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1
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0031024670
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Conserved clusters of functionally related genes in two bacterial genomes
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•], compares some of the completely sequenced genomes and describes the manner in which gene order and chromosome organization have evolved in bacteria. By first classifying genes into one of several functional classes and then examining their relative positions, the authors find that in both Escherichia coli and Haemophilus influenzae functionally related genes tend to be neighbors more often than functionally unrelated genes.
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Tamames, J.1
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Watanabe H, Mori H, Itoh T, Gojobori T: Genome plasticity as a paradigm of eubacterial evolution. J Mol Evol 1997, 44:S57-S64. By examining the locations of homologous genes in several sequenced genomes, these authors detect very few evolutionary conserved gene clusters and conclude that bacterial genomes are subject to repeated events that alter the chromosome structure.
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J Mol Evol
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Watanabe, H.1
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Genes and their organization in the replication region of the bacterial chromosome
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Strand asymmetry in bacterial and large viral genomes
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Mrázek J, Karlin S: Strand asymmetry in bacterial and large viral genomes. Proc Natl Acad Sci USA 1998, 95:3720-3725. Most bacterial chromosomes are polarized around their origins of replication, both in terms of base composition and gene distribution. This paper examines the extent of GC skew - the excess of G over C in the leading strand of replication - in several sequenced genomes and discusses the potential forces generating the strand asymmetry in base composition.
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Proc Natl Acad Sci USA
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Mrázek, J.1
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Measuring genome evolution
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Huynen MA, Bork P: Measuring genome evolution. Proc Natl Acad Sci USA 1998, 95:5849-5856. This is a superb analysis of the organization and evolution of bacterial chromosomes as reconstructed from complete genome sequences. The authors describe the relative rates at which differ features of the genome, ranging from protein sequence to overall chromosome content and structure, have changed over an evolutionary timescale.
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Proc Natl Acad Sci USA
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Huynen, M.A.1
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Prokaryotic genomes: The emerging paradigm of genome-based microbiology
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Koonin EV, Galperin MY: Prokaryotic genomes: the emerging paradigm of genome-based microbiology. Curr Opin Genet Dev 1997, 7:757-763. A comparison of the complete sequences of several eubacterial and archael genomes shows that while families of proteins are conserved among taxa, gene order and gene families are not. On the basis of the heterogeneity among genomes, the authors conclude that horizontal transfer plays a significant role in the evolution of genomes.
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Koonin, E.V.1
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The evolutionary relationships between the two bacteria Escherichia coli and Haemophilus influenzae and their putative last common ancestor
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De Rosa R, Labedan B: The evolutionary relationships between the two bacteria Escherichia coli and Haemophilus influenzae and their putative last common ancestor. Mol Biol Evol 1998, 15:17-27. On the basis of an analysis of the genes common to E. coli and H. influenzae, these authors hypothesize that the common ancestor of these species had a genome size similar to that of present day E. coli. Several gene duplications are ancestral and common to both species; except for few small regions, gene order has not been conserved since these species diverged.
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Mol Biol Evol
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De Rosa, R.1
Labedan, B.2
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10
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0027236788
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Genomic mapping with I-Ceu I, an intron-encoded endonuclease specific for genes for ribosomal RNA, in Salmonella spp
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Liu, S.-L.1
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Genome size variation among recent human isolates of Salmonella typhi
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Thong KL, Puthucheary SD, Pang T: Genome size variation among recent human isolates of Salmonella typhi. Res Microbiol 1997, 148:229-235. On the basis of multilocus enzyme electrophoresis data, natural isolates of Typhi are thought to be genetically homogeneous; however, this study shows that strains of Typhi exhibit extraordinary plasticity in chromosome size and organization, with genomes that vary from 3.9 to 4.9 Mb in length.
