-
2
-
-
0023184331
-
Bacterial evolution
-
C.R. Woese Bacterial evolution Microbiol Rev 51 1987 221 271
-
(1987)
Microbiol Rev
, vol.51
, pp. 221-271
-
-
Woese, C.R.1
-
3
-
-
9144247750
-
Reductive evolution suggested from the complete genome sequence of a plant-pathogenic phytoplasma
-
K. Oshima, S. Kakizawa, H. Nishigawa, H.Y. Jung, W. Wei, S. Suzuki, R. Arashida, D. Nakata, S. Miyata, M. Ugaki, and S. Namba Reductive evolution suggested from the complete genome sequence of a plant-pathogenic phytoplasma Nat Genet 36 2004 27 29
-
(2004)
Nat Genet
, vol.36
, pp. 27-29
-
-
Oshima, K.1
Kakizawa, S.2
Nishigawa, H.3
Jung, H.Y.4
Wei, W.5
Suzuki, S.6
Arashida, R.7
Nakata, D.8
Miyata, S.9
Ugaki, M.10
Namba, S.11
-
4
-
-
0032512051
-
The genome sequence of Rickettsia prowazekii and the origin of mitochondria
-
S.G. Andersson, A. Zomorodipour, J.O. Andersson, T. Sicheritz-Ponten, U.C. Alsmark, R.M. Podowski, A.K. Naslund, A.S. Eriksson, H.H. Winkler, and C.G. Kurland The genome sequence of Rickettsia prowazekii and the origin of mitochondria Nature 396 1998 133 140
-
(1998)
Nature
, vol.396
, pp. 133-140
-
-
Andersson, S.G.1
Zomorodipour, A.2
Andersson, J.O.3
Sicheritz-Ponten, T.4
Alsmark, U.C.5
Podowski, R.M.6
Naslund, A.K.7
Eriksson, A.S.8
Winkler, H.H.9
Kurland, C.G.10
-
5
-
-
19344378727
-
Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: A streamlined genome overrun by mobile genetic elements
-
M. Wu, L.V. Sun, J. Vamathevan, M. Riegler, R. Deboy, J.C. Brownlie, E.A. McGraw, W. Martin, C. Esser, and N. Ahmadinejad Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: a streamlined genome overrun by mobile genetic elements PLoS Biol 2 2004 E69 This is an odd genome; it is overrun with apparent mobile elements, but otherwise has many features of the highly reduced genomes of long-term symbionts such as a small size and a base compositional bias favoring A+T.
-
(2004)
PLoS Biol
, vol.2
-
-
Wu, M.1
Sun, L.V.2
Vamathevan, J.3
Riegler, M.4
Deboy, R.5
Brownlie, J.C.6
McGraw, E.A.7
Martin, W.8
Esser, C.9
Ahmadinejad, N.10
-
6
-
-
2342423344
-
Illuminating the evolutionary history of chlamydiae
-
M. Horn, A. Collingro, S. Schmitz-Esser, C.L. Beier, U. Purkhold, B. Fartmann, P. Brandt, G.J. Nyakatura, M. Droege, and D. Frishman Illuminating the evolutionary history of chlamydiae Science 304 2004 728 730
-
(2004)
Science
, vol.304
, pp. 728-730
-
-
Horn, M.1
Collingro, A.2
Schmitz-Esser, S.3
Beier, C.L.4
Purkhold, U.5
Fartmann, B.6
Brandt, P.7
Nyakatura, G.J.8
Droege, M.9
Frishman, D.10
-
7
-
-
11144358038
-
Comparison of the genome of the oral pathogen Treponema denticola with other spirochete genomes
-
R. Seshadri, G.S. Myers, H. Tettelin, J.A. Eisen, J.F. Heidelberg, R.J. Dodson, T.M. Davidsen, R.T. DeBoy, D.E. Fouts, and D.H. Haft Comparison of the genome of the oral pathogen Treponema denticola with other spirochete genomes Proc Natl Acad Sci USA 101 2004 5646 5651 The comparison of T. denticola with T. pallidum indicates that gene loss and rearrangements can be important in the genome evolution of host-restricted pathogens and provides an example in which specialized pathogens continue to show dynamic genomic change.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 5646-5651
-
-
Seshadri, R.1
Myers, G.S.2
Tettelin, H.3
Eisen, J.A.4
Heidelberg, J.F.5
Dodson, R.J.6
Davidsen, T.M.7
Deboy, R.T.8
Fouts, D.E.9
Haft, D.H.10
-
8
-
-
0034618559
-
Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS
-
S. Shigenobu, H. Watanabe, M. Hattori, Y. Sakaki, and H. Ishikawa Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS Nature 407 2000 81 86
-
(2000)
Nature
, vol.407
, pp. 81-86
-
-
Shigenobu, S.1
Watanabe, H.2
Hattori, M.3
Sakaki, Y.4
Ishikawa, H.5
-
9
-
-
0037189373
-
50 million years of genomic stasis in endosymbiotic bacteria
-
I. Tamas, L. Klasson, B. Canback, A.K. Naslund, A.S. Eriksson, J.J. Wernegreen, J.P. Sandstrom, N.A. Moran, and S.G. Andersson 50 million years of genomic stasis in endosymbiotic bacteria Science 296 2002 2376 2379
-
(2002)
Science
, vol.296
, pp. 2376-2379
-
-
Tamas, I.1
Klasson, L.2
Canback, B.3
Naslund, A.K.4
Eriksson, A.S.5
Wernegreen, J.J.6
Sandstrom, J.P.7
Moran, N.A.8
Andersson, S.G.9
-
10
-
-
0036842986
-
