Sequence variability of Rhizobiales orthologs and relationship with physico-chemical characteristics of proteins

Biology Direct

Volumn 6, Issue , 2011, Pages

  Peralta, Humberto ^a   Guerrero, Gabriela ^a   Aguilar, Alejandro ^a   Mora, Jaime ^a  

^a INSTITUTO DE CIENCIAS FÍSICAS   (Mexico)

Author keywords

Adaptation; Comparative genomics; Evolutionary rates; Nonsynonymous substitution; Rhizobia

Indexed keywords

AGROBACTERIUM TUMEFACIENS; ANIMALIA; BRUCELLA MELITENSIS; RHIZOBIACEAE; RHIZOBIALES;

BACTERIAL PROTEIN; MEMBRANE PROTEIN;

AMINO ACID SUBSTITUTION; ARTICLE; BACTERIAL CHROMOSOME; BACTERIAL GENE; CHEMISTRY; CLASSIFICATION; COMPARATIVE STUDY; GENETICS; ISOELECTRIC POINT; MOLECULAR EVOLUTION; PHYLOGENY; PHYSICAL CHEMISTRY; PROTEIN SECONDARY STRUCTURE; RHIZOBIACEAE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SPECIES DIFFERENCE; SYNTENY;

AMINO ACID SUBSTITUTION; BACTERIAL PROTEINS; CHROMOSOMES, BACTERIAL; EVOLUTION, MOLECULAR; GENES, BACTERIAL; ISOELECTRIC POINT; MEMBRANE PROTEINS; PHYLOGENY; PHYSICOCHEMICAL PROCESSES; PROTEIN STRUCTURE, SECONDARY; RHIZOBIACEAE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN; SEQUENCE HOMOLOGY, AMINO ACID; SPECIES SPECIFICITY; SYNTENY;

EID: 80053548046     PISSN: None     EISSN: 17456150     Source Type: Journal    
DOI: 10.1186/1745-6150-6-48     Document Type: Article

References (63)

