Order and disorder in bacterial genomes

Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2)

Bentley, S. D., Chater, K. F., Cerdeño-Tárraga, A. M., Challis, G. L., Thomson, N. R., James, K., Harris, D. E., Quail, M. A., Kieser, H. M., Harper, D., et al. (2002) · Nature · doi:10.1038/417141a · Cited by 3,226 · see citing works

Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori

Alm, R. A., Ling, L.-S. L., Moir, D. T., King, B. L., Brown, E. D., Doig, P. C., Smith, D. R., Noonan, B., Guild, B. C., deJonge, B. L., et al. (1999) · Nature · doi:10.1038/16495 · Cited by 1,893 · see citing works

rRNA Operon Copy Number Reflects Ecological Strategies of Bacteria

Klappenbach, J. A., Dunbar, J., & Schmidt, T. M. (2000) · Applied and Environmental Microbiology · doi:10.1128/aem.66.4.1328-1333.2000 · Cited by 1,140 · see citing works

Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica

Parkhill, J., Sebaihia, M., Preston, A., Murphy, L. D., Thomson, N., Harris, D. E., Holden, M. T. G., Churcher, C. M., Bentley, S. D., Mungall, K. L., et al. (2003) · Nature Genetics · doi:10.1038/ng1227 · Cited by 1,037 · see citing works

A bacterial genome in flux: the twelve linear and nine circular extrachromosomal DNAs in an infectious isolate of the Lyme disease spirochete Borrelia burgdorferi

Casjens, S., Palmer, N., van Vugt, R., Huang, W. M., Stevenson, B., Rosa, P. A., Lathigra, R. B., Sutton, G. G., Peterson, J. D., Dodson, R. J., et al. (2000) · Molecular Microbiology · doi:10.1046/j.1365-2958.2000.01698.x · Cited by 834 · see citing works

Adaptive evolution of highly mutable loci in pathogenic bacteria

Moxon, E. R., Rainey, P. B., Nowak, M. A., & Lenski, R. E. (1994) · Current Biology · doi:10.1016/s0960-9822(00)00005-1 · Cited by 755 · see citing works

Short-sequence DNA repeats in prokaryotic genomes

van Belkum, A., Scherer, S., van Alphen, L., & Verbrugh, H. (1998) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.62.2.275-293.1998 · Cited by 737 · see citing works

Evolution of rhizobia by acquisition of a 500-kb symbiosis island that integrates into a phe-tRNA gene

Sullivan, J. T., & Ronson, C. W. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.9.5145 · Cited by 603 · see citing works

Complete genome sequence of the marine planctomycete Pirellula sp. strain 1

Glöckner, F. O., Kube, M., Bauer, M., Teeling, H., Lombardot, T., Ludwig, W., Gade, D., Beck, A., Borzym, K., Heitmann, K., et al. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1431443100 · Cited by 482 · see citing works

Genome sequence of Streptococcus agalactiae, a pathogen causing invasive neonatal disease

Glaser, P., Rusniok, C., Buchrieser, C., Chevalier, F., Frangeul, L., Msadek, T., Zouine, M., Couvé, E., Lalioui, L., Poyart, C., et al. (2002) · Molecular Microbiology · doi:10.1046/j.1365-2958.2002.03126.x · Cited by 476 · see citing works

GENETICS OF BACTERIAL RIBOSOMES

Nomura, M., Morgan, E. A., & Jaskunas, S. R. (1977) · Annual Review of Genetics · doi:10.1146/annurev.ge.11.120177.001501 · Cited by 320 · see citing works

The replication-related organization of bacterial genomes

Rocha, E. P. C. (2004) · Microbiology · doi:10.1099/mic.0.26974-0 · Cited by 279 · see citing works

Genome Sequence of an M3 Strain of Streptococcus pyogenes Reveals a Large-Scale Genomic Rearrangement in Invasive Strains and New Insights into Phage EvolutionPreprint