Genome sequence of the endocellular obligate symbiont of tsetse flies, Wigglesworthia glossinidia
-
L. Akman, A. Yamashita, H. Watanabe, K. Oshima, T. Shiba, M. Hattori, and S. Aksoy Genome sequence of the endocellular obligate symbiont of tsetse flies, Wigglesworthia glossinidia Nat Genet 32 2002 402 407
-
(2002)
Nat Genet
, vol.32
, pp. 402-407
-
-
Akman, L.1
Yamashita, A.2
Watanabe, H.3
Oshima, K.4
Shiba, T.5
Hattori, M.6
Aksoy, S.7
-
11
-
-
0037457901
-
Reductive genome evolution in Buchnera aphidicola
-
R.C. van Ham, J. Kamerbeek, C. Palacios, C. Rausell, F. Abascal, U. Bastolla, J.M. Fernandez, L. Jimenez, M. Postigo, and F.J. Silva Reductive genome evolution in Buchnera aphidicola Proc Natl Acad Sci USA 100 2003 581 586 This comparison of the three completed Buchnera genomes demonstrates that continued, slow rates of gene loss can be ongoing even in the extremely reduced genomes of organisms that are anciently host-dependent.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 581-586
-
-
Van Ham, R.C.1
Kamerbeek, J.2
Palacios, C.3
Rausell, C.4
Abascal, F.5
Bastolla, U.6
Fernandez, J.M.7
Jimenez, L.8
Postigo, M.9
Silva, F.J.10
-
12
-
-
0041422250
-
The genome sequence of Blochmannia floridanus: Comparative analysis of reduced genomes
-
R. Gil, F.J. Silva, E. Zientz, F. Delmotte, F. Gonzalez-Candelas, A. Latorre, C. Rausell, J. Kamerbeek, J. Gadau, and B. Holldobler The genome sequence of Blochmannia floridanus: comparative analysis of reduced genomes Proc Natl Acad Sci USA 100 2003 9388 9393
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 9388-9393
-
-
Gil, R.1
Silva, F.J.2
Zientz, E.3
Delmotte, F.4
Gonzalez-Candelas, F.5
Latorre, A.6
Rausell, C.7
Kamerbeek, J.8
Gadau, J.9
Holldobler, B.10
-
13
-
-
0027254254
-
A molecular clock in endosymbiotic bacteria is calibrated using the insect hosts
-
N.A. Moran, M.A. Munson, B. Baumann, and H. Ishikawa A molecular clock in endosymbiotic bacteria is calibrated using the insect hosts Proc R Soc Lond B Biol Sci 253 1993 167 171
-
(1993)
Proc R Soc Lond B Biol Sci
, vol.253
, pp. 167-171
-
-
Moran, N.A.1
Munson, M.A.2
Baumann, B.3
Ishikawa, H.4
-
14
-
-
0035058359
-
Evolution of prokaryotic gene order: Genome rearrangements in closely related species
-
M. Suyama, and P. Bork Evolution of prokaryotic gene order: genome rearrangements in closely related species Trends Genet 17 2001 10 13
-
(2001)
Trends Genet
, vol.17
, pp. 10-13
-
-
Suyama, M.1
Bork, P.2
-
15
-
-
0035749612
-
The process of genome shrinkage in the obligate symbiont, Buchnera aphidicola
-
N.A. Moran, and A. Mira The process of genome shrinkage in the obligate symbiont, Buchnera aphidicola Genome Biol 2 2001 research0054.1-research0054.12
-
(2001)
Genome Biol
, vol.2
-
-
Moran, N.A.1
Mira, A.2
-
16
-
-
0035500843
-
Genome size reduction through multiple events of gene disintegration in Buchnera APS
-
F.J. Silva, A. Latorre, and A. Moya Genome size reduction through multiple events of gene disintegration in Buchnera APS Trends Genet 17 2001 615 618
-
(2001)
Trends Genet
, vol.17
, pp. 615-618
-
-
Silva, F.J.1
Latorre, A.2
Moya, A.3
-
17
-
-
18644378721
-
Genome sequence of Shigella flexneri 2a: Insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157
-
Q. Jin, Z. Yuan, J. Xu, Y. Wang, Y. Shen, W. Lu, J. Wang, H. Liu, J. Yang, and F. Yang Genome sequence of Shigella flexneri 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157 Nucleic Acids Res 30 2002 4432 4441
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 4432-4441
-
-
Jin, Q.1
Yuan, Z.2
Xu, J.3
Wang, Y.4
Shen, Y.5
Lu, W.6
Wang, J.7
Liu, H.8
Yang, J.9
Yang, F.10
-
18
-
-
0242416999
-
Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457T
-
J. Wei, M.B. Goldberg, V. Burland, M.M. Venkatesan, W. Deng, G. Fournier, G.F. Mayhew, G. Plunkett III, D.J. Rose, and A. Darling Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457T Infect Immun 71 2003 2775 2786 The Shigella strains represent host-restricted strains derived from E. coli. They are characterized by an abundance of insertion sequence (IS) elements, some mediating chromosomal rearrangements and some causing gene inactivations. In this strain, most of the recent pseudogenes are attributed to base substitutions.
