Divergent evolution and purifying selection of the flaA gene sequences in Aeromonas

Biology Direct

Volumn 4, Issue , 2009, Pages

  Farfán, Maribel ^a   Miñana Galbis, David ^a   Fusté, M Carmen ^a   Lorén, J Gaspar ^a  

^a UNIVERSITY OF BARCELONA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

AEROMONAS; AEROMONAS ALLOSACCHAROPHILA; AEROMONAS POPOFFII; ANIMALIA; BACTERIA (MICROORGANISMS);

FLAA PROTEIN, BACTERIA; FLAGELLIN;

AEROMONAS; ARTICLE; BIOLOGY; GENETIC SELECTION; GENETICS; MOLECULAR EVOLUTION; STATISTICAL MODEL;

AEROMONAS; COMPUTATIONAL BIOLOGY; EVOLUTION, MOLECULAR; FLAGELLIN; LIKELIHOOD FUNCTIONS; SELECTION (GENETICS);

EID: 68949201025     PISSN: None     EISSN: 17456150     Source Type: Journal    
DOI: 10.1186/1745-6150-4-23     Document Type: Article

References (51)

1. AL Bergey's Manual of Systematic Bacteriology. part B New York: Springer Brenner DJ, Krieg NR, Staley JT, Garrity GM 2005, 2:557-578.
2. Rabaan AA Gryllos I Tomás JM Shaw JG Motility and the polar flagellum are required for Aeromonas caviae adherence to Hep-2 cells Infect Immun 2001, 69:4257-4267. 98495 11401962 10.1128/ IAI.69.7.4257-4267.2001
3. Kirov SDM Castrisios M Shaw JG Aeromonas flagella (polar and lateral) are enterocyte adhesins that contribute to biofilm formation on surfaces Infect Immun 2004, 72:1939-1945. 375165 15039313 10.1128/ IAI.72.4.1939-1945.2004
4. Josenhaus C Suerbaun S The role of motility as a virulence factor in bacteria Int J Med Microbiol 2002, 291:605-614. 10.1078/1438-4221-00173 12008914
5. Pallen MJ Penn CW Chandhuri RR Bacterial flagellar diversity in the post-genomic era Trends Microbiol 2005, 13:143-149. 10.1016/ j.tim.2005.02.008 15817382
6. Ramos JHC Rumbo M Sirard JC Bacterial flagellins: Mediators of pathogenicity and host immune responses in mucosa Trends Microbiol 2004, 12:509-517. 10.1016/j.tim.2004.09.002 15488392
7. Andersen-Nissen E Smith KD Strobe KL Rassoulian Barrett SL Cookson BT Logan SM Aderem A Evasion of Toll-like receptor 5 by flagellated bacteria Proc Natl Acad Sci USA 2005, 102:9247-9252. 1166605 15956202 10.1073/pnas.0502040102
8. Westerlund-Wikstrom B Peptide display on bacterial flagella: Principles and applications Int J Med Microbiol 2000, 290:223-230. 10959724
9. Ely B Ely TW Crymes WB Jr Minnich SA A family of six flagellin genes contributes to the Caulobacter crescentus flagellar filament J Bacteriol 2000, 182:5001-5004. 111384 10940048 10.1128/JB.182.17.5001-5004.2000
10. Beatson SA Minamino T Pallen MJ Variation in bacterial flagellins: From sequence to structure Trends Microbiol 2006, 14:151-155. 10.1016/ j.tim.2006.02.008 16540320
11. Umelo E Trust TJ Identification and molecular characterization of two tandemly located flagellin genes from Aeromonas salmonicida A449 J Bacteriol 1997, 179:5292-5299. 179395 9286979
12. Monday SR Minnich SA Feng PCA 12-base-pair deletion in the flagellar master control gene fliC causes nonmotility of the pathogenic German sorbitol fermenting Escherichia coli O157:H strains J Bacteriol 2004, 186:2319-2327. 412172 15060034 10.1128/JB.186.8.2319-2327.2004
13. Ren CP Beatson SA Parkhill J Pallen MJ The flag 2 locus, an ancestral gene cluster, is potentially associated with a novel flagellar system from Escherichia coli J Bacteriol 2005, 187:1430-1440. 545627 15687208 10.1128/JB.187.4.1430-1440.2005
14. Fretin D Fauconnier A Köhler S Halling S Léonard S Nijskens C Ferooz J Lestrate P Delrue RM Danese I Vandenhaute J Tibor A DeBolle X Letesson JJ The sheathed flagellum of Brucella melitensis is involved in persistence in a murine model of infection Cell Microbiol 2005, 7:687-698. 10.1111/j.1462-5822.2005.00502.x 15839898
15. Pallen MJ Matzke NJ From the origin of species to the origin of bacterial flagella Nature reviews 2006, 4:784-790. 10.1038/nrmicro1493 16953248
16. Yang Z PAML 4: A program package for phylogenetic analysis by maximum likelihood Mol Biol Evol 2007, 24:1586-1591. http://abacus.gene.ucl.ac.uk/software/paml.html 10.1093/molbev/msm088 17483113
17. Jukes TH Cantor CR Evolution of protein molecules Mammalian Protein Metabolism New York: Academic Press Munro HN 1969, III:21-132.
18. Kimura M A simple method for estimating evolutionary rate of base substitution through comparative studies of nucleotide sequences J Mol Evol 1980, 16:111-120. 10.1007/BF01731581 7463489
19. Felsenstein J Evolutionary trees from DNA sequences: A maximum likelihood approach J Mol Evol 1981, 17:368-376. 10.1007/BF01734359 7288891
20. Felsenstein J PHYLIP - phylogeny inference package (version 3.2) Cladistics 1989, 5:164-166.
21. Hasegawa M Kishino H Yano T Dating the human-ape splitting by a molecular clock of mitochondrial DNA J Mol Evol 1985, 22:160-174. 10.1007/BF02101694 3934395