Nakagawa, I., Kurokawa, K., Yamashita, A., Nakata, M., Tomiyasu, Y., Okahashi, N., Kawabata, S., Yamazaki, K., Shiba, T., Yasunaga, T., et al. (2003) · Genome Research · doi:10.1101/gr.1096703 · Cited by 275 · see citing works

Comparative analysis of the genomes of the bacteria Mycoplasma pneumoniae and Mycoplasma genitalium

Himmelreich, R., Plagens, H., Hilbert, H., Reiner, B., & Herrmann, R. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.4.701 · Cited by 261 · see citing works

The role of co‐transcriptional translation and protein translocation (transertion) in bacterial chromosome segregation

Woldringh, C. L. (2002) · Molecular Microbiology · doi:10.1046/j.1365-2958.2002.02993.x · Cited by 253 · see citing works

GENE AMPLIFICATION AND GENOMIC PLASTICITY IN PROKARYOTES

Romero, D., & Palacios, R. (1997) · Annual Review of Genetics · doi:10.1146/annurev.genet.31.1.91 · Cited by 237 · see citing works

Generating and Exploiting Polarity in Bacteria

Shapiro, L., McAdams, H. H., & Losick, R. M. (2002) · Science · doi:10.1126/science.1072163 · Cited by 228 · see citing works

Repeat‐associated phase variable genes in the complete genome sequence of Neisseria meningitidis strain MC58

Saunders, N. J. S. G., Jeffries, A. C., Peden, J. F., Hood, D. W., Tettelin, H., Rappuoli, R., & Moxon, E. R. (2000) · Molecular Microbiology · doi:10.1046/j.1365-2958.2000.02000.x · Cited by 227 · see citing works

Gene context conservation of a higher order than operons.

Lathe, W. C., Snel, B., & Bork, P. (2000) · TIBS -Trends in Biochemical Sciences. Regular ed · doi:10.1016/s0968-0004(00)01663-7 · Cited by 224 · see citing works

Comparative Analysis of Superintegrons: Engineering Extensive Genetic Diversity in the VibrionaceaePreprint

Rowe‐Magnus, D. A., Guérout, A.-M., Biskri, L., Bouige, P., & Mazel, D. (2003) · Genome Research · doi:10.1101/gr.617103 · Cited by 224 · see citing works

Essentiality, not expressiveness, drives gene-strand bias in bacteria

Rocha, E. P. C., & Danchin, A. (2003) · Nature Genetics · doi:10.1038/ng1209 · Cited by 211 · see citing works

Analysis of genomic context: prediction of functional associations from conserved bidirectionally transcribed gene pairs

Korbel, J., Jensen, L., von Mering, C., & Bork, P. (2004) · Nature Biotechnology · doi:10.1038/nbt988 · Cited by 210 · see citing works

Genome rearrangement by replication-directed translocation

Tillier, E. R. M., & Collins, R. A. (2000) · Nature Genetics · doi:10.1038/79918 · Cited by 192 · see citing works

Tropheryma whipplei Twist: A Human Pathogenic Actinobacteria With a Reduced GenomePreprint

Raoult, D., Ogata, H., Audic, S., Robert, C., Suhre, K., Drancourt, M., & Claverie, J. (2003) · Genome Research · doi:10.1101/gr.1474603 · Cited by 189 · see citing works

Organization of the Prokaryotic Genome

(1999) · ASM Press eBooks · doi:10.1128/9781555818180 · Cited by 170 · see citing works

Gene essentiality determines chromosome organisation in bacteria

Rocha, E. P. C. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg859 · Cited by 166 · see citing works

Genomic islands and the evolution of catabolic pathways in bacteria

van der Meer, J. R., & Sentchilo, V. (2003) · Current Opinion in Biotechnology · doi:10.1016/s0958-1669(03)00058-2 · Cited by 162 · see citing works

Once the circle has been broken: dynamics and evolution of Streptomyces chromosomes

Chen, C. W., Huang, C., Lee, H.-H., et al. (2002) · Trends in Genetics · doi:10.1016/s0168-9525(02)02752-x · Cited by 144 · see citing works

Extensive repetitive DNA facilitates prokaryotic genome plasticity

Aras, R. A., Kang, J., Tschumi, A. I., Harasaki, Y., & Blaser, M. J. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1735481100 · Cited by 138 · see citing works

Does RNA polymerase help drive chromosome segregation in bacteria?

