Prevalence of SOS-mediated control of integron integrase expression as an adaptive trait of chromosomal and mobile integrons

Mobile DNA

Volumn 2, Issue 1, 2011, Pages

  Cambray, Guillaume ^a   Sanchez Alberola, Neus ^b,c   Campoy, Susana ^b   Guerin, Émilie ^d   Da Re, Sandra ^d   González Zorn, Bruno ^e   Ploy, Marie Cécile ^d   Barbé, Jordi ^c   Mazel, Didier ^a   Erill, Ivan ^c  

^a CNRS   (France)

^b UNIVERSITAT AUTÒNOMA DE BARCELONA   (Spain)

^c UNIVERSITY OF MARYLAND BALTIMORE COUNTY   (United States)

^d UNIVERSITY OF LIMOGES   (France)

^e UNIVERSIDAD COMPLUTENSE DE MADRID   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

INTEGRASE; LEXA PROTEIN;

ADAPTIVE TRAIT; ANTIBIOTIC RESISTANCE; ARTICLE; BINDING KINETICS; BINDING SITE; CHROMOSOME; DNA REPAIR; ESCHERICHIA COLI; GENE SEQUENCE; GENETIC CORRELATION; GENETIC EPIDEMIOLOGY; GENETIC REGULATION; GENETIC TRAIT; GENETIC VARIABILITY; HUMAN; INTEGRON; PREVALENCE; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN EXPRESSION; VIBRIO CHOLERAE;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; NEGIBACTERIA; VIBRIO; VIBRIO CHOLERAE;

EID: 80053586991     PISSN: None     EISSN: 17598753     Source Type: Journal    
DOI: 10.1186/1759-8753-2-6     Document Type: Article

References (100)