1. Hulsen T, Hynen MA, De Vlieg J, Groenen PMA. Benchmarking ortholog identification methods using functional genomics data. Genome Biol 2006, 7(4):R31. 10.1186/gb-2006-7-4-r31, 1557999, 16613613.
2. Huynen MA, Bork P. Measuring genome evolution. Proc Natl Acad Sci USA 1998, 95:5849-5856. 10.1073/pnas.95.11.5849, 34486, 9600883.
3. Zheng XH, Lu F, Wang ZY, Zhong F, Hoover J, Mural R. Using shared genomic synteny and shared protein functions to enhance the identification of orthologous gene pairs. Bioinformatics 2005, 21(6):703-710. 10.1093/bioinformatics/bti045, 15458983.
4. Guerrero G, Peralta H, Aguilar A, Diaz R, Villalobos MA, Medrano-Soto A, Mora J. Evolutionary, structural and functional relationships revealed by comparative analysis of syntenic genes in Rhizobiales. BMC Evol Biol 2005, 5:55. 10.1186/1471-2148-5-55, 1276791, 16229745.
5. Soskine M, Tawfik DS. Mutational effects and the evolution of new protein functions. Nat Rev Genet 2010, 11:572-582.
6. Hughes AL, Nei M. Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection. Nature 1988, 335:167-170. 10.1038/335167a0, 3412472.
7. Yang Z, Bielawski JP. Statistical methods for detecting molecular adaptation. Trends Ecol Evol 2000, 15:496-503. 10.1016/S0169-5347(00)01994-7, 11114436.
8. Yang Z. Maximum-likelihood models for combined analyses of multiple sequence data. J Mol Evol 1996, 42:587-596. 10.1007/BF02352289, 8662011.
9. Atchley WR, Zhao J, Fernandes AD, Drüke T. Solving the protein sequence metric problem. Proc Natl Acad Sci USA 2005, 102(18):6395-6400. 10.1073/pnas.0408677102, 1088356, 15851683.
10. Wood DW, Setubal JC, Kaul R, Monks DE, Kitajima JP, Okura VK, Zhou Y, Chen L, Wood GE, Almeida NF, Woo L, Chen Y, Paulsen IT, Eisen JA, Karp PD, Bovee D, Chapman P, Clendenning J, Deatherage G, Gillet W, Grant C, Kutyavin T, Levy R, Li MJ, McClelland E, Palmieri A, Raymond C, Rouse G, Saenphimmachak C, Wu Z, Romero P, Gordon D, Zhang S, Yoo H, Tao Y, Biddle P, Jung M, Krespan W, Perry M, Gordon-Kamm B, Liao L, Kim S, Hendrick C, Zhao ZY, Dolan M, Chumley F, Tingey SV, Tomb JF, Gordon MP, Olson MV, Nester EW. The genome of the natural genetic engineer Agrobacterium tumefaciens C58. Science 2001, 294(5550):2317-2323. 10.1126/science.1066804, 11743193.
11. DelVecchio VG, Kapatral V, Redkar RJ, Patra G, Mujer C, Los T, Ivanova N, Anderson I, Bhattacharyya A, Lykidis A, Reznik G, Jablonski L, Larsen N, D'Souza M, Bernal A, Mazur M, Goltsman E, Selkov E, Elzer PH, Hagius S, O'Callaghan D, Letesson JJ, Haselkorn R, Kyrpides N, Overbeek R. The genome sequence of the facultative intracellular pathogen Brucella melitensis. Proc Natl Acad Sci USA 2002, 99(1):443-448. 10.1073/pnas.221575398, 117579, 11756688.
12. Goodner B, Hinkle G, Gattung S, Miller N, Blanchard M, Qurollo B, Goldman BS, Cao Y, Askenazi M, Halling C, Mullin L, Houmiel K, Gordon J, Vaudin M, Iartchouk O, Epp A, Liu F, Wollam C, Allinger M, Doughty D, Scott C, Lappas C, Markelz B, Flanagan C, Crowell C, Gurson J, Lomo C, Sear C, Strub G, Cielo C, Slater S. Genome sequence of the plant pathogen and biotechnology agent Agrobacterium tumefaciens C58. Science 2001, 294(5550):2323-2328. 10.1126/science.1066803, 11743194.
13. Paulsen IT, Seshadri R, Nelson KE, Eisen JA, Heidelberg JF, Read TD, Dodson RJ, Umayam L, Brinkac LM, Beanan MJ, Daugherty SC, Deboy RT, Durkin AS, Kolonay JF, Madupu R, Nelson WC, Ayodeji B, Kraul M, Shetty J, Malek J, Van Aken SE, Riedmuller S, Tettelin H, Gill SR, White O, Salzberg SL, Hoover DL, Lindler LE, Halling SM, Boyle SM, Fraser CM. The Brucella suis genome reveals fundamental similarities between animal and plant pathogens and symbionts. Proc Natl Acad Sci USA 2002, 99(20):13148-13153. 10.1073/pnas.192319099, 130601, 12271122.