-
(2003)
Infect Immun
, vol.71
, pp. 2775-2786
-
-
Wei, J.1
Goldberg, M.B.2
Burland, V.3
Venkatesan, M.M.4
Deng, W.5
Fournier, G.6
Mayhew, G.F.7
Plunkett III, G.8
Rose, D.J.9
Darling, A.10
-
19
-
-
0035807385
-
Genome sequence of Yersinia pestis, the causative agent of plague
-
J. Parkhill, B.W. Wren, N.R. Thomson, R.W. Titball, Holden MTG, M.B. Prentice, M. Sebaihia, K.D. James, C. Churcher, and K.L. Mungall Genome sequence of Yersinia pestis, the causative agent of plague Nature 413 2001 523 527
-
(2001)
Nature
, vol.413
, pp. 523-527
-
-
Parkhill, J.1
Wren, B.W.2
Thomson, N.R.3
Titball, R.W.4
Holden, M.T.G.5
Prentice, M.B.6
Sebaihia, M.7
James, K.D.8
Churcher, C.9
Mungall, K.L.10
-
20
-
-
10744220624
-
The genome sequence of the entomopathogenic bacterium Photorhabdus luminescens
-
E. Duchaud, C. Rusniok, L. Frangeul, C. Buchrieser, S. Taourit, S. Bocs, C. Boursaux-Eude, M. Chandler, E. Dassa, and R. Derose The genome sequence of the entomopathogenic bacterium Photorhabdus luminescens Nat Biotechnol 21 2003 1307 1313 This genome, like that of Yersinia pestis, shows that symbiotic bacteria of invertebrates can share many of the features of host-restricted mammalian pathogens, including an increase in insertion sequence element load and chromosomal rearrangements.
-
(2003)
Nat Biotechnol
, vol.21
, pp. 1307-1313
-
-
Duchaud, E.1
Rusniok, C.2
Frangeul, L.3
Buchrieser, C.4
Taourit, S.5
Bocs, S.6
Boursaux-Eude, C.7
Chandler, M.8
Dassa, E.9
Derose, R.10
-
21
-
-
0042073066
-
Loss of DNA recombinational repair enzymes in the initial stages of genome degeneration in mutualistic bacterial endosymbionts
-
C. Dale, B. Wang, N. Moran, and H. Ochman Loss of DNA recombinational repair enzymes in the initial stages of genome degeneration in mutualistic bacterial endosymbionts Mol Biol Evol 20 2003 1188 1194 This obligate symbiont of weevils, a member of the enteric bacteria, shows remarkable changes owing to the transposition of insertion sequence elements, resulting in the inactivation of some rRNA operons. Among the inactivated genes is recA, and loss of homologous recombination is likely to underlie some of the observed changes, such as the unusual divergence of rRNA operons in the genome. This illustrates a common feature of reduced genomes: namely, the elimination of repair gene function can lead to an increase in mutations and possibly to a faster accumulation of genomic changes.
