chromosome (4,171,146 bp, encoding 2,432 protein coding sequences) indicates a reduced coding capacity of 51\%. Furthermore, the chromosome contains 972 pseudogenes, an inordinately high number compared with that of other bacterial species. A high proportion of these pseudogenes are homologs of known proteins that function either in defense or in the transport and metabolism of carbohydrates and inorganic ions, suggesting               Sodalis               ' degenerative adaptations to the immunity and restricted nutritional status of the host.               Sodalis               possesses three chromosomal symbiosis regions (SSR): SSR-1, SSR-2, and SSR-3, with gene inventories similar to the Type-III secretion system (TTSS) ysa from               Yersinia enterolitica               and SPI-1 and SPI-2 from               Salmonella               , respectively. While core components of the needle structure have been conserved, some of the effectors and regulators typically associated with these systems in pathogenic microbes are modified or eliminated in               Sodalis               . Analysis of SSR-specific               invA               transcript abundance in               Sodalis               during host development indicates that the individual symbiosis regions may exhibit different temporal expression profiles. In addition, the               Sodalis               chromosome encodes a complete flagella structure, key components of which are expressed in immature host developmental stages. These features may be important for the transmission and establishment of symbiont infections in the intra-uterine progeny. The data suggest that               Sodalis               represents an evolutionary intermediate transitioning from a free-living to a mutualistic lifestyle.},
  langid = {english}
}

@article{travers2005,
  title = {{{DNA}} Supercoiling \textemdash{} a Global Transcriptional Regulator for Enterobacterial Growth?},
  author = {Travers, Andrew and Muskhelishvili, Georgi},
  year = {2005},
  month = feb,
  journal = {Nature Reviews Microbiology},
  volume = {3},
  number = {2},
  pages = {157--169},
  issn = {1740-1526, 1740-1534},
  doi = {10.1038/nrmicro1088},
  abstract = {A fundamental principle of exponential bacterial growth is that no more ribosomes are produced than are necessary to support the balance between nutrient availability and protein synthesis. Although this conclusion was first expressed more than 40 years ago, a full understanding of the molecular mechanisms involved remains elusive and the issue is still controversial. There is currently agreement that, although many different systems are undoubtedly involved in fine-tuning this balance, an important control, and in our opinion perhaps the main control, is regulation of the rate of transcription initiation of the stable (ribosomal and transfer) RNA transcriptons. In this review, we argue that regulation of DNA supercoiling provides a coherent explanation for the main modes of transcriptional control \textemdash stringent control, growth-rate control and growth-phase control \textemdash{} during the normal growth of Escherichia coli.},
  langid = {english}
}

@article{travers2005a,
  title = {Bacterial Chromatin},
  author = {Travers, Andrew and Muskhelishvili, Georgi},
  year = {2005},
  month = oct,
  journal = {Current Opinion in Genetics \& Development},
  volume = {15},
  number = {5},
  pages = {507--514},
  issn = {0959437X},
  doi = {10.1016/j.gde.2005.08.006},
  langid = {english}
}

@inproceedings{vadee-le-brun2016,
  title = {In {{Silico Experimental Evolution}} Suggests a Complex Intertwining of Selection, Robustness and Drift in the Evolution of Genetic Networks Complexity},
  booktitle = {Proceedings of the {{Artificial Life Conference}} 2016},
  author = {{Vad{\'e}e-Le-Brun}, Yoram and Beslon, Guillaume and {Rouzaud-Cornabas}, Jonathan},
  year = {2016},
  pages = {180--187},
  publisher = {{MIT Press}},
  address = {{Cancun, Mexico}},
  doi = {10.7551/978-0-262-33936-0-ch036},
  abstract = {Using the RAevol model we investigate whether the molecular complexity of evolving organisms is linked to the ``complexity'' of their environment. Here, the complexity is considered as the number of different states environments can have. Results strikingly show that the number of genes acquired by an organism during its evolution does not increase when the number of states of the environment increases but that the connectivity of their genetic regulation network actually does. On the opposite, we show that the mutation rate has an important influence on the gene content. We interpret these results as a complex intertwining of direct selective pressures (the more genes, the better the organisms can be) and robustness and drift thresholds that limit the maximum number of genes at different values depending on the mutation rates.},
  isbn = {978-0-262-33936-0},
  langid = {english}
}