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Res Microbiol
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Thong, K.L.1
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12
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0031963154
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Distribution of chromosome length variation in natural isolates of Escherichia coli
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Bergthorsson U, Ochman H: Distribution of chromosome length variation in natural isolates of Escherichia coli. Mol Biol Evol 1998, 15:9-16. Among natural isolates of E. coli, chromosome sizes range from 4.5 to 5.5 Mb. The distribution of this length variation is not random: strains with larger chromosomes are primarily found in certain subspecific groups and the chromosome size variation has a symmetric distribution with respect to the replication origin.
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Mol Biol Evol
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Bergthorsson, U.1
Ochman, H.2
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Bergthorsson U, Ochman H: Heterogeneity of genome sizes among natural isolates of Escherichia coli. J Bacteriol 1995, 177:5784-5789.
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Highly plastic chromosomal organization in Salmonella typhi
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Liu S-L, Sanderson KE: Highly plastic chromosomal organization in Salmonella typhi. Proc Natl Acad Sci USA 1996, 93:10303-10308.
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Proc Natl Acad Sci USA
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Liu, S.-L.1
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Chromosomal rearrangements in enteric bacteria
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Sanderson KE, Liu S-L: Chromosomal rearrangements in enteric bacteria. Electrophoresis 1998, 19:569-572. A review on the variation in chromosome organization found within Salmonella enterica which describes physical mapping techniques and the types of structural changes that have been detected by these procedures. Serovars of S. enterica showing little or no host specificity appear to have more conserved chromosome structure than do serovars adapted to a single host.
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Electrophoresis
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Sanderson, K.E.1
Liu, S.-L.2
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Gene transfer is a major factor in bacterial evolution
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Lan R, Reeves PR: Gene transfer is a major factor in bacterial evolution. Mol Biol Evol 1996, 13:47-55.
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Lan, R.1
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Pathogenicity islands: Bacterial evolution in quantum leaps
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Groisman EA, Ochman H: Pathogenicity islands: bacterial evolution in quantum leaps. Cell 1996, 87:791-794.
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Pathogenicity islands of virulent bacteria: Structure, function and impact on microbial evolution
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Hacker J, Blum-Oehler G Mühldorfer I, Tschäpe H: Pathogenicity islands of virulent bacteria: structure, function and impact on microbial evolution. Mol Microbiol 1997, 23:1089-1097.
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Mol Microbiol
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19
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Chromosomal regions specific to pathogenic isolates of Escherichia coli have a phylogenetically clustered distribution
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Boyd EF, Hartl DL: Chromosomal regions specific to pathogenic isolates of Escherichia coli have a phylogenetically clustered distribution. J Bacteriol 1998, 5:1159-1165. The distribution of four virulence determinants associated with pathogenicity islands is clustered in the subspecific groups of E. coli having larger genomes. The distribution suggests that these virulence genes were present in the ancestors of these subgroups despite the fact that the majority of these strains were originally isolated from healthy hosts.
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A role for bacteriophages in the evolution and transfer of bacterial virulence determinants
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Cheetam BF, Katz ME: A role for bacteriophages in the evolution and transfer of bacterial virulence determinants. Mol Microbiol 1995, 18:201-208.
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Cheetam, B.F.1
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0031895930
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The complete sequence of the locus of enterocyte effacement (LEE) from enteropathogenic Escherichia coli E2348/69
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Elliott SJ, Wainwright LA, McDaniel TD, Jarvis KG, Deng YK, Lai LC, McNamara BP, Donnenberg MS, Kaper JB: The complete sequence of the locus of enterocyte effacement (LEE) from enteropathogenic Escherichia coli E2348/69. Mol Microbiol 1998, 28:1-4. The insertion of the LEE island can, in a single step, convert a benign strain of E. coli into a pathogen. This paper provides the newly determined sequence of the entire insert; and aside from containing genes that are apparently specific to LEE, this region also encodes a type III secretion apparatus homologous to those present in pathogenicity islands of other enteric pathogens, including Salmonella, Shigella and Yersinia.