-
(2003)
Mol Biol Evol
, vol.20
, pp. 1188-1194
-
-
Dale, C.1
Wang, B.2
Moran, N.3
Ochman, H.4
-
22
-
-
85158048416
-
Insertion sequences revisited
-
N.L. Craig R. Craigie M. Gellert A.M. Lambowitz ASM Press Washington DC
-
M. Chandler, and J. Mahillon Insertion sequences revisited N.L. Craig R. Craigie M. Gellert A.M. Lambowitz Mobile DNA II 2002 ASM Press Washington DC 305 366
-
(2002)
Mobile DNA II
, pp. 305-366
-
-
Chandler, M.1
Mahillon, J.2
-
23
-
-
0042355274
-
Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica
-
J. Parkhill, M. Sebaihia, A. Preston, L.D. Murphy, N. Thomson, D.E. Harris, Holden MTG, C.M. Churcher, S.D. Bentley, and K.L. Mungall Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica Nat Genet 35 2003 32 40 This paper, based on three complete Bordetella genome sequences, provides the best comparison so far between genomes that differ in host restriction. B. pertussis and B. parapertussis are independently derived, host-restricted species that evolved from B. bronchiseptica, which can live independently of hosts in the environment. The derived strains have undergone a considerable increase in insertion sequence (IS) elements, the inactivation of many genes resulting in several pseudogenes (358 and 220, respectively, or 5-10% of open reading frames) and numerous deletions of up to 120 kb. The deletions have caused an overall decrease in genome size, from 5.3 Mb in B. bronchiseptica to 4.1 Mb and 4.8 Mb in the two host-restricted lineages. Many chromosomal rearrangements have occurred in the two host-restricted strains, particularly in B. pertussis. IS elements positioned at the boundaries of nearly all rearranged and deleted regions provide strong evidence that homologous recombination between these sequences is the mechanistic basis for the inversions, translocations and deletions. Mobile element transposition has also apparently caused substantial gene inactivation in the host-dependent Bordetella, with most identifiable pseudogenes containing IS elements. These extensive genomic changes have occurred over an estimated 0.3 to 4 million years on the basis of the sequence divergence of homologous genes.
-
(2003)
Nat Genet
, vol.35
, pp. 32-40
-
-
Parkhill, J.1
Sebaihia, M.2
Preston, A.3
Murphy, L.D.4
Thomson, N.5
Harris, D.E.6
Holden, M.T.G.7
Churcher, C.M.8
Bentley, S.D.9
Mungall, K.L.10
-
24
-
-
1342325443
-
Bordetella species are distinguished by patterns of substantial gene loss and host adaptation
-
C.A. Cummings, M.M. Brinig, P.W. Lepp, S. van de Pas, and D.A. Relman Bordetella species are distinguished by patterns of substantial gene loss and host adaptation J Bacteriol 186 2004 1484 1492 This analysis shows that B. bronchiseptica is a paraphyletic taxon with some diversity and that B. pertussis and B. parapertussis represent two independently derived clades of host-restricted pathogens. The authors propose that gene loss, mediated by transposable elements, has been important in adaptation of the strains.
-
(2004)
J Bacteriol
, vol.186
, pp. 1484-1492
-
-
Cummings, C.A.1
Brinig, M.M.2
Lepp, P.W.3
Van De Pas, S.4
Relman, D.A.5
-
25
-
-
0037596510
-
The complete genome sequence of Mycobacterium bovis
-
T. Garnier, K. Eiglmeier, J.C. Camus, N. Medina, H. Mansoor, M. Pryor, S. Duthoy, S. Grondin, C. Lacroix, and C. Monsempe The complete genome sequence of Mycobacterium bovis Proc Natl Acad Sci USA 100 2003 7877 7882 M. bovis seems to have evolved from an ancestor very close to M. tuberculosis, from which it has diverged very little at homologous genes (>99.9% sequence identity). Owing to gene deletion, it has lost metabolic self-sufficiency, and it represents a very recent stage of genome deterioration in a pathogen, in contrast to the highly degraded genome of M. leprae described in [27].
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 7877-7882
-
-
Garnier, T.1
Eiglmeier, K.2
Camus, J.C.3
Medina, N.4
Mansoor, H.5
Pryor, M.6
Duthoy, S.7
Grondin, S.8
Lacroix, C.9
Monsempe, C.10
-
26
-
-
0038222539
-
Complete genome sequence of the Q-fever pathogen Coxiella burnetii
-
R. Seshadri, I.T. Paulsen, J.A. Eisen, T.D. Read, K.E. Nelson, W.C. Nelson, N.L. Ward, H. Tettelin, T.M. Davidsen, and M.J. Beanan Complete genome sequence of the Q-fever pathogen Coxiella burnetii Proc Natl Acad Sci USA 100 2003 5455 5460 This is another apparent example of genomic degradation following host restriction; the 2 Mb genome contains relatively high loads of both insertion sequence elements (32 in total) and pseudogenes (83 in total).