@article{vinuelas2007,
  title = {Conservation of the Links between Gene Transcription and Chromosomal Organization in the Highly Reduced Genome of {{Buchnera}} Aphidicola},
  author = {Vi{\~n}uelas, Jos{\'e} and Calevro, Federica and Remond, Didier and Bernillon, Jacques and Rahb{\'e}, Yvan and Febvay, G{\'e}rard and Fayard, Jean-Michel and Charles, Hubert},
  year = {2007},
  journal = {BMC Genomics},
  volume = {8},
  number = {1},
  pages = {143},
  issn = {14712164},
  doi = {10.1186/1471-2164-8-143},
  abstract = {Background: Genomic studies on bacteria have clearly shown the existence of chromosomal organization as regards, for example, to gene localization, order and orientation. Moreover, transcriptomic analyses have demonstrated that, in free-living bacteria, gene transcription levels and chromosomal organization are mutually influenced. We have explored the possible conservation of relationships between mRNA abundances and chromosomal organization in the highly reduced genome of Buchnera aphidicola, the primary endosymbiont of the aphids, and a close relative to Escherichia coli. Results: Using an oligonucleotide-based microarray, we normalized the transcriptomic data by genomic DNA signals in order to have access to inter-gene comparison data. Our analysis showed that mRNA abundances, gene organization (operon) and gene essentiality are correlated in Buchnera (i.e., the most expressed genes are essential genes organized in operons) whereas no link between mRNA abundances and gene strand bias was found. The effect of Buchnera genome evolution on gene expression levels has also been analysed in order to assess the constraints imposed by the obligate symbiosis with aphids, underlining the importance of some gene sets for the survival of the two partners. Finally, our results show the existence of spatial periodic transcriptional patterns in the genome of Buchnera. Conclusion: Despite an important reduction in its genome size and an apparent decay of its capacity for regulating transcription, this work reveals a significant correlation between mRNA abundances and chromosomal organization of the aphid-symbiont Buchnera.},
  langid = {english}
}

@article{visser2022,
  title = {Psoralen Mapping Reveals a Bacterial Genome Supercoiling Landscape Dominated by Transcription},
  author = {Visser, Bryan J and Sharma, Sonum and Chen, Po J and McMullin, Anna B and Bates, Maia L and Bates, David},
  year = {2022},
  month = may,
  journal = {Nucleic Acids Research},
  volume = {50},
  number = {8},
  pages = {4436--4449},
  issn = {0305-1048, 1362-4962},
  doi = {10.1093/nar/gkac244},
  abstract = {DNA supercoiling is a key regulator of all DNA metabolic processes including replication, transcription, and recombination, yet a reliable genomic assay for supercoiling is lacking. Here, we present a robust and flexible method (Psora-seq) to measure whole-genome supercoiling at high resolution. Using this tool in Escherichia coli, we observe a supercoiling landscape that is well correlated to transcription. Supercoiling twin-domains generated by RNA polymerase complexes span 25 kb in each direction \textendash{} an order of magnitude farther than previous measurements in any organism. Thus, ribosomal and many other highly expressed genes strongly affect the topology of about 40 neighboring genes each, creating highly integrated gene circuits. Genomic patterns of supercoiling revealed by Psora-seq could be aptly predicted from modeling based on gene expression levels alone, indicating that transcription is the major determinant of chromosome supercoiling. Large-scale supercoiling patterns were highly symmetrical between left and right chromosome arms (replichores), indicating that DNA replication also strongly influences supercoiling. Skew in the axis of symmetry from the natural ori-ter axis supports previous indications that the rightward replication fork is delayed several minutes after initiation. Implications of supercoiling on DNA replication and chromosome domain structure are discussed.},
  langid = {english}
}