1. A novel family of potentially mobile DNA elements encoding site-specific gene-integration functions: integrons. Stokes HW, Hall RM, Molecular microbiology 1989 3 1669 1683 10.1111/j.1365-2958.1989.tb00153.x 2560119 (Pubitemid 20023246)
2. Integron-encoded IntI integrases preferentially recognize the adjacent cognate attI site in recombination with a 59-be site. Collis CM, Kim MJ, Stokes HW, Hall RM, Molecular microbiology 2002 46 1415 1427 10.1046/j.1365-2958.2002. 03260.x 12453226 (Pubitemid 36961274)
3. Diversity and relative strength of tandem promoters for the antibiotic-resistance genes of several integrons. Levesque C, Brassard S, Lapointe J, Roy PH, Gene 1994 142 49 54 10.1016/0378-1119(94)90353-0 8181756
4. Expression of antibiotic resistance genes in the integrated cassettes of integrons. Collis CM, Hall RM, Antimicrobial agents and chemotherapy 1995 39 155 162 7695299
5. The role of integrons in antibiotic resistance gene capture. Rowe-Magnus DA, Mazel D, Int J Med Microbiol 2002 292 115 125 10.1078/1438-4221-00197 12195734 (Pubitemid 34842182)
6. Resistance integrons and super-integrons. Fluit AC, Schmitz FJ, Clin Microbiol Infect 2004 10 272 288 10.1111/j.1198-743X.2004.00858.x 15059115 (Pubitemid 38519353)
7. Gene cassettes and cassette arrays in mobile resistance integrons. Partridge SR, Tsafnat G, Coiera E, Iredell JR, FEMS microbiology reviews 2009 33 757 784 10.1111/j.1574-6976.2009.00175.x 19416365
8. Integrons. Cambray G, Guerout AM, Mazel D, Annual review of genetics 2010 44 141 166 10.1146/annurev-genet-102209-163504 20707672
9. Integrons: agents of bacterial evolution. Mazel D, Nature reviews 2006 4 608 620 10.1038/nrmicro1462 16845431 (Pubitemid 44317023)
10. Integrons: mobilizable platforms that promote genetic diversity in bacteria. Boucher Y, Labbate M, Koenig JE, Stokes HW, Trends in microbiology 2007 15 301 309 10.1016/j.tim.2007.05.004 17566739 (Pubitemid 47017712)
11. A distinctive class of integron in the Vibrio cholerae genome. Mazel D, Dychinco B, Webb VA, Davies J, Science (New York, NY) 1998 280 605 608 10.1126/science.280.5363.605 (Pubitemid 28227767)
12. Super-integrons. Rowe-Magnus DA, Guerout AM, Mazel D, Research in microbiology 1999 150 641 651 10.1016/S0923-2508(99)00127-8 10673003 (Pubitemid 30035885)
13. The evolutionary history of chromosomal super-integrons provides an ancestry for multiresistant integrons. Rowe-Magnus DA, Guerout AM, Ploncard P, Dychinco B, Davies J, Mazel D, Proceedings of the National Academy of Sciences of the United States of America 2001 98 652 657 10.1073/pnas.98.2.652 11209061 (Pubitemid 32105098)
14. Discovery and distribution of super-integrons among pseudomonads. Vaisvila R, Morgan RD, Posfai J, Raleigh EA, Molecular microbiology 2001 42 587 601 11722728 (Pubitemid 33064472)
15. Comparative analysis of superintegrons: engineering extensive genetic diversity in the Vibrionaceae. Rowe-Magnus DA, Guerout AM, Biskri L, Bouige P, Mazel D, Genome research 2003 13 428 442 10.1101/gr.617103 12618374 (Pubitemid 36395401)
16. Integrons in Xanthomonas: a source of species genome diversity. Gillings MR, Holley MP, Stokes HW, Holmes AJ, Proceedings of the National Academy of Sciences of the United States of America 2005 102 4419 4424 10.1073/pnas. 0406620102 15755815 (Pubitemid 40397127)
17. Bacterial resistance evolution by recruitment of super-integron gene cassettes. Rowe-Magnus DA, Guerout AM, Mazel D, Molecular microbiology 2002 43 1657 1669 10.1046/j.1365-2958.2002.02861.x 11952913 (Pubitemid 34595555)