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 5455-5460
-
-
Seshadri, R.1
Paulsen, I.T.2
Eisen, J.A.3
Read, T.D.4
Nelson, K.E.5
Nelson, W.C.6
Ward, N.L.7
Tettelin, H.8
Davidsen, T.M.9
Beanan, M.J.10
-
27
-
-
0035931926
-
Massive gene decay in the leprosy bacillus
-
S.T. Cole, K. Eiglmeier, J. Parkhill, K.D. James, N.R. Thomson, P.R. Wheeler, N. Honore, T. Garnier, C. Churcher, and D. Harris Massive gene decay in the leprosy bacillus Nature 409 2001 1007 1011
-
(2001)
Nature
, vol.409
, pp. 1007-1011
-
-
Cole, S.T.1
Eiglmeier, K.2
Parkhill, J.3
James, K.D.4
Thomson, N.R.5
Wheeler, P.R.6
Honore, N.7
Garnier, T.8
Churcher, C.9
Harris, D.10
-
28
-
-
0035479142
-
Deletional bias and the evolution of bacterial genomes
-
A. Mira, H. Ochman, and N.A. Moran Deletional bias and the evolution of bacterial genomes Trends Genet 17 2001 589 596
-
(2001)
Trends Genet
, vol.17
, pp. 589-596
-
-
Mira, A.1
Ochman, H.2
Moran, N.A.3
-
29
-
-
0036667684
-
Proliferation and deterioration of Rickettsia palindromic elements
-
H. Amiri, C.M. Alsmark, and S.G.E. Andersson Proliferation and deterioration of Rickettsia palindromic elements Mol Biol Evol 19 2002 1234 1243
-
(2002)
Mol Biol Evol
, vol.19
, pp. 1234-1243
-
-
Amiri, H.1
Alsmark, C.M.2
Andersson, S.G.E.3
-
30
-
-
0142222533
-
Birth and death of orphan genes in Rickettsia
-
H. Amiri, W. Davids, and S.G.E. Andersson Birth and death of orphan genes in Rickettsia Mol Biol Evol 20 2003 1575 1587 Comparing the two completed Rickettsia genomes shows that sequence repeats are important in mediating deletions of chromosomal fragments. Gene loss is ongoing in these small genomes.
-
(2003)
Mol Biol Evol
, vol.20
, pp. 1575-1587
-
-
Amiri, H.1
Davids, W.2
Andersson, S.G.E.3
-
31
-
-
0029866448
-
Accelerated evolution and Muller's ratchet in endosymbiotic bacteria
-
N.A. Moran Accelerated evolution and Muller's ratchet in endosymbiotic bacteria Proc Natl Acad Sci USA 93 1996 2873 2878
-
(1996)
Proc Natl Acad Sci USA
, vol.93
, pp. 2873-2878
-
-
Moran, N.A.1
-
32
-
-
0242657423
-
Comparative genomics of insect-symbiotic bacteria: Influence of host environment on microbial genome composition
-
R.V. Rio, C. Lefevre, A. Heddi, and S. Aksoy Comparative genomics of insect-symbiotic bacteria: influence of host environment on microbial genome composition Appl Environ Microbiol 69 2003 6825 6832 The use of microarrays to examine gene inventories reveals extensive gene loss in two insect symbionts: Sodalis glossinidius of tsetse flies; and Sitophilus oryzae, the obligate symbiont of the rice grant weevil.
-
(2003)
Appl Environ Microbiol
, vol.69
, pp. 6825-6832
-
-
Rio, R.V.1
Lefevre, C.2
Heddi, A.3
Aksoy, S.4
-
33
-
-
85158032422
-
Eubacterial genomes
-
N.L. Craig R. Craigie M. Gellert A.M. Lambowitz ASM Press Washington DC
-
A. Campbell Eubacterial genomes N.L. Craig R. Craigie M. Gellert A.M. Lambowitz Mobile DNA II 2002 ASM Press Washington DC 1024 1038
-
(2002)
Mobile DNA II
, pp. 1024-1038
-
-
Campbell, A.1
-
34
-
-
0038075530
-
Transposable elements in clonal lineages: Lethal hangover from sex
-
S.V. Nuzhdin, and D.A. Petrov Transposable elements in clonal lineages: lethal hangover from sex Biol J Linn Soc 79 2003 33 41
-
(2003)
Biol J Linn Soc
, vol.79
, pp. 33-41
-
-
Nuzhdin, S.V.1
Petrov, D.A.2
-
35
-
-
0036728258
-
The rate of recombination in Wolbachia bacteria
-