14. Halling SM, Peterson-Burch BD, Bricker BJ, Zuerner RL, Qing Z, Li LL, Kapur V, Alt DP, Olsen SC. Completion of the genome sequence of Brucella abortus and comparison to the highly similar genomes of Brucella melitensis and Brucella suis. J Bacteriol 2005, 187(8):2715-2726. 10.1128/JB.187.8.2715-2726.2005, 1070361, 15805518.
15. Alsmark CM, Frank AC, Karlberg EO, Legault BA, Ardell DH, Canbäck B, Eriksson AS, Näslund AK, Handley SA, Huvet M, La Scola B, Holmberg M, Andersson SG. The louse-borne human pathogen Bartonella quintana is a genomic derivative of the zoonotic agent Bartonella henselae. Proc Natl Acad Sci USA 2004, 101(26):9716-9721. 10.1073/pnas.0305659101, 470741, 15210978.
16. Galibert F, Finan TM, Long SR, Puhler A, Abola P, Ampe F, Barloy-Hubler F, Barnett MJ, Becker A, Boistard P, Bothe G, Boutry M, Bowser L, Buhrmester J, Cadieu E, Capela D, Chain P, Cowie A, Davis RW, Dreano S, Federspiel NA, Fisher RF, Gloux S, Godrie T, Goffeau A, Golding B, Gouzy J, Gurjal M, Hernandez-Lucas I, Hong A, Huizar L, Hyman RW, Jones T, Kahn D, Kahn ML, Kalman S, Keating DH, Kiss E, Komp C, Lelaure V, Masuy D, Palm C, Peck MC, Pohl TM, Portetelle D, Purnelle B, Ramsperger U, Surzycki R, Thebault P, Vandenbol M, Vorholter FJ, Weidner S, Wells DH, Wong K, Yeh KC, Batut J. The composite genome of the legume symbiont Sinorhizobium meliloti. Science 2001, 293(5530):668-672. 10.1126/science.1060966, 11474104.
17. Kaneko T, Nakamura Y, Sato S, Asamizu E, Kato T, Sasamoto S, Watanabe A, Idesawa K, Ishikawa A, Kawashima K, Kimura T, Kishida Y, Kiyokawa C, Kohara M, Matsumoto M, Matsuno A, Mochizuki Y, Nakayama S, Nakazaki N, Shimpo S, Sugimoto M, Takeuchi C, Yamada M, Tabata S. Complete genome structure of the nitrogen-fixing symbiotic bacterium Mesorhizobium loti. DNA Res 2000, 7(6):331-338. 10.1093/dnares/7.6.331, 11214968.
18. González V, Santamaría RI, Bustos P, Hernández-González I, Medrano-Soto A, Moreno-Hagelsieb G, Janga SC, Ramírez MA, Jiménez-Jacinto V, Collado-Vides J, Dávila G. The partitioned Rhizobium etli genome: genetic and metabolic redundancy in seven interacting replicons. Proc Natl Acad Sci USA 2006, 103(10):3834-3839. 10.1073/pnas.0508502103, 1383491, 16505379.
19. Pearson WR, Lipman DJ. Improved tools for biological sequence comparison. Proc Natl Acad Sci USA 1988, 85(8):2444-2448. 10.1073/pnas.85.8.2444, 280013, 3162770.
20. Thompson JD, Higgins DG, Gibson TJ. CLUSTALW: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucl Acids Res 1994, 22(22):4673-4680. 10.1093/nar/22.22.4673, 308517, 7984417.
21. PHYLIP Program for inferring phylogenies. , http://evolution.genetics.washington.edu/phylip.html
22. Yang Z. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 1997, 13(5):555-556.
23. Saeed AI, Sharov V, White J, Li J, Liang W, Bhagabati N, Braisted J, Klapa M, Currier T, Thiagarajan M, Sturn A, Snuffin M, Rezantsev A, Popov D, Ryltsov A, Kostukovich E, Borisovsky I, Liu Z, Vinsavich A, Trush V, Quackenbush J. TM4: a free, open-source system for microarray data management and analysis. Biotechniques 2003, 34(2):374-378.
24. Olivares-Hernandez R, Bordel S, Nielsen J. Codon usage variability determines the correlation between proteome and transcriptome fold changes. BMC Syst Biol 2011, 5:33. 10.1186/1752-0509-5-33, 3058016, 21352515.
25. Persson B, Argos P. Prediction of transmembrane segments in proteins utilising multiple sequence alignments. J Mol Biol 1994, 237(2):182-192. 10.1006/jmbi.1994.1220, 8126732.
26. Llóret L, Martínez-Romero E. Evolucion y filogenia de Rhizobium. Rev Lat Microbiol 2005, 47:43-60.
27. Capaldi RA, Vanderkooi G. The low polarity of many membrane proteins. Proc Natl Acad Sci USA 1972, 69(4):930-932. 10.1073/pnas.69.4.930, 426597, 4502942.
