Insight into the Evolution of the Histidine Triad Protein (HTP) Family in Streptococcus

PLoS ONE

Volumn 8, Issue 3, 2013, Pages

  Shao, Zhu Qing ^a   Zhang, Yan Mei ^a   Pan, Xiu Zhen ^b   Wang, Bin ^a   Chen, Jian Qun ^a  

^a NANJING UNIVERSITY   (China)

^b Research Institute for Medicine of Nanjing Command   (China)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; HISTIDINE TRIAD PROTEIN; LEUCINE; NUCLEOTIDE; UNCLASSIFIED DRUG;

ARTICLE; BACTERIAL GENE; BACTERIAL GENOME; CARBOXY TERMINAL SEQUENCE; CONTROLLED STUDY; GENE DOSAGE; GENE LOSS; GENUS; HOUSEKEEPING GENE; HTP GENE; MOLECULAR EVOLUTION; MOLECULAR RECOGNITION; NONHUMAN; NUCLEIC ACID BASE SUBSTITUTION; PHYLOGENY; PROTEIN DOMAIN; PROTEIN FAMILY; PYOGENIC BACTERIUM; SEQUENCE HOMOLOGY; SPECIES; STREPTOCOCCUS BOVIS; STREPTOCOCCUS MUTANS; STREPTOCOCCUS PNEUMONIAE; STREPTOCOCCUS SALIVARIUS; STREPTOCOCCUS SUIS; SUBSPECIES;

CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; EVOLUTION, MOLECULAR; GENE DOSAGE; GENETIC VARIATION; HYDROLASES; MULTIGENE FAMILY; PHYLOGENY; PROTEIN STRUCTURE, TERTIARY; SPECIES SPECIFICITY; STREPTOCOCCUS;

EID: 84875202216     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0060116     Document Type: Article

References (58)