F.M. Jiggins The rate of recombination in Wolbachia bacteria Mol Biol Evol 19 2002 1640 1643
-
(2002)
Mol Biol Evol
, vol.19
, pp. 1640-1643
-
-
Jiggins, F.M.1
-
36
-
-
0035916791
-
Recombination in Wolbachia
-
J.H. Werren, and J.D. Bartos Recombination in Wolbachia Curr Biol 11 2001 431 435
-
(2001)
Curr Biol
, vol.11
, pp. 431-435
-
-
Werren, J.H.1
Bartos, J.D.2
-
37
-
-
0036782602
-
Wolbachia infections of tephritid fruit flies: Molecular evidence for five distinct strains in a single host species
-
W. Jamnongluk, P. Kittayapong, V. Baimai, and S.L. O'Neill Wolbachia infections of tephritid fruit flies: molecular evidence for five distinct strains in a single host species Curr Microbiol 45 2002 255 260
-
(2002)
Curr Microbiol
, vol.45
, pp. 255-260
-
-
Jamnongluk, W.1
Kittayapong, P.2
Baimai, V.3
O'Neill, S.L.4
-
38
-
-
0038032021
-
High levels of multiple Wolbachia infection and recombination in the ant Formica exsecta
-
M. Reuter, and L. Keller High levels of multiple Wolbachia infection and recombination in the ant Formica exsecta Mol Biol Evol 20 2003 748 753
-
(2003)
Mol Biol Evol
, vol.20
, pp. 748-753
-
-
Reuter, M.1
Keller, L.2
-
40
-
-
0032584169
-
'Black holes' and bacterial pathogenicity: A large genomic deletion that enhances the virulence of Shigella spp. and enteroinvasive Escherichia coli
-
A.T. Maurelli, R.E. Fernández, C.A. Bloch, C.K. Rode, and A. Fasano '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 95 1998 3943 3948
-
(1998)
Proc Natl Acad Sci USA
, vol.95
, pp. 3943-3948
-
-
Maurelli, A.T.1
Fernández, R.E.2
Bloch, C.A.3
Rode, C.K.4
Fasano, A.5
-
41
-
-
0037219570
-
Impact of large chromosomal inversions on the adaptation and evolution of Pseudomonas aeruginosa chronically colonizing cystic fibrosis lungs
-
A.U. Kresse, S.D. Dinesh, K. Larbig, and U. Romling Impact of large chromosomal inversions on the adaptation and evolution of Pseudomonas aeruginosa chronically colonizing cystic fibrosis lungs Mol Microbiol 47 2003 145 158 Strains that cause chronic infections show accelerated chromosomal evolution, mediated by transposition of IS6100. These elements form the basis for both chromosomal rearrangements and the inactivation of numerous genes.
-
(2003)
Mol Microbiol
, vol.47
, pp. 145-158
-
-
Kresse, A.U.1
Dinesh, S.D.2
Larbig, K.3
Romling, U.4
-
42
-
-
0141742352
-
Application of DNA microarrays to study the evolutionary genomics of Yersinia pestis and Yersinia pseudotuberculosis
-
S.J. Hinchliffe, K.E. Isherwood, R.A. Stabler, M.B. Prentice, A. Rakin, R.A. Nichols, P.C. Oyston, J. Hinds, R.W. Titball, and B.W. Wren Application of DNA microarrays to study the evolutionary genomics of Yersinia pestis and Yersinia pseudotuberculosis Genome Res 13 2003 2018 2029 The authors propose that Y. pestis evolved quickly from Y. pseudotuberculosis, a mammalian enteropathogen that occurs widely in the environment, to become a more host-restricted lineage that is symbiotic in insects and blood-borne in mammals, and has limited ability to live outside these hosts. The authors identify numerous genomic differences between Y. pestis and Y. pseudotuberculosis and suggest that "genome rearrangements, particularly as a result of the recombination of insertion sequence elements and the accumulation of pseudogenes, may also have played a significant role in the rapid evolution of Y. pestis", which is estimated to have diversified over a period of only 20 000 years.