Dworkin, J. E., & Losick, R. M. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.182539899 · Cited by 131 · see citing works

Why are the genomes of endosymbiotic bacteria so stable?

Silva, F. J., Latorre, A., & Moyá, A. (2003) · Trends in Genetics · doi:10.1016/s0168-9525(03)00041-6 · Cited by 119 · see citing works

Prokaryotic Chromosomes and Disease

Hacker, J. H., Hentschel, U., & Dobrindt, U. (2003) · Science · doi:10.1126/science.1086802 · Cited by 116 · see citing works

Impact of large chromosomal inversions on the adaptation and evolution of Pseudomonas aeruginosa chronically colonizing cystic fibrosis lungs

Kresse, A. U., Sriramulu, D. D., Larbig, K. D., & Römling, U. (2002) · Molecular Microbiology · doi:10.1046/j.1365-2958.2003.03261.x · Cited by 114 · see citing works

Rearrangement of the Bacterial Chromosome: Forbidden Inversions

Segall, A. M., Mahan, M. J., & Roth, J. R. (1988) · Science · doi:10.1126/science.3045970 · Cited by 107 · see citing works

The effect of gene concentration and relative gene dosage on gene output inEscherichia coli

Chandler, M., & Pritchard, R. H. (1975) · Molecular and General Genetics MGG · doi:10.1007/bf02428117 · Cited by 101 · see citing works

Effects of chromosomal inversion on cell fitness in Escherichia coli K-12.

Hill, C. W. L., & Gray, J. A. (1988) · Genetics · doi:10.1093/genetics/119.4.771 · Cited by 100 · see citing works

Loss of DNA Recombinational Repair Enzymes in the Initial Stages of Genome Degeneration

Dale, C. (2003) · Molecular Biology and Evolution · doi:10.1093/molbev/msg138 · Cited by 96 · see citing works

Is there a role for replication fork asymmetry in the distribution of genes in bacterial genomes?

Rocha, E. P. C. (2002) · Trends in Microbiology · doi:10.1016/s0966-842x(02)02420-4 · Cited by 96 · see citing works

Associations Between Inverted Repeats and the Structural Evolution of Bacterial Genomes

Achaz, G., Coissac, É., Netter, P., & Rocha, E. P. C. (2003) · Genetics · doi:10.1093/genetics/164.4.1279 · Cited by 95 · see citing works

Adaptive mutation: General mutagenesis is not a programmed response to stress but results from rare coamplification of dinB with lac

Slechta, E. S., Bunny, K. L., Kugelberg, E., Kofoid, E., Andersson, D. I., & Roth, J. R. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1735464100 · Cited by 94 · see citing works

Detection and possible role of two large nondivisible zones on the Escherichia coli chromosome.

Rebollo, J. E., François, V, & Louarn, J. M. (1988) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.85.24.9391 · Cited by 90 · see citing works

Genome deterioration: loss of repeated sequences and accumulation of junk DNA

Frank, A. C., Amiri, H., & Andersson, S. G. E. (2002) · Genetica · doi:10.1023/a:1016064511533 · Cited by 89 · see citing works

Natural Genomic Design in Sinorhizobium meliloti: Novel Genomic ArchitecturesPreprint

Guo, X., Flores, M., Mavingui, P., et al. (2003) · Genome Research · doi:10.1101/gr.1260903 · Cited by 88 · see citing works