28. González V, Acosta JL, Santamaría RI, Bustos P, Fernández JL, Hernández-González IL, Díaz R, Flores M, Palacios R, Mora J, Dávila G. Conserved symbiotic plasmid DNA sequences in the multireplicon pangenomic structure of Rhizobium etli. Appl Environ Microbiol 2010, 76(5):1604-1614. 10.1128/AEM.02039-09, 2832352, 20048063.
29. Díaz R, Vargas-Lagunas C, Villalobos MA, Peralta H, Mora Y, Encarnación S, Girard L, Mora J. argC orthologs from Rhizobiales show diverse transcriptional efficiency and functionality in Sinorhizobium meliloti. J Bacteriol 2011, 193:460-472. 10.1128/JB.01010-10, 3019832, 21075924.
30. Jordan IK, Rogozin IB, Wolf YI, Koonin EV. Microevolutionary genomics of bacteria. Theor Popul Biol 2002, 61(4):435-447. 10.1006/tpbi.2002.1588, 12167363.
31. Jordan IK, Rogozin IB, Wolf YI, Koonin EV. Essential genes are more evolutionarily conserved than are nonessential genes in bacteria. Genome Res 2002, 12(6):962-968. 1383730, 12045149.
32. Jordan IK, Wolf YI, Koonin EV. No simple dependence between protein evolution rate and the number of protein-protein interactions: only the most prolific interactors tend to evolve slowly. BMC Evol Biol 2003, 3:1. 10.1186/1471-2148-3-1, 140311, 12515583.
33. Koonin EV. Comparative genomics, minimal gene sets, and the last universal common ancestor. Nat Rev Microbiol 2003, 1:127-136. 10.1038/nrmicro751, 15035042.
34. Danchin A. Genomes and evolution. Curr Issues Mol Biol 2003, 5:37-42.
35. Young JP, Crossman LC, Johnston AW, Thomson NR, Ghazoui ZF, Hull KH, Wexler M, Curson AR, Todd JD, Poole PS, Mauchline TH, East AK, Quail MA, Churcher C, Arrowsmith C, Cherevach I, Chillingworth T, Clarke K, Cronin A, Davis P, Fraser A, Hance Z, Hauser H, Jagels K, Moule S, Mungall K, Norbertczak H, Rabbinowitsch E, Sanders M, Simmonds M, Whitehead S, Parkhill J. The genome of Rhizobium leguminosarum has recognizable core and accessory components. Genome Biol 2006, 7(4):R34. 10.1186/gb-2006-7-4-r34, 1557990, 16640791.
36. Koonin EV, Wolf YI. Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world. Nucl Acids Res 2008, 36:6688-6719. 10.1093/nar/gkn668, 2588523, 18948295.
37. Philippe H, Casane D, Gribaldo S, Lopez P, Meunier J. Heterotachy and functional shift in protein evolution. IUBMB Life 2003, 55:257-265. 10.1080/1521654031000123330, 12880207.
38. Amitai G, Gupta RD, Tawfik DS. Latent evolutionary potentials under the neutral mutational drift of an enzyme. HFSP J 2007, 1:67-78. 2645560, 19404461.
39. Wagner A. Neutralism and selectionism: a network-based reconciliation. Nat Rev Gen 2008, 9:965-974.
40. Wagner A. Robustness, evolvability, and neutrality. FEBS Letters 2005, 579:1772-1778. 10.1016/j.febslet.2005.01.063, 15763550.
41. Chamary JV, Parmley JL, Hurst LD. Hearing silence: non-neutral evolution at silent sites in mammals. Nat Rev Genet 2006, 7:98-108. 10.1038/nrg1770, 16418745.
42. Gray MW, Lukes J, Archibald JM, Keeling PJ, Doolittle WF. Irremediable complexity?. Science 2010, 330:920-921. 10.1126/science.1198594, 21071654.
43. Ortlund EA, Bridgham JT, Redinbo MR, Thornton JW. Crystal structure of an ancient protein: evolution by conformational epistasis. Science 2007, 317:1544-1548. 10.1126/science.1142819, 2519897, 17702911.
44. Lind PA, Berg OG, Andersson DI. Mutational robustness of ribosomal protein genes. Science 2010, 330:825-827. 10.1126/science.1194617, 21051637.
45. Kristensen DM, Wolf YI, Mushegian AR, Koonin EV. Computational methods for gene orthology inference. Brief Bioinf 2011,
46. Lind PA, Tobin C, Berg OG, Kurland CG, Andersson DI. Compensatory gene amplification restores fitness after inter-species gene replacements. Mol Microbiol 2010, 75:1078-1089. 10.1111/j.1365-2958.2009.07030.x, 20088865.