-
(2003)
Genome Res
, vol.13
, pp. 2018-2029
-
-
Hinchliffe, S.J.1
Isherwood, K.E.2
Stabler, R.A.3
Prentice, M.B.4
Rakin, A.5
Nichols, R.A.6
Oyston, P.C.7
Hinds, J.8
Titball, R.W.9
Wren, B.W.10
-
43
-
-
0031684504
-
Identification and characterization of IS1411, a new insertion sequence which causes transcriptional activation of the phenol degradation genes in Pseudomonas putida
-
A. Kallastu, R. Hõrak, and M. Kivisaar Identification and characterization of IS1411, a new insertion sequence which causes transcriptional activation of the phenol degradation genes in Pseudomonas putida J Bacteriol 180 1998 5306 5312
-
(1998)
J Bacteriol
, vol.180
, pp. 5306-5312
-
-
Kallastu, A.1
Hõrak, R.2
Kivisaar, M.3
-
44
-
-
0035036957
-
Multiple mobile promoter regions for the rare carbapenem resistance gene of Bacteroides fragilis
-
I. Podglajen, J. Breuil, A. Rohaut, C. Monsempes, and E. Collatz Multiple mobile promoter regions for the rare carbapenem resistance gene of Bacteroides fragilis J Bacteriol 183 2001 3531 3535
-
(2001)
J Bacteriol
, vol.183
, pp. 3531-3535
-
-
Podglajen, I.1
Breuil, J.2
Rohaut, A.3
Monsempes, C.4
Collatz, E.5
-
45
-
-
0242500750
-
Identification in methicillin-susceptible Staphylococcus hominis of an active primordial mobile genetic element for the staphylococcal cassette chromosome mec of methicillin-resistant Staphylococcus aureus
-
Y. Katayama, F. Takeuchi, T. Ito, X.X. Ma, Y. Ui-Mizutani, I. Kobayashi, and K. Hiramatsu Identification in methicillin-susceptible Staphylococcus hominis of an active primordial mobile genetic element for the staphylococcal cassette chromosome mec of methicillin-resistant Staphylococcus aureus J Bacteriol 185 2003 2711 2722
-
(2003)
J Bacteriol
, vol.185
, pp. 2711-2722
-
-
Katayama, Y.1
Takeuchi, F.2
Ito, T.3
Ma, X.X.4
Ui-Mizutani, Y.5
Kobayashi, I.6
Hiramatsu, K.7
-
46
-
-
3142706519
-
IS6110 functions as a mobile, monocyte-activated promoter in Mycobacterium tuberculosis
-
H. Safi, P.F. Barnes, D.L. Lakey, H. Shams, B. Samten, R. Vankayalapati, and S.T. Howard IS6110 functions as a mobile, monocyte-activated promoter in Mycobacterium tuberculosis Mol Microbiol 52 2004 999 1012 This study provides an example of a mobile element that mediates apparent adaptive change. In some M. tuberculosis strains, IS6110 upregulates the Rv1468c gene, which plays a presumptive role in evading host immune recognition.
-
(2004)
Mol Microbiol
, vol.52
, pp. 999-1012
-
-
Safi, H.1
Barnes, P.F.2
Lakey, D.L.3
Shams, H.4
Samten, B.5
Vankayalapati, R.6
Howard, S.T.7
-
47
-
-
11144356962
-
Functional and evolutionary genomics of Mycobacterium tuberculosis: Insights from genomic deletions in 100 strains
-
A.G. Tsolaki, A.E. Hirsh, K. DeRiemer, J.A. Enciso, M.Z. Wong, M. Hannan, de la Salmoniere YOL, K. Aman, M. Kato-Maeda, and P.M. Small Functional and evolutionary genomics of Mycobacterium tuberculosis: insights from genomic deletions in 100 strains Proc Natl Acad Sci USA 101 2004 4865 4870 On the basis of microarray assays of 100 M. tuberculosis clinical isolates, deletions are shown to be strongly clustered on the chromosome, on the scale of 15 kb and less. Some clusters are confined to a particular phylogenetic lineage and are possibly due to an insertion sequence element localized in one region. But most clusters involve particular regions that incur deletions in distinct lineages, indicating that region-specific properties have made them more vulnerable to deletion. This can be explained if the regions contain genes that are neutral or negative with respect to fitness in host-associated strains. This study is one of a few in which sufficient strains have been studied to determine whether the distribution of deletion frequencies is repeated in independent lineages of host-restricted bacteria.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 4865-4870
-
-
Tsolaki, A.G.1
Hirsh, A.E.2
Deriemer, K.3
Enciso, J.A.4
Wong, M.Z.5
Hannan, M.6
De La Salmoniere, Y.O.L.7
Aman, K.8
Kato-Maeda, M.9
Small, P.M.10
-
48
-
-
0344838395
-
Evolutionary relationships among strains of Mycobacterium tuberculosis with few copies of IS6110
-
J.W. Dale, H. Al-Ghusein, S. Al-Hashmi, P. Butcher, A.L. Dickens, F. Drobniewski, K.J. Forbes, S.H. Gillespie, D. Lamprecht, and T.D. McHugh Evolutionary relationships among strains of Mycobacterium tuberculosis with few copies of IS6110 J Bacteriol 185 2003 2555 2562
-
(2003)
J Bacteriol
, vol.185
, pp. 2555-2562
-
-
Dale, J.W.1
Al-Ghusein, H.2
Al-Hashmi, S.3
Butcher, P.4
Dickens, A.L.5
Drobniewski, F.6
Forbes, K.J.7
Gillespie, S.H.8
Lamprecht, D.9
McHugh, T.D.10
-
49
-
-
0037853350
-
How clonal is Staphylococcus aureus?