18. New carbenicillin-hydrolyzing beta-lactamase (CARB-7) from Vibrio cholerae non-O1, non-O139 strains encoded by the VCR region of the V. cholerae genome. Melano R, Petroni A, Garutti A, Saka HA, Mange L, Pasteran F, Rapoport M, Rossi A, Galas M, Antimicrobial agents and chemotherapy 2002 46 2162 2168 10.1128/AAC.46.7.2162-2168.2002 12069969 (Pubitemid 34665911)
19. CARB-9, a carbenicillinase encoded in the VCR region of Vibrio cholerae non-O1, non-O139 belongs to a family of cassette-encoded beta-lactamases. Petroni A, Melano RG, Saka HA, Garutti A, Mange L, Pasteran F, Rapoport M, Miranda M, Faccone D, Rossi A, Hoffman PS, Galas MF, Antimicrobial agents and chemotherapy 2004 48 4042 4046 10.1128/AAC.48.10.4042-4046.2004 15388476 (Pubitemid 39304645)
20. Genome sequence of Vibrio splendidus: an abundant planctonic marine species with a large genotypic diversity. Le Roux F, Zouine M, Chakroun N, Binesse J, Saulnier D, Bouchier C, Zidane N, Ma L, Rusniok C, Lajus A, Buchrieser C, Médigue C, Polz MF, Mazel D, Environmental microbiology 2009 11 1959 1970 10.1111/j.1462-2920.2009.01918.x 19364337
21. Use of chromosomal integron arrays as a phylogenetic typing system for Vibrio cholerae pandemic strains. Labbate M, Boucher Y, Joss MJ, Michael CA, Gillings MR, Stokes HW, Microbiology (Reading, England) 2007 153 1488 1498 10.1099/mic.0.2006/001065-0 (Pubitemid 46780005)
22. Structural basis for broad DNA-specificity in integron recombination. MacDonald D, Demarre G, Bouvier M, Mazel D, Gopaul DN, Nature 2006 440 1157 1162 10.1038/nature04643 16641988
23. Structural features of single-stranded integron cassette attC sites and their role in strand selection. Bouvier M, Ducos-Galand M, Loot C, Bikard D, Mazel D, PLoS genetics 2009 5 1000632 10.1371/journal.pgen.1000632 19730680
24. Integron cassette insertion: a recombination process involving a folded single strand substrate. Bouvier M, Demarre G, Mazel D, The EMBO journal 2005 24 4356 4367 10.1038/sj.emboj.7600898 16341091 (Pubitemid 41828910)
25. The SOS Response Controls Integron Recombination. Guerin E, Cambray G, Sanchez-Alberola N, Campoy S, Erill I, Da Re S, Gonzalez-Zorn B, Barbe J, Ploy M-C, Mazel D, Science 2009 324 1034 10.1126/science.1172914 19460999
26. Mutagenesis and inducible responses to deoxyribonucleic acid damage in Escherichia coli. Walker GC, Microbiol Rev 1984 48 60 93 6371470 (Pubitemid 14150426)
27. Aeons of distress: an evolutionary perspective on the bacterial SOS response. Erill I, Campoy S, Barbe J, FEMS microbiology reviews 2007 31 637 656 10.1111/j.1574-6976.2007.00082.x 17883408 (Pubitemid 47621761)
28. Upstream of the SOS response: figure out the trigger. Aertsen A, Michiels CW, Trends in microbiology 2006 14 421 423 10.1016/j.tim.2006.08.006 16934473 (Pubitemid 44375021)
29. Nature of the SOS-inducing signal in Escherichia coli. The involvement of DNA replication. Sassanfar M, Roberts JW, Journal of molecular biology 1990 212 79 96 10.1016/0022-2836(90)90306-7 2108251 (Pubitemid 20120299)
30. Mechanism of specific LexA cleavage: autodigestion and the role of RecA coprotease. Little JW, Biochimie 1991 73 411 421 10.1016/0300-9084(91)90108-D 1911941
31. Identification of additional genes belonging to the LexA regulon in Escherichia coli. Fernandez De Henestrosa AR, Ogi T, Aoyagi S, Chafin D, Hayes JJ, Ohmori H, Woodgate R, Molecular microbiology 2000 35 1560 1572 10760155 (Pubitemid 30175530)
32. Phage regulatory circuits and virulence gene expression. Waldor MK, Friedman DI, Current opinion in microbiology 2005 8 459 465 10.1016/j.mib.2005. 06.001 15979389 (Pubitemid 41021908)
33. Activation of the Vibrio cholerae SOS response is not required for intestinal cholera toxin production or colonization. Quinones M, Davis BM, Waldor MK, Infection and immunity 2006 74 927 930 10.1128/IAI.74.2.927-930.2006 16428736 (Pubitemid 43185526)