47. Drummond DA, Wilke CO. Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution. Cell 2008, 134(2):341-352. 10.1016/j.cell.2008.05.042, 2696314, 18662548.
48. Wolf MY, Wolf YI, Koonin EV. Comparable contributions of structural functional constraints and expression level to the rate of protein sequence evolution. Biol Direct 2008, 3:40. 10.1186/1745-6150-3-40, 2572155, 18840284.
49. Wolf Y, Gopich IV, Lipman DJ, Koonin EV. Relative contributions of intrinsic structural-function constraints and translation rate to the evolution of protein-coding genes. Genome Biol Evol 2010, 2:190-199. 10.1093/gbe/evq010, 2940324, 20624725.
50. Zeng Y, Gu X. Genome factor and gene pleiotropy hypotheses in protein evolution. Biol Direct 2010, 5:37. 10.1186/1745-6150-5-37, 2889903, 20497565.
51. Mondal UK, Sur S, Bothra AK, Sen A. Comparative analysis of codon usage patterns and identification of predicted highly expressed genes in five Salmonella genomes. Indian J Med Microbiol 2008, 26:313-321. 10.4103/0255-0857.43558, 18974482.
52. Das S, Ghosh S, Pan A, Dutta C. Compositional variation in bacterial genes and proteins with potential expression level. FEBS Lett 2005, 579:5205-5210. 10.1016/j.febslet.2005.08.042, 16165133.
53. Carbone A, Zinovyev A, Képès F. Codon adaptation index as a measure of dominating codon bias. Bioinformatics 2003, 19:2005-2015. 10.1093/bioinformatics/btg272, 14594704.
54. Rocha EP, Danchin A. An analysis of determinants of amino acids substitution rates in bacterial proteins. Mol Biol Evol 2004, 21(1):108-116.
55. Krylov DM, Wolf YI, Rogozin IB, Koonin EV. Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution. Genome Res 2003, 13(10):2229-2235. 10.1101/gr.1589103, 403683, 14525925.
56. Drummond AD, Bloom JD, Adami C, Wilke CO, Arnold FH. Why highly expressed proteins evolve slowly?. Proc Natl Acad Sci USA 2005, 102(40):14338-14343. 10.1073/pnas.0504070102, 1242296, 16176987.
57. Marsella L, Sirocco F, Trovato A, Seno F, Tosatto SCE. REPETITA: detection and discrimination of the periodicity of protein solenoid repeats by discrete Fourier transform. Bioinformatics 2009, 25:i289-i295. 10.1093/bioinformatics/btp232, 2687986, 19478001.
58. Smole Z, Nikolic N, Supek F, Smuc T, Sbalzarini IF, Krisko A. Proteome sequence features carry signatures of the environmental niche of prokaryotes. BMC Evol Biol 2011, 11:26. 10.1186/1471-2148-11-26, 3045906, 21269423.
59. Kiraga J, Mackiewicz P, Mackiewicz D, Kowalczuk M, Biecek P, Polak N, Smolarczyk K, Dudek MR, Cebrat S. The relationships between the isoelectric point and: length of proteins, taxonomy and ecology of organisms. BMC Genomics 2007, 8:163. 10.1186/1471-2164-8-163, 1905920, 17565672.
60. Williams DL, Slayden RA, Amin A, Martinez AN, Pittman TL, Mira A, Mitra A, Nagaraja V, Morrison NE, Moraes M, Gillis TP. Implications of high level pseudogene transcription in Mycobacterium leprae. BMC Genomics 2009, 10:397. 10.1186/1471-2164-10-397, 2753549, 19706172.
61. Gómez-Valero L, Rocha EPC, Latorre A, Silva FJ. Reconstructing the ancestor of Mycobacterium leprae: The dynamics of gene loss and genome reduction. Genome Res 2007, 17(8):1178-1185. 10.1101/gr.6360207, 1933519, 17623808.
62. Ran L, Larsson J, Vigil-Stenman T, Nylander JAA, Ininbergs K, Zheng WW, Lapidus A, Lowry S, Haselkorn R, Bergman B. Genome erosion in a nitrogen-fixing vertically transmitted endosymbiotic multicellular cyanobacterium. PLoS One 2010, 5(7):e11486. 10.1371/journal.pone.0011486, 2900214, 20628610.
63. Willenbrock H, Friis C, Friis AS, Ussery DW. An environmental signature for 323 microbial genomes based on codon adaptation indices. Genome Biol 2006, 7(12):R114. 10.1186/gb-2006-7-12-r114, 1794427, 17156429.