Pyrococcus genome comparison evidences chromosome shuffling-driven evolution

Zivanovic, Y. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.9.1902 · Cited by 85 · see citing works

Gene Organization: Selection, Selfishness, and Serendipity

Lawrence, J. G. (2003) · Annual Review of Microbiology · doi:10.1146/annurev.micro.57.030502.090816 · Cited by 83 · see citing works

Genome plasticity in Acinetobacter: new degradative capabilities acquired by the spontaneous amplification of large chromosomal segments

Reams, A. B., & Neidle, E. L. (2003) · Molecular Microbiology · doi:10.1046/j.1365-2958.2003.03342.x · Cited by 80 · see citing works

An Appraisal of the Potential for Illegitimate Recombination in Bacterial Genomes and Its Consequences: From Duplications to Genome ReductionPreprint

Rocha, E. P. C. (2003) · Genome Research · doi:10.1101/gr.966203 · Cited by 69 · see citing works

Chromosomal constraints in Gram‐positive bacteria revealed by artificial inversions

Campo, N., Dias, M. J., Daveran‐Mingot, M. ‐., Ritzenthaler, P., & Le Bourgeois, P. (2004) · Molecular Microbiology · doi:10.1046/j.1365-2958.2003.03847.x · Cited by 68 · see citing works

Occurrence of deletions, associated with genetic instability in Streptomyces ambofaciens, is independent of the linearity of the chromosomal DNA

Fischer, G., Decaris, B., & Leblond, P. (1997) · Journal of Bacteriology · doi:10.1128/jb.179.14.4553-4558.1997 · Cited by 65 · see citing works

Experimental surgery to create subgenomes of Bacillus subtilis 168

Itaya, M., & Tanaka, T. (1997) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.94.10.5378 · Cited by 61 · see citing works

DNA repeats lead to the accelerated loss of gene order in bacteria

Rocha, E. P. C. (2003) · Trends in Genetics · doi:10.1016/j.tig.2003.09.011 · Cited by 59 · see citing works

Mapping the bacterial cell architecture into the chromosome

Danchin, A., Guerdoux-Jamet, P., Moszer, I., et al. (2000) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2000.0557 · Cited by 58 · see citing works

Cassette-like variation of restriction enzyme genes in Escherichia coli C and relatives

Sibley, M. H. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh194 · Cited by 56 · see citing works

Asymmetric activation of Xer site‐specific recombination by FtsK

Massey, T. H., Aussel, L., Barre, F., & Sherratt, D. J. (2004) · EMBO Reports · doi:10.1038/sj.embor.7400116 · Cited by 54 · see citing works

Flip-flop around the origin and terminus of replication in prokaryotic genomes.

Mackiewicz, P., Mackiewicz, D., Kowalczuk, M., & Cebrat, S. (2001) · Genome biology · doi:10.1186/gb-2001-2-12-interactions1004 · Cited by 51 · see citing works

A strand‐specific model for chromosome segregation in bacteria

Rocha, E. P. C., Fralick, J. A., Vediyappan, G., Danchin, A., & Norris, V. (2003) · Molecular Microbiology · doi:10.1046/j.1365-2958.2003.03606.x · Cited by 47 · see citing works

Unequal access of chromosomal regions to each other in <i>Salmonella</i>: probing chromosome structure with phage λ integrase‐mediated long‐range rearrangements

Garcia‐Russell, N., Harmon, T. G., Le, T. Q., Amaladas, N. H., Mathewson, R. D., & Segall, A. M. (2004) · Molecular Microbiology · doi:10.1111/j.1365-2958.2004.03976.x · Cited by 43 · see citing works

From Genes to Genomes: Universal Scale-invariant Properties of Microbial Chromosome Organisation

Audit, B., & Ouzounis, C. A. (2003) · Journal of Molecular Biology · doi:10.1016/s0022-2836(03)00811-8 · Cited by 42 · see citing works

Genomic Rearrangements at rrn Operons in Salmonella

Helm, R. A., Lee, A., Christman, H. D., & Maloy, S. (2003) · Genetics · doi:10.1093/genetics/165.3.951 · Cited by 37 · see citing works

End‐to‐end fusion of linear deleted chromosomes initiates a cycle of genome instability in Streptomyces ambofaciens

Wenner, T., Roth, V., Fischer, G., et al. (2003) · Molecular Microbiology · doi:10.1046/j.1365-2958.2003.03698.x · Cited by 35 · see citing works

Sulphur islands in the Escherichia coli genome: markers of the cell's architecture?