34. Toxin gene expression by shiga toxin-producing Escherichia coli: the role of antibiotics and the bacterial SOS response. Kimmitt PT, Harwood CR, Barer MR, Emerging infectious diseases 2000 6 458 465 10.3201/eid0605.000503 10998375
35. High and low UV-dose responses in SOS-induction of the precise excision of transposons tn1, Tn5 and Tn10 in Escherichia coli. Aleshkin GI, Kadzhaev KV, Markov AP, Mutation research 1998 401 179 191 9639701 (Pubitemid 28293849)
36. Antibiotic-induced SOS response promotes horizontal dissemination of pathogenicity island-encoded virulence factors in staphylococci. Ubeda C, Maiques E, Knecht E, Lasa I, Novick RP, Penades JR, Molecular microbiology 2005 56 836 844 10.1111/j.1365-2958.2005.04584.x 15819636 (Pubitemid 40562374)
37. Lex marks the spot: the virulent side of SOS and a closer look at the LexA regulon. Kelley WL, Molecular microbiology 2006 62 1228 1238 10.1111/j.1365-2958.2006.05444.x 17042786 (Pubitemid 44707190)
38. SOS response promotes horizontal dissemination of antibiotic resistance genes. Beaber JW, Hochhut B, Waldor MK, Nature 2004 427 72 74 10.1038/nature02241 14688795 (Pubitemid 38094823)
39. Induction of the SOS response by new 4-quinolones. Phillips I, Culebras E, Moreno F, Baquero F, The Journal of antimicrobial chemotherapy 1987 20 631 638 10.1093/jac/20.5.631 3323160 (Pubitemid 18036576)
40. SOS response induction by beta-lactams and bacterial defense against antibiotic lethality. Miller C, Thomsen LE, Gaggero C, Mosseri R, Ingmer H, Cohen SN, Science (New York, NY) 2004 305 1629 1631 10.1126/science.1101630 (Pubitemid 39296359)
41. beta-lactam antibiotics induce the SOS response and horizontal transfer of virulence factors in Staphylococcus aureus. Maiques E, Ubeda C, Campoy S, Salvador N, Lasa I, Novick RP, Barbe J, Penades JR, Journal of bacteriology 2006 188 2726 2729 10.1128/JB.188.7.2726-2729.2006 16547063
42. Ciprofloxacin and trimethoprim cause phage induction and virulence modulation in Staphylococcus aureus. Goerke C, Koller J, Wolz C, Antimicrobial agents and chemotherapy 2006 50 171 177 10.1128/AAC.50.1.171-177.2006 16377683 (Pubitemid 43042918)
43. New approaches to combating antimicrobial drug resistance. Avison MB, Genome biology 2005 6 243 10.1186/gb-2005-6-13-243 16420675 (Pubitemid 44725592)
44. Mobile gene cassettes: a fundamental resource for bacterial evolution. Michael CA, Gillings MR, Holmes AJ, Hughes L, Andrew NR, Holley MP, Stokes HW, The American naturalist 2004 164 1 12 10.1086/421733 15266366 (Pubitemid 38991827)
45. Mutational analysis of the Rhizobium etli recA operator. Tapias A, Barbe J, Journal of bacteriology 1998 180 6325 6331 9829943 (Pubitemid 28544265)
46. LexA-independent DNA damage-mediated induction of gene expression in Myxococcus xanthus. Campoy S, Fontes M, Padmanabhan S, Cortes P, Llagostera M, Barbe J, Molecular microbiology 2003 49 769 781 12864858 (Pubitemid 36918695)
47. Reconstruction of the evolutionary history of the LexA-binding sequence. Mazon G, Erill I, Campoy S, Cortes P, Forano E, Barbe J, Microbiology 2004 150 3783 3795 10.1099/mic.0.27315-0 15528664 (Pubitemid 39545324)
48. Geobacter sulfurreducens has two autoregulated lexA genes whose products do not bind the recA promoter: differing responses of lexA and recA to DNA damage. Jara M, Nunez C, Campoy S, Fernandez de Henestrosa AR, Lovley DR, Barbe J, Journal of bacteriology 2003 185 2493 2502 10.1128/JB.185.8.2493-2502.2003 12670973 (Pubitemid 36417973)
49. Expression of canonical SOS genes is not under LexA repression in Bdellovibrio bacteriovorus. Campoy S, Salvador N, Cortes P, Erill I, Barbe J, Journal of bacteriology 2005 187 5367 5375 10.1128/JB.187.15.5367-5375.2005 16030231 (Pubitemid 41022956)