-
E.J. Feil, J.E. Cooper, H. Grundmann, D.A. Robinson, M.C. Enright, T. Berendt, S.J. Peacock, J.M. Smith, M. Murphy, and B.G. Spratt How clonal is Staphylococcus aureus? J Bacteriol 185 2003 3307 3316 This paper is one of several from this group that address the extent of clonality versus recombination in pathogenic bacteria, an issue that has repercussions for the extent of genetic drift and the fixation of novel mutations. The data presented here show that point mutations are 15 times more important than recombination in producing new alleles in S. aureus. The relative impact of recombination and mutation in producing novelty varies among species, with recombination much more important in the previously studied species Neisseria meningitidis and Streptococcus pneumoniae. This study also documents high levels of nonsynonymous substitutions between isolates belonging to the same clonal complex, suggesting that purifying selection is inefficient; in other words, high levels of genetic drift are occurring in these host-restricted lineages, enabling deleterious alleles to become common.
-
(2003)
J Bacteriol
, vol.185
, pp. 3307-3316
-
-
Feil, E.J.1
Cooper, J.E.2
Grundmann, H.3
Robinson, D.A.4
Enright, M.C.5
Berendt, T.6
Peacock, S.J.7
Smith, J.M.8
Murphy, M.9
Spratt, B.G.10
-
50
-
-
0036754331
-
Escherichia coli in disguise: Molecular origins of Shigella
-
R. Lan, and P.R. Reeves Escherichia coli in disguise: molecular origins of Shigella Microbes Infect 4 2002 1125 1132
-
(2002)
Microbes Infect
, vol.4
, pp. 1125-1132
-
-
Lan, R.1
Reeves, P.R.2
-
51
-
-
0842326187
-
The bacterial insertion sequence element IS256 occurs preferentially in nosocomial Staphylococcus epidermidis isolates: Association with biofilm formation and resistance to aminoglycosides
-
S. Kozitskaya, S.H. Cho, K. Dietrich, R. Marre, K. Naber, and W. Ziebuhr The bacterial insertion sequence element IS256 occurs preferentially in nosocomial Staphylococcus epidermidis isolates: association with biofilm formation and resistance to aminoglycosides Infect Immun 72 2004 1210 1215 Clinical isolates of Staphylococcus epidermidis, which have a relatively restricted occurrence in hosts, show relatively high frequencies of IS256.
-
(2004)
Infect Immun
, vol.72
, pp. 1210-1215
-
-
Kozitskaya, S.1
Cho, S.H.2
Dietrich, K.3
Marre, R.4
Naber, K.5
Ziebuhr, W.6
-
52
-
-
3042718925
-
Complete genomes of two clinical Staphylococcus aureus strains: Evidence for the rapid evolution of virulence and drug resistance
-
M.T. Holden, E.J. Feil, J.A. Lindsay, S.J. Peacock, N.P. Day, M.C. Enright, T.J. Foster, C.E. Moore, L. Hurst, and R. Atkin Complete genomes of two clinical Staphylococcus aureus strains: evidence for the rapid evolution of virulence and drug resistance Proc Natl Acad Sci USA 101 2004 9786 9791 This comparison of a more generalized 'community acquired' strain with a more restricted clinical strain of S. aureus illustrates the link between mobile elements, genomic plasticity and the rapid evolution of host-restricted bacteria.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 9786-9791
-
-
Holden, M.T.1
Feil, E.J.2
Lindsay, J.A.3
Peacock, S.J.4
Day, N.P.5
Enright, M.C.6
Foster, T.J.7
Moore, C.E.8
Hurst, L.9
Atkin, R.10
-
53
-
-
0033598784
-
Yersinia pestis, the cause of plague, is a recently emerged clone of Yersinia pseudotuberculosis
-
M. Achtman, K. Zurth, G. Morelli, G. Torrea, A. Guiyoule, and E. Carniel Yersinia pestis, the cause of plague, is a recently emerged clone of Yersinia pseudotuberculosis Proc Natl Acad Sci USA 96 1999 14043 14048
-
(1999)
Proc Natl Acad Sci USA
, vol.96
, pp. 14043-14048
-
-
Achtman, M.1
Zurth, K.2
Morelli, G.3
Torrea, G.4
Guiyoule, A.5
Carniel, E.6
-
54
-
-
2942593885
-
Differential plague-transmission dynamics determine Yersinia pestis population genetic structure on local, regional, and global scales
-
J.M. Girard, D.M. Wagner, A.J. Vogler, C. Keys, C.J. Allender, L.C. Drickamer, and P. Keim Differential plague-transmission dynamics determine Yersinia pestis population genetic structure on local, regional, and global scales Proc Natl Acad Sci USA 101 2004 8408 8413
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 8408-8413
-
-
Girard, J.M.1
Wagner, D.M.2
Vogler, A.J.3
Keys, C.4
Allender, C.J.5
Drickamer, L.C.6
Keim, P.7
|