22. Tamura K Nei M Estimation of the number of nucleotide substitutions when there are strong transition-transversion and G+C content biases Mol Biol Evol 1993, 9:678-687.
23. Yang Z Estimating the pattern of nucleotide substitution J Mol Evol 1994, 39:105-111. 8064867
24. Zharkikh A Estimation of evolutionary distances between nucleotide sequences J Mol Evol 1994, 39:315-329. 10.1007/BF00160155 7932793
25. Akaike H Information measures and model selection Int Stat Inst 1983, 22:277-291.
26. Nielsen R Yang Z Likelihood models for detecting positively amino acid sites and applications to the HIV-1 envelope gene Genetics 1998, 148:929-936. 1460041 9539414
27. Yang Z Nielsen R Goldman N Pedersen AM Codon-substitution models for heterogeneous selection pressure at amino acid sites Genetics 2000, 155:431-449. 1461088 10790415
28. Goldman N Yang Z A codon-based model of nucleotide substitution for protein-coding DNA sequences Mol Biol Evol 1994, 11:725-736. 7968486
29. Nei M Gojobori T Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions Mol Biol Evol 1986, 3:418-426. 3444411
30. Yang Z Swanson WJ Codon-substitution models to detect adaptive evolution that account for heterogeneous selective pressures among site classes Mol Biol Evol 2002, 19:49-57. 11752189
31. Yang Z Swanson WJ Vacquier VD Maximum-Likelihood analysis of molecular adaptation in Abalone sperm lysin reveals selective pressures among lineages and sites Mol Biol Evol 2000, 17:1446-1455. 11018152
32. Yang Z Bielawski JP Statistical models for detecting molecular adaptation Trends Ecol Evol 2000, 15:496-502. 10.1016/ S0169-5347(00)01994-7 11114436
33. Yang Z Nielsen R Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages Mol Biol Evol 2002, 19:908-917. 12032247
34. Yang Z Wong WSW Nielsen R Bayes empirical Bayes inference of amino acid sites under positive selection Mol Biol Evol 2005, 22:1197-1118.
35. Zhang J Nielsen R Yang Z Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level Mol Biol Evol 2005, 22:2472-2479. 10.1093/molbev/msi237 16107592
36. Yang Z Kumar S Nei M A new method of inference of nucleotide and amino acid ancestral sequences Genetics 1995, 141:1641-1650. 1206894 8601501
37. Winstanley C Morgan JAW The bacterial flagellin gene as a biomarker for detection, population genetics and epidemiological analysis Microbiol 1997, 143:3071-3084. 10.1099/00221287-143-10-3071
38. Reid SD Selander RK Whittam TS Sequence diversity of flagellin (fliC) alleles in pathogenic Escherichia coli J Bacteriol 1999, 181:153-160. 103544 9864325
39. Jordan K Rogozin IB Wolf YI Koonin EV Microevolutionary genomics of bacteria Theor Pop Biol 2002, 61:435-447. 10.1006/tpbi.2002.1588
40. Mamirova L Popadin K Gelfand MS Purifying selection in mitochondria, free-living and obligate intracellular proteobacteria BMC Evol Biol 2007, 7:17-29. 1803777 17295908 10.1186/1471-2148-7-17
41. Zhang J Rates of conservative and radical nonsynonymous nucleotide substitutions in mammalian nuclear genes J Mol Evol 2000, 50:56-68. 10654260
42. Yang Z Maximum likelihood estimation on large phylogenies and analysis of adaptive evolution in human influenza virus A J Mol Evol 2000, 51:423-432. 11080365
43. Yang Z Maximum likelihood analysis of adaptive evolution in HIV-1 gp120 env gene Pac Symp Biocomput 2001, 226-237. 11262943
44. Canals R Ramirez S Vilches S Horsburgh G Shaw JG Tomás JM Merino S Polar flagellum biogenesis in Aeromonas hydrophila J Bacteriol 2006, 188:542-555. 1347287 16385045 10.1128/JB.188.2.542-555.2006
45. Thompson JD Gibson TJ Plewniak F Jeanmougin F Higgins DG The ClustalX windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools Nucleic Acids Res 1997, 25:4876-4882. 147148 9396791 10.1093/nar/25.24.4876
46. Guindon S Gascuel O A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood Syst Biol 2003, 52:696-704. 10.1080/10635150390235520 14530136
47. Johnson JB Omland KS Model selection in ecology and evolution Trends Ecol Evol 2004, 19:101-108. 10.1016/j.tree.2003.10.013 16701236
48. Paradis E Claude J Strimmer K APE: Analyses of phylogenetics and evolution in R languages Bioinformatics 2004, 20:289-290. 10.1093/ bioinformatics/btg412 14734327
49. R Development Core Team R: A language and environment for statistical computing R Foundation for Statistical Computing, Vienna, Austria 2007 http://www.R-project.orG
50. Rozas J Sánchez del Barrio JC Messeguer X Rozas R DnaSP, DNA polymorphism analyses by the coalescent and other methods Bioinformatics 2003, 19:2496-2497. 10.1093/bioinformatics/btg359 14668244
51. Tamura K Dudley J Nei M Kumar S MEGA 4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0 Mol Biol Evol 2007, 24:1596-1599. 10.1093/molbev/msm092 17488738