50. Molecular differentiation of common promoters in Salmonella class 1 integrons. Kim T-E, Kwon H-J, Cho S-H, Kim S, Lee B-K, Yoo H-S, Park Y-H, Kim S-J, Journal of Microbiological Methods 2007 68 453 457 10.1016/j.mimet.2006.09. 019 17123653 (Pubitemid 46329146)
51. Inverse correlation between promoter strength and excision activity in class 1 integrons. Jove T, Da Re S, Denis F, Mazel D, Ploy MC, PLoS genetics 2010 6 1000793 10.1371/journal.pgen.1000793 20066027
52. Genetic basis for dissemination of armA. Gonzalez-Zorn B, Catalan A, Escudero JA, Dominguez L, Teshager T, Porrero C, Moreno MA, The Journal of antimicrobial chemotherapy 2005 56 583 585 10.1093/jac/dki246 16027145 (Pubitemid 41264140)
53. Insights and inferences about integron evolution from genomic data. Nemergut DR, Robeson MS, Kysela RF, Martin AP, Schmidt SK, Knight R, BMC genomics 2008 9 261 10.1186/1471-2164-9-261 18513439 (Pubitemid 351837408)
54. Characterization of Xanthomonas axonopodis pv. citri LexA: recognition of the LexA binding site. Yang MK, Yang YC, Hsu CH, Mol Genet Genomics 2002 268 477 487 10.1007/s00438-002-0754-6 12471445 (Pubitemid 35435851)
55. A new regulatory DNA motif of the gamma subclass Proteobacteria: identification of the LexA protein binding site of the plant pathogen Xylella fastidiosa. Campoy S, Mazon G, Fernandez de Henestrosa AR, Llagostera M, Monteiro PB, Barbe J, Microbiology (Reading, England) 2002 148 3583 3597 (Pubitemid 35414468)
56. An analysis of the evolutionary relationships of integron integrases, with emphasis on the prevalence of class 1 integrons in Escherichia coli isolates from clinical and environmental origins. Diaz-Mejia JJ, Amabile-Cuevas CF, Rosas I, Souza V, Microbiology (Reading, England) 2008 154 94 102 10.1099/mic.0.2007/008649-0 (Pubitemid 351201390)
57. Recovery and evolutionary analysis of complete integron gene cassette arrays from Vibrio. Boucher Y, Nesbo CL, Joss MJ, Robinson A, Mabbutt BC, Gillings MR, Doolittle WF, Stokes HW, BMC Evolutionary Biology 2006 6 3 10.1186/1471-2148-6-3 16417647
58. Analysis by mutagenesis of a chromosomal integron integrase from Shewanella amazonensis SB2BT. Larouche A, Roy PH, Journal of bacteriology 2009 191 1933 1940 10.1128/JB.01537-08 19136589
59. The evolution of class 1 integrons and the rise of antibiotic resistance. Gillings M, Boucher Y, Labbate M, Holmes A, Krishnan S, Holley M, Stokes HW, Journal of bacteriology 2008 190 5095 5100 10.1128/JB.00152-08 18487337 (Pubitemid 351991077)
60. Whole-genome reciprocal BLAST analysis reveals that planctomycetes do not share an unusually large number of genes with Eukarya and Archaea. Fuchsman CA, Rocap G, Applied and environmental microbiology 2006 72 6841 6844 10.1128/AEM.00429-06 17021241 (Pubitemid 44582933)
61. Identification of operators and promoters that control SXT conjugative transfer. Beaber JW, Waldor MK, Journal of bacteriology 2004 186 5945 5949 10.1128/JB.186.17.5945-5949.2004 15317801 (Pubitemid 39128669)
62. LexA-binding sequences in Gram-positive and cyanobacteria are closely related. Mazon G, Lucena JM, Campoy S, Fernandez de Henestrosa AR, Candau P, Barbe J, Mol Genet Genomics 2004 271 40 49 10.1007/s00438-003-0952-x 14652736 (Pubitemid 38299684)
63. The Leptospira interrogans lexA gene is not autoregulated. Cune J, Cullen P, Mazon G, Campoy S, Adler B, Barbe J, Journal of bacteriology 2005 187 5841 5845 10.1128/JB.187.16.5841-5845.2005 16077133 (Pubitemid 41134323)
