Immunoglobulin-like domains on bacteriophage: weapons of modest damage?

Current Opinion in Microbiology

Volumn 10, Issue 4, 2007, Pages 382-387

  Fraser, James S ^a   Maxwell, Karen L ^b   Davidson, Alan R ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF TORONTO   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

CARBOHYDRATE; IMMUNOGLOBULIN; MEMBRANE PROTEIN; POLYSACCHARIDE;

ADSORPTION; BACTERIOPHAGE; CARBOXY TERMINAL SEQUENCE; CELL SURFACE; HOST CELL; MORPHOGENESIS; NONHUMAN; PROTEIN BINDING; PROTEIN STRUCTURE; REVIEW; RIBOSOMAL FRAMESHIFTING;

BACTERIA; CAUDOVIRALES; PROTEIN STRUCTURE, TERTIARY; VIRAL PROTEINS;

EID: 34548671924     PISSN: 13695274     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mib.2007.05.018     Document Type: Review

References (42)

1. Pedulla M.L., Ford M.E., Houtz J.M., Karthikeyan T., Wadsworth C., Lewis J.A., Jacobs-Sera D., Falbo J., Gross J., Pannunzio N.R., et al. Origins of highly mosaic mycobacteriophage genomes. Cell 113 (2003) 171-182
2. Hendrix R.W. Bacteriophage genomics. Curr Opin Microbiol 6 (2003) 506-511
3. Fraser J.S., Yu Z., Maxwell K.L., and Davidson A.R. Ig-like domains on bacteriophages: a tale of promiscuity and deceit. J Mol Biol 359 (2006) 496-507. A comprehensive bioinformatics-based search of all sequenced phage genomes reveals rampant horizontal exchange of Ig-like domains. The functional role of the discovered domains and associated frameshifts is not currently known.
4. McMahon S.A., Miller J.L., Lawton J.A., Kerkow D.E., Hodes A., Marti-Renom M.A., Doulatov S., Narayanan E., Sali A., Miller J.F., et al. The C-type lectin fold as an evolutionary solution for massive sequence variation. Nat Struct Mol Biol 12 (2005) 886-892
5. Doulatov S., Hodes A., Dai L., Mandhana N., Liu M., Deora R., Simons R.W., Zimmerly S., and Miller J.F. Tropism switching in Bordetella bacteriophage defines a family of diversity-generating retroelements. Nature 431 (2004) 476-481
6. Bateman A., Eddy S.R., and Mesyanzhinov V.V. A member of the immunoglobulin superfamily in bacteriophage T4. Virus Genes 14 (1997) 163-165
7. Fokine A., Chipman P.R., Leiman P.G., Mesyanzhinov V.V., Rao V.B., and Rossmann M.G. Molecular architecture of the prolate head of bacteriophage T4. Proc Natl Acad Sci USA 101 (2004) 6003-6008. The authors describe the structure of the T4 head by cryo-electron microscopy. They locate the HOC protein on the surface and rule out a structural role for its Ig-like domains.
8. Morais M.C., Choi K.H., Koti J.S., Chipman P.R., Anderson D.L., and Rossmann M.G. Conservation of the capsid structure in tailed dsDNA bacteriophages: the pseudoatomic structure of phi29. Mol Cell 18 (2005) 149-159
9. Katsura I. Structure and function of the major tail protein of bacteriophage lambda. Mutants having small major tail protein molecules in their virion. J Mol Biol 146 (1981) 493-512
10. Maruyama I.N., Maruyama H.I., and Brenner S. Lambda foo: a lambda phage vector for the expression of foreign proteins. Proc Natl Acad Sci USA 91 (1994) 8273-8277
11. Dunn I.S. Assembly of functional bacteriophage lambda virions incorporating C-terminal peptide or protein fusions with the major tail protein. J Mol Biol 248 (1995) 497-506
12. Kuwabara I., Maruyama H., Mikawa Y.G., Zuberi R.I., Liu F.T., and Maruyama I.N. Efficient epitope mapping by bacteriophage lambda surface display. Nat Biotechnol 15 (1997) 74-78
13. Effantin G., Boulanger P., Neumann E., Letellier L., and Conway J.F. Bacteriophage T5 structure reveals similarities with HK97 and T4 suggesting evolutionary relationships. J Mol Biol 361 (2006) 993-1002. This electron microscopy study shows that phage T5 possesses a protein with similar properties to the HOC protein of phage T4. This T5 protein, pb10, possesses an Ig-like domain.
14. Letarov A., Manival X., Desplats C., and Krisch H.M. gpwac of the T4-type bacteriophages: structure, function, and evolution of a segmented coiled-coil protein that controls viral infectivity. J Bacteriol 187 (2005) 1055-1066. It is shown that fibritin proteins from various T4-like phages possess different C-terminal domains. Some have Ig-like domains.
15. Sullivan M.B., Coleman M.L., Weigele P., Rohwer F., and Chisholm S.W. Three Prochlorococcus cyanophage genomes: signature features and ecological interpretations. PLoS Biol 3 (2005) e144
16. Little E., Bork P., and Doolittle R.F. Tracing the spread of fibronectin type III domains in bacterial glycohydrolases. J Mol Evol 39 (1994) 631-643
17. Baranov P.V., Fayet O., Hendrix R.W., and Atkins J.F. Recoding in bacteriophages and bacterial IS elements. Trends Genet 22 (2006) 174-181
18. Xu J., Hendrix R.W., and Duda R.L. Conserved translational frameshift in dsDNA bacteriophage tail assembly genes. Mol Cell 16 (2004) 11-21
19. Pajunen M., Kiljunen S., and Skurnik M. Bacteriophage phiYeO3-12, specific for Yersinia enterocolitica serotype O:3, is related to coliphages T3 and T7. J Bacteriol 182 (2000) 5114-5120
20. Rodriguez I., Garcia P., and Suarez J.E. A second case of -1 ribosomal frameshifting affecting a major virion protein of the Lactobacillus bacteriophage A2. J Bacteriol 187 (2005) 8201-8204
21. Garcia P., Rodriguez I., and Suarez J.E. A -1 ribosomal frameshift in the transcript that encodes the major head protein of bacteriophage A2 mediates biosynthesis of a second essential component of the capsid. J Bacteriol 186 (2004) 1714-1719
22. Condreay J.P., Wright S.E., and Molineux I.J. Nucleotide sequence and complementation studies of the gene 10 region of bacteriophage T3. J Mol Biol 207 (1989) 555-561
23. Luo Y., Frey E.A., Pfuetzner R.A., Creagh A.L., Knoechel D.G., Haynes C.A., Finlay B.B., and Strynadka N.C. Crystal structure of enteropathogenic Escherichia coli intimin-receptor complex. Nature 405 (2000) 1073-1077
24. Halaby D.M., and Mornon J.P. The immunoglobulin superfamily: an insight on its tissular, species, and functional diversity. J Mol Evol 46 (1998) 389-400
25. Geller B.L., Ngo H.T., Mooney D.T., Su P., and Dunn N. Lactococcal 936-species phage attachment to surface of Lactococcus lactis. J Dairy Sci 88 (2005) 900-907
26. Dupont K., Vogensen F.K., Neve H., Bresciani J., and Josephsen J. Identification of the receptor-binding protein in 936-species lactococcal bacteriophages. Appl Environ Microbiol 70 (2004) 5818-5824
27. Spinelli S., Campanacci V., Blangy S., Moineau S., Tegoni M., and Cambillau C. Modular structure of the receptor binding proteins of Lactococcus lactis