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Mol Microbiol
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Elliott, S.J.1
Wainwright, L.A.2
McDaniel, T.D.3
Jarvis, K.G.4
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McNamara, B.P.7
Donnenberg, M.S.8
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The Salmonella selC locus contains a pathogenicity island mediating intramacrophage survival
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Blanc-Potard A, Groisman EA: The Salmonella selC locus contains a pathogenicity island mediating intramacrophage survival. EMBO J 1997, 16:5376-5385. The selC locus has been shown to be a common target for pathogenicity islands in Escherichia coli, and this study takes the clever approach of surveying the corresponding site in the Salmonella genome. The authors discover a 17 kb insert required for virulence, adding to the growing list of pathogenicity islands in Salmonella.
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EMBO J
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Blanc-Potard, A.1
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Construction of chromosomal rearrangements in Salmonella by transduction: Inversions of nonpermissive segments are not lethal
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Miesel L, Segall A, Roth JR: Construction of chromosomal rearrangements in Salmonella by transduction: inversions of nonpermissive segments are not lethal. Genetics 1994, 137:919-932.
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Selfish operons: Horizontal transfer may drive the evolution of gene clusters
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Lawrence JG, Roth JR: Selfish operons: horizontal transfer may drive the evolution of gene clusters. Genetics 1996, 143:1843-1860. This paper very convincingly makes the case that bacterial genes specifying a single metabolic function are typically arranged into operons because this organization often facilitates efficient horizontal transfer of genes among organisms. Their model accounts for the mosaic structure of some bacterial genomes whereby ancestral chromosomal material is interspersed with horizontally transferred operons providing novel metabolic functions.
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Genetics
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Lawrence, J.G.1
Roth, J.R.2
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Identification of a pathogenicity island required for Salmonella survival in host cells
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Proc Natl Acad Sci USA
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Groisman, E.A.4
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Identification of a virulence locus encoding a second type III secretion system in Salmonella typhimurium
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Shea JE, Hensel M, Gleeson C, Holden DW: Identification of a virulence locus encoding a second type III secretion system in Salmonella typhimurium. Proc Natl Acad Sci USA 1996, 93:2593-2597.
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Holden, D.W.4
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0032584169
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"Black holes" and bacterial pathogenicity: A large genomic deletion that enhances the virulence of Shigella spp. and enteroinvasive Escherichia coli
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Maurelli AT, Fernandez RE, Bloch CA, Rode CK, Fasano A: "Black holes" and bacterial pathogenicity: a large genomic deletion that enhances the virulence of Shigella spp. and enteroinvasive Escherichia coli. Proc Natl Acad Sci USA 1998, 95:3943-3948. Strains of Shigella and enteroinvasive E. coli were found to have chromosomal deletions of cadA and the surrounding region. The presence of cadA inhibits enterotoxin activity and attenuates virulence in Shigella and these deletions are likely to have played a large role in the evolution of these pathogens. A similar situation exists for ompT, a surface protease which is present in E. coli K12 but not in Shigella and enteroinvasive E. coli.
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Proc Natl Acad Sci USA
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Maurelli, A.T.1
Fernandez, R.E.2
Bloch, C.A.3
Rode, C.K.4
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Adams J, Puskas-Rozsa S, Simlar J, Wilke CM: Adaptation and major chromosomal changes in populations of Saccharomyces cerevisiae. Curr Genet 1992, 22:13-19.
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Amelioration of bacterial genomes: Rates of change and exchange
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Lawrence, JG, Ochman H: Amelioration of bacterial genomes: rates of change and exchange. J Mol Evol 1997, 44:383-397. Based on their GC contents, genes acquired through horizontal transfer can be distinguished from ancestral DNA. At the time of introduction, horizontally transferred genes reflect the base composition of the donor genome; but, over time, these sequences will ameliorate to reflect the DNA composition of the new genome, this paper develops a method to estimate the time of acquisition of horizontally transferred genes, which makes it possible to establish the age of transferred genes and the rate at which DNA has been acquired on an evolutionary timescale.
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J Mol Evol
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