64. Recombination activity of a distinctive integron-gene cassette system associated with Pseudomonas stutzeri populations in soil. Holmes AJ, Holley MP, Mahon A, Nield B, Gillings M, Stokes HW, Journal of bacteriology 2003 185 918 928 10.1128/JB.185.3.918-928.2003 12533467 (Pubitemid 36139450)
65. Excision and integration of cassettes by an integron integrase of Nitrosomonas europaea. Leon G, Roy PH, Journal of bacteriology 2003 185 2036 2041 10.1128/JB.185.6.2036-2041.2003 12618471 (Pubitemid 36297907)
66. Conjugative DNA transfer induces the bacterial SOS response and promotes antibiotic resistance development through integron activation. Baharoglu Z, Bikard D, Mazel D, PLoS genetics 2010 6 1001165 10.1371/journal.pgen.1001165 20975940
67. New qnr Gene Cassettes Associated with Superintegron Repeats in Vibrio cholerae O1. Fonseca EL, Dos Santos Freitas F, Vieira VV, Vicente AC, Emerging infectious diseases 2008 14 1129 1131 10.3201/eid1407.080132 18598639 (Pubitemid 351920448)
68. The biological cost of antibiotic resistance. Andersson DI, Levin BR, Current opinion in microbiology 1999 2 489 493 10.1016/S1369-5274(99)00005-3 10508723 (Pubitemid 29477174)
69. Directed enzyme evolution via small and effective neutral drift libraries. Gupta RD, Tawfik DS, Nature methods 2008 5 939 942 10.1038/nmeth.1262 18931667
70. Integron integrases possess a unique additional domain necessary for activity. Messier N, Roy PH, Journal of bacteriology 2001 183 6699 6706 10.1128/JB.183.22.6699-6706.2001 11673443 (Pubitemid 33026764)
71. Mutagenesis and homology modeling of the Tn21 integron integrase IntI1. Johansson C, Boukharta L, Eriksson J, Aqvist J, Sundstrom L, Biochemistry 2009 48 1743 1753 10.1021/bi8020235 19199791
72. Point mutations in the integron integrase IntI1 that affect recombination and/or substrate recognition. Gravel A, Messier N, Roy PH, Journal of bacteriology 1998 180 5437 5442 9765577 (Pubitemid 28471542)
73. Identification of key structural determinants of the IntI1 integron integrase that influence attC × attI1 recombination efficiency. Demarre G, Frumerie C, Gopaul DN, Mazel D, Nucleic acids research 2007 35 6475 6489 10.1093/nar/gkm709 17884913 (Pubitemid 350111616)
74. The relaxed requirements of the integron cleavage site allow predictable changes in integron target specificity. Frumerie C, Ducos-Galand M, Gopaul DN, Mazel D, Nucleic acids research 2010 38 559 569 10.1093/nar/gkp990 19914932
75. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Edgar RC, Nucleic acids research 2004 32 1792 1797 10.1093/nar/gkh340 15034147 (Pubitemid 38832724)
76. The IntI-like tyrosine recombinase of Shewanella oneidensis is active as an integron integrase. Drouin F, Melancon J, Roy PH, Journal of bacteriology 2002 184 1811 1815 10.1128/JB.184.6.1811-1815.2002 11872738 (Pubitemid 34188238)
77. Characterization of the class 3 integron and the site-specific recombination system it determines. Collis CM, Kim MJ, Partridge SR, Stokes HW, Hall RM, Journal of bacteriology 2002 184 3017 3026 10.1128/JB.184.11.3017-3026. 2002 12003943 (Pubitemid 34517825)
78. IntI2 integron integrase in Tn7. Hansson K, Sundstrom L, Pelletier A, Roy PH, Journal of bacteriology 2002 184 1712 1721 10.1128/JB.184.6.1712-1721.2002 11872723 (Pubitemid 34188223)
79. Comparative study of class 1 integron and Vibrio cholerae superintegron integrase activities. Biskri L, Bouvier M, Guerout AM, Boisnard S, Mazel D, Journal of bacteriology 2005 187 1740 1750 10.1128/JB.187.5.1740-1750.2005 15716446 (Pubitemid 40289376)
80. Genetic elements involved in Tn21 site-specific integration, a novel mechanism for the dissemination of antibiotic resistance genes. Martinez E, de la Cruz F, The EMBO journal 1990 9 1275 1281 2157593