1. Kawamura Y, Hou XG, Sultana F, Miura H, Ezaki T, (1995) Determination of 16S rRNA sequences of Streptococcus mitis and Streptococcus gordonii and phylogenetic relationships among members of the genus Streptococcus. Int J Syst Bacteriol 45: 406-408.
2. Jarva H, Jokiranta TS, Wurzner R, Meri S, (2003) Complement resistance mechanisms of streptococci. Mol Immunol 40: 95-107.
3. Soriani M, Telford JL, (2010) Relevance of pili in pathogenic streptococci pathogenesis and vaccine development. Future Microbiol 5: 735-747.
4. Anisimova M, Bielawski J, Dunn K, Yang Z, (2007) Phylogenomic analysis of natural selection pressure in Streptococcus genomes. BMC Evol Biol 7: 154.
5. Bessen DE, (2009) Population biology of the human restricted pathogen, Streptococcus pyogenes. Infect Genet Evol 9: 581-593.
6. Lefebure T, Stanhope MJ, (2007) Evolution of the core and pan-genome of Streptococcus: positive selection, recombination, and genome composition. Genome Biol 8: R71.
7. Marri PR, Hao W, Golding GB, (2006) Gene gain and gene loss in streptococcus: is it driven by habitat? Mol Biol Evol 23: 2379-2391.
8. Brochet M, Rusniok C, Couve E, Dramsi S, Poyart C, et al. (2008) Shaping a bacterial genome by large chromosomal replacements, the evolutionary history of Streptococcus agalactiae. Proc Natl Acad Sci U S A 105: 15961-15966.
9. Gogarten JP, Townsend JP, (2005) Horizontal gene transfer, genome innovation and evolution. Nat Rev Microbiol 3: 679-687.
10. Boggs JM, South AH, Hughes AL, (2012) Phylogenetic analysis supports horizontal gene transfer of L-amino acid oxidase gene in Streptococcus oligofermentans. Infect Genet Evol 12: 1005-1009.
11. Lindahl G, Stalhammar-Carlemalm M, Areschoug T, (2005) Surface proteins of Streptococcus agalactiae and related proteins in other bacterial pathogens. Clin Microbiol Rev 18: 102-127.
12. Richards VP, Lang P, Bitar PD, Lefebure T, Schukken YH, et al. (2011) Comparative genomics and the role of lateral gene transfer in the evolution of bovine adapted Streptococcus agalactiae. Infect Genet Evol 11: 1263-1275.
13. Nobbs AH, Lamont RJ, Jenkinson HF (2009) Streptococcus adherence and colonization. Microbiol Mol Biol Rev 73: 407-450, Table of Contents.
14. Kadioglu A, Weiser JN, Paton JC, Andrew PW, (2008) The role of Streptococcus pneumoniae virulence factors in host respiratory colonization and disease. Nat Rev Microbiol 6: 288-301.
15. Mitchell TJ, (2003) The pathogenesis of streptococcal infections: from tooth decay to meningitis. Nat Rev Microbiol 1: 219-230.
16. Ogunniyi AD, Grabowicz M, Mahdi LK, Cook J, Gordon DL, et al. (2009) Pneumococcal histidine triad proteins are regulated by the Zn2+-dependent repressor AdcR and inhibit complement deposition through the recruitment of complement factor H. FASEB J. 23: 731-738.
17. Maruvada R, Prasadarao NV, Rubens CE, (2009) Acquisition of factor H by a novel surface protein on group B Streptococcus promotes complement degradation. FASEB J 23: 3967-3977.
18. Kunitomo E, Terao Y, Okamoto S, Rikimaru T, Hamada S, et al. (2008) Molecular and biological characterization of histidine triad protein in group A streptococci. Microbes Infect 10: 414-423.
19. Adamou JE, Heinrichs JH, Erwin AL, Walsh W, Gayle T, et al. (2001) Identification and characterization of a novel family of pneumococcal proteins that are protective against sepsis. Infect Immun 69: 949-958.
20. Zhang Y, Masi AW, Barniak V, Mountzouros K, Hostetter MK, et al. (2001) Recombinant PhpA protein, a unique histidine motif-containing protein from Streptococcus pneumoniae, protects mice against intranasal pneumococcal challenge. Infect Immun 69: 3827-3836.
21. Hamel J, Charland N, Pineau I, Ouellet C, Rioux S, et al. (2004) Prevention of pneumococcal disease in mice immunized with conserved surface-accessible proteins. Infect Immun 72: 2659-2670.
22. Reid SD, Montgomery AG, Voyich JM, DeLeo FR, Lei B, et al. (2003) Characterization of an extracellular virulence factor made by group A Streptococcus with homology to the Listeria monocytogenes internalin family of proteins. Infect Immun 71: 7043-7052.
23. Waldemarsson J, Areschoug T, Lindahl G, Johnsson E, (2006) The streptococcal Blr and Slr proteins define a family of surface proteins with leucine-rich repeats: camouflaging by other surface structures. J Bacteriol 188: 378-388.
24. Shao Z, Pan X, Li X, Liu W, Han M, et al. (2011) HtpS, a novel immunogenic cell surface-exposed protein of Streptococcus suis, confers protection in mice. FEMS Microbiol Lett 314: 174-182.
25. Aranda J, Garrido ME, Fittipaldi N, Cortes P, Llagostera M, et al. (2009) Protective capacities of cell surface-associated proteins of Streptococcus suis mutants deficient in divalent cation-uptake regulators. Microbiology 155: 1580-1587.
26. Plumptre CD, Ogunniyi AD, Paton JC, (2012) Polyhistidine triad proteins of pathogenic streptococci. Trends Microbiol 20: 485-493.
27. Riboldi-Tunnicliffe A, Bent CJ, Isaacs NW, Mitchell TJ, (2004) Expression, purification and X-ray characterization of residues 18-230 from the pneumococcal histidine triad protein A (PhtA) from Streptococcus pneumoniae. Acta Crystallogr D Biol Crystallogr 60: 926-928.
28. Riboldi-Tunnicliffe A, Isaacs NW, Mitchell TJ, (2005) 1.2 Angstroms crystal structure of the S. pneumoniae PhtA histidine triad domain a novel zinc binding fold. FEBS Lett 579: 5353-5360.