@article{webber2013,
  title = {Clinically {{Relevant Mutant DNA Gyrase Alters Supercoiling}}, {{Changes}} the {{Transcriptome}}, and {{Confers Multidrug Resistance}}},
  author = {Webber, Mark A. and Ricci, Vito and Whitehead, Rebekah and Patel, Meha and Fookes, Maria and Ivens, Alasdair and Piddock, Laura J. V.},
  editor = {Bush, Karen},
  year = {2013},
  month = aug,
  journal = {mBio},
  volume = {4},
  number = {4},
  issn = {2161-2129, 2150-7511},
  doi = {10.1128/mBio.00273-13},
  abstract = {Bacterial DNA is maintained in a supercoiled state controlled by the action of topoisomerases. Alterations in supercoiling affect fundamental cellular processes, including transcription. Here, we show that substitution at position 87 of GyrA of Salmonella influences sensitivity to antibiotics, including nonquinolone drugs, alters global supercoiling, and results in an altered transcriptome with increased expression of stress response pathways. Decreased susceptibility to multiple antibiotics seen with a GyrA Asp87Gly mutant was not a result of increased efflux activity or reduced reactive-oxygen production. These data show that a frequently observed and clinically relevant substitution within GyrA results in altered expression of numerous genes, including those important in bacterial survival of stress, suggesting that GyrA mutants may have a selective advantage under specific conditions. Our findings help contextualize the high rate of quinolone resistance in pathogenic strains of bacteria and may partly explain why such mutant strains are evolutionarily successful. IMPORTANCE Fluoroquinolones are a powerful group of antibiotics that target bacterial enzymes involved in helping bacteria maintain the conformation of their chromosome. Mutations in the target enzymes allow bacteria to become resistant to these antibiotics, and fluoroquinolone resistance is common. We show here that these mutations also provide protection against a broad range of other antimicrobials by triggering a defensive stress response in the cell. This work suggests that fluoroquinolone resistance mutations may be beneficial under a range of conditions.},
  langid = {english}
}

@misc{wortel2021,
  title = {Towards Evolutionary Predictions: Current Promises and Challenges},
  shorttitle = {Towards Evolutionary Predictions},
  author = {Wortel, Meike T. and Agashe, Deepa and Bailey, Susan F. and Bank, Claudia and Bisschop, Karen and Blankers, Thomas and Cairns, Johannes and Colizzi, Enrico Sandro and Cusseddu, Davide and Desai, Michael M. and {van Dijk}, Bram and Egas, Martijn and Ellers, Jacintha and Groot, Astrid T. and Hackel, David G. and Johnson, Marcelle L. and Kraaijeveld, Ken and Krug, Joachim and Laan, Liedewij and Laessig, Michael and Lind, Peter A. and Meijer, Jeroen and Noble, Luke M. and Okasha, Samir and Rainey, Paul B. and Rozen, Daniel E. and Shitut, Shraddha and Tans, Sander J. and Tenaillon, Olivier and Teotonio, Henrique and {de Visser}, J. Arjan G. M. and Visser, Marcel Erik and Vroomans, Renske M. A. and Werner, Gijsbert D. A. and Wertheim, Bregje and Pennings, Pleuni S.},
  year = {2021},
  month = aug,
  institution = {{EcoEvoRxiv}},
  doi = {10.32942/osf.io/4u3mg},
  abstract = {Evolution has traditionally been a historical and descriptive science and predicting future evolutionary processes has long been considered impossible. However, evolutionary predictions are increasingly being developed and used in medicine, agriculture, biotechnology and conservation biology. Evolutionary predictions may be used for different purposes, such as to prepare for the future, to try and change the course of evolution or to determine how well we understand evolutionary processes. Similarly, the exact aspect of the evolved population that we want to predict may also differ, for example we could try to predict which genotype will dominate, the fitness of the population, or the extinction probability of a population. In addition, there are many uses of evolutionary predictions that may not always be recognized as such. The main goal of this review is to increase awareness of methods and data that are used to make these predictions in different research fields by showing the breadth of situations in which evolutionary predictions are made. We describe how diverse evolutionary predictions share a common structure described by the predictive scope, time scale and precision. Then, by using examples ranging from SARS-CoV2 and influenza to CRISPR-based gene drives and sustainable product formation in biotechnology, we discuss the methods for predicting evolution, the factors that affect predictability, and how predictions can be used to prevent evolution in undesirable directions or to promote beneficial evolution (i.e. evolutionary control). We hope that this review will stimulate collaboration between fields by creating a common language for evolutionary predictions.},
  langid = {english},
  note = {\url{https://ecoevorxiv.org/4u3mg/}}
}