81. A reexamination of information theory-based methods for DNA-binding site identification. Erill I, O'Neill MC, BMC bioinformatics 2009 10 57 10.1186/1471-2105-10-57 19210776
82. xFITOM: a generic GUI tool to search for transcription factor binding sites. Bhargava N, Erill I, Bioinformation 2010 5 49 50 21346861
83. Information Content of Individual Genetic Sequences. Schneider TD, Journal of Theoretical Biology 1997 189 427 441 10.1006/jtbi.1997.0540 9446751 (Pubitemid 28048211)
84. Cohabitation of two different lexA regulons in Pseudomonas putida. Abella M, Campoy S, Erill I, Rojo F, Barbe J, Journal of bacteriology 2007 189 8855 8862 10.1128/JB.01213-07 17933893
85. Elucidation of regulatory elements that control damage induction and competence induction of the Bacillus subtilis SOS system. Cheo DL, Bayles KW, Yasbin RE, Journal of bacteriology 1993 175 5907 5915 7690748 (Pubitemid 23277439)
86. Characterization of Mycobacterium tuberculosis LexA: recognition of a Cheo (Bacillus-type SOS) box. Movahedzadeh F, Colston MJ, Davis EO, Microbiology (Reading, England) 1997 143 Pt 3 929 936 (Pubitemid 27192771)
87. Identification of the Rhodobacter sphaeroides SOS box. Fernandez de Henestrosa AR, Rivera E, Tapias A, Barbe J, Molecular microbiology 1998 28 991 1003 10.1046/j.1365-2958.1998.00860.x 9663685 (Pubitemid 28258996)
88. Dispersal and regulation of an adaptive mutagenesis cassette in the bacteria domain. Erill I, Campoy S, Mazon G, Barbe J, Nucleic acids research 2006 34 66 77 10.1093/nar/gkj412 16407325 (Pubitemid 43160035)
89. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Thompson JD, Higgins DG, Gibson TJ, Nucleic acids research 1994 22 4673 4680 10.1093/nar/22.22.4673 7984417 (Pubitemid 24354800)
90. T-Coffee: A novel method for fast and accurate multiple sequence alignment. Notredame C, Higgins DG, Heringa J, Journal of molecular biology 2000 302 205 217 10.1006/jmbi.2000.4042 10964570
91. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Castresana J, Molecular biology and evolution 2000 17 540 552 10742046 (Pubitemid 30210700)
92. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Guindon S, Gascuel O, Systematic biology 2003 52 696 704 10.1080/10635150390235520 14530136 (Pubitemid 37365050)
93. TreeView: an application to display phylogenetic trees on personal computers. Page RD, Comput Appl Biosci 1996 12 357 358 8902363
94. Mesquite: a modular system for evolutionary analysis. Version 2.72. http://mesquiteproject.org
95. The maximum likelihood approach to reconstructing ancestral character states of discrete characters on phylogenies. Pagel M, Systematic biology 1999 48 612 622 10.1080/106351599260184 (Pubitemid 129479567)
96. Likelihood of ancestor states in adaptive radiation. Schluter D, Price T, Mooers AO, Ludwig D, Evolution 1997 51 1699 1711 10.2307/2410994 (Pubitemid 28104532)
97. The assumptions and challenges of ancestral state reconstructions. Omland KE, Systematic biology 1999 48 604 611 10.1080/106351599260175 (Pubitemid 129479566)
98. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Datsenko KA, Wanner BL, Proceedings of the National Academy of Sciences of the United States of America 2000 97 6640 6645 10.1073/pnas. 120163297 10829079 (Pubitemid 30412767)
99. Widespread distribution of a lexA-regulated DNA damage-inducible multiple gene cassette in the Proteobacteria phylum. Abella M, Erill I, Jara M, Mazon G, Campoy S, Barbe J, Molecular microbiology 2004 54 212 222 10.1111/j.1365-2958. 2004.04260.x 15458417 (Pubitemid 39315170)
100. WebLogo: a sequence logo generator. Crooks GE, Hon G, Chandonia JM, Brenner SE, Genome research 2004 14 1188 1190 10.1101/gr.849004 15173120 (Pubitemid 38811555)