Rocha, E. P. C., Sekowska, A., & Danchin, A. (2000) · FEBS Letters · doi:10.1016/s0014-5793(00)01660-4 · Cited by 33 · see citing works

Polarization of the Escherichia coli chromosome. A view from the terminus

Capiaux, H., Cornet, F., Corre, J., Guijo, M. I., Pérals, K., Rebollo, J. E., & Louarn, J. (2001) · Biochimie · doi:10.1016/s0300-9084(00)01202-5 · Cited by 32 · see citing works

Multiplication of a restriction–modification gene complex

Sadykov, M. R., Asami, Y., Niki, H., Handa, N., Itaya, M., Tanokura, M., & Kobayashi, I. (2003) · Molecular Microbiology · doi:10.1046/j.1365-2958.2003.03464.x · Cited by 32 · see citing works

Impact of Homologous Recombination on Genome Organization and Stability

Hughes, D. (2014) · ASM Press eBooks · doi:10.1128/9781555818180.ch7 · Cited by 23 · see citing works

Influence of disruption of the recA gene on genetic instability and genome rearrangement in Streptomyces lividans

Volff, J., & Altenbuchner, J. (1997) · Journal of Bacteriology · doi:10.1128/jb.179.7.2440-2445.1997 · Cited by 18 · see citing works

Highly plastic genome of Microcystis aeruginosa PCC 7806, a ubiquitous toxic freshwater cyanobacterium

Frangeul, L., Quillardet, P., Castets, A.-M., Humbert, J.-F., Matthijs, H. C., Cortez, D., Tolonen, A., Zhang, C.-C., Gribaldo, S., Kehr, J.-C., et al. (2008) · BMC Genomics · doi:10.1186/1471-2164-9-274 · Cited by 221 · see citing works

Persistence drives gene clustering in bacterial genomes

Fang, G., Rocha, E. P., & Danchin, A. (2008) · BMC Genomics · doi:10.1186/1471-2164-9-4 · Cited by 112 · see citing works

Whole genomic DNA sequencing and comparative genomic analysis of<i>Arthrospira platensis</i>: high genome plasticity and genetic diversity

Xu, T., Qin, S., Hu, Y., Song, Z., Ying, J., Li, P., Dong, W., Zhao, F., Yang, H., & Bao, Q. (2016) · DNA Research · doi:10.1093/dnares/dsw023 · Cited by 37 · see citing works

Isolating Bacterial Artificial Chromosome (BAC) DNA from Bacterial Cultures Using the NucleoBond SystemPreprint

Saunders, T. L. (2006) · Cold Spring Harbor Protocols · doi:10.1101/pdb.prot4390

Dynamic bacterial genome organization

Kolstø, A. (1997) · Molecular Microbiology · doi:10.1046/j.1365-2958.1997.3501715.x · Cited by 113 · see citing works

Properties of polylysogens containing derepressed λN− prophages

Mandal, N. C., Crochet, M., & Lieb, M. (1974) · Virology · doi:10.1016/0042-6822(74)90110-x · Cited by 11 · see citing works

Bacterial Cell Division

Lutkenhaus, J. (2001) · Encyclopedia of Life Sciences · doi:10.1038/npg.els.0000294

Chromosome conformation capture assays in bacteria

Umbarger, M. A. (2012) · Methods · doi:10.1016/j.ymeth.2012.06.017 · Cited by 8 · see citing works