29. Loisel E, Chimalapati S, Bougault C, Imberty A, Gallet B, et al. (2011) Biochemical characterization of the histidine triad protein PhtD as a cell surface zinc-binding protein of pneumococcus. Biochemistry 50: 3551-3558.
30. Panina EM, Mironov AA, Gelfand MS, (2003) Comparative genomics of bacterial zinc regulons: enhanced ion transport, pathogenesis, and rearrangement of ribosomal proteins. Proc Natl Acad Sci U S A 100: 9912-9917.
31. Bober M, Morgelin M, Olin AI, von Pawel-Rammingen U, Collin M, (2011) The membrane bound LRR lipoprotein Slr, and the cell wall-anchored M1 protein from Streptococcus pyogenes both interact with type I collagen. PLoS One 6: e20345.
32. Simell B, Ahokas P, Lahdenkari M, Poolman J, Henckaerts I, et al. (2009) Pneumococcal carriage and acute otitis media induce serum antibodies to pneumococcal surface proteins CbpA and PhtD in children. Vaccine 27: 4615-4621.
33. Holmlund E, Quiambao B, Ollgren J, Jaakkola T, Neyt C, et al. (2009) Antibodies to pneumococcal proteins PhtD, CbpA, and LytC in Filipino pregnant women and their infants in relation to pneumococcal carriage. Clin Vaccine Immunol 16: 916-923.
34. Lebon A, Verkaik NJ, Labout JA, de Vogel CP, Hooijkaas H, et al. (2011) Natural antibodies against several pneumococcal virulence proteins in children during the pre-pneumococcal-vaccine era: the generation R study. Infect Immun 79: 1680-1687.
35. Denoel P, Philipp MT, Doyle L, Martin D, Carletti G, et al. (2011) A protein-based pneumococcal vaccine protects rhesus macaques from pneumonia after experimental infection with Streptococcus pneumoniae. Vaccine 29: 5495-5501.
36. Gillespie JJ, Wattam AR, Cammer SA, Gabbard JL, Shukla MP, et al. (2011) PATRIC: the comprehensive bacterial bioinformatics resource with a focus on human pathogenic species. Infect Immun 79: 4286-4298.
37. Meyers BC, Kozik A, Griego A, Kuang H, Michelmore RW, (2003) Genome-wide analysis of NBS-LRR-encoding genes in Arabidopsis. Plant Cell 15: 809-834.
38. Rioux S, Neyt C, Di Paolo E, Turpin L, Charland N, et al. (2011) Transcriptional regulation, occurrence and putative role of the Pht family of Streptococcus pneumoniae. Microbiology 157: 336-348.
39. Librado P, Rozas J, (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25: 1451-1452.
40. Aranda J, Teixido L, Fittipaldi N, Cortes P, Llagostera M, et al. (2012) Inactivation of the gene encoding zinc-binding lipoprotein 103 impairs the infectivity of Streptococcus suis. Can J Vet Res 76: 72-76.
41. Shao ZQ, Zhang YM, Feng XY, Wang B, Chen JQ, (2012) Synonymous codon ordering: a subtle but prevalent strategy of bacteria to improve translational efficiency. PLoS One 7: e33547.
42. Wang B, Shao ZQ, Xu Y, Liu J, Liu Y, et al. (2011) Optimal codon identities in bacteria: implications from the conflicting results of two different methods. PLoS One 6: e22714.
43. Croucher NJ, Harris SR, Fraser C, Quail MA, Burton J, et al. (2011) Rapid pneumococcal evolution in response to clinical interventions. Science 331: 430-434.
44. Kakizawa S, Oshima K, Jung HY, Suzuki S, Nishigawa H, et al. (2006) Positive selection acting on a surface membrane protein of the plant-pathogenic phytoplasmas. J Bacteriol 188: 3424-3428.
45. Petersen L, Bollback JP, Dimmic M, Hubisz M, Nielsen R, (2007) Genes under positive selection in Escherichia coli. Genome Res 17: 1336-1343.
46. Fabre A, Danet JL, Foissac X, (2011) The stolbur phytoplasma antigenic membrane protein gene stamp is submitted to diversifying positive selection. Gene 472: 37-41.
47. Xu Z, Chen H, Zhou R, (2011) Genome-wide evidence for positive selection and recombination in Actinobacillus pleuropneumoniae. BMC Evol Biol 11: 203.
48. Andrews TD, Gojobori T, (2004) Strong positive selection and recombination drive the antigenic variation of the PilE protein of the human pathogen Neisseria meningitidis. Genetics 166: 25-32.
49. Liu C, Chen Z, Tan C, Liu W, Xu Z, et al. (2012) Immunogenic characterization of outer membrane porins OmpC and OmpF of porcine extraintestinal pathogenic Escherichia coli. FEMS Microbiol Lett 337: 104-111.
50. Gangwer KA, Shaffer CL, Suerbaum S, Lacy DB, Cover TL, et al. (2010) Molecular evolution of the Helicobacter pylori vacuolating toxin gene vacA. J Bacteriol 192: 6126-6135.
51. Nogueira T, Touchon M, Rocha EP, (2012) Rapid evolution of the sequences and gene repertoires of secreted proteins in bacteria. PLoS One 7: e49403.
52. Lechner M, Findeiss S, Steiner L, Marz M, Stadler PF, et al. (2011) Proteinortho: detection of (co-)orthologs in large-scale analysis. BMC Bioinformatics 12: 124.
53. Criscuolo A, (2011) morePhyML: improving the phylogenetic tree space exploration with PhyML 3. Mol Phylogenet Evol 61: 944-948.
54. Thompson JD, Gibson TJ, Higgins DG (2002) Multiple sequence alignment using ClustalW and ClustalX. Curr Protoc Bioinformatics Chapter 2: Unit 2 3.
55. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, et al. (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28: 2731-2739.
56. Delorme C, Bartholini C, Bolotine A, Ehrlich SD, Renault P, (2010) Emergence of a cell wall protease in the Streptococcus thermophilus population. Appl Environ Microbiol 76: 451-460.
57. Delorme C, Poyart C, Ehrlich SD, Renault P, (2007) Extent of horizontal gene transfer in evolution of Streptococci of the salivarius group. J Bacteriol 189: 1330-1341.
58. Martin DP, Lemey P, Lott M, Moulton V, Posada D, et al. (2010) RDP3: a flexible and fast computer program for analyzing recombination. Bioinformatics 26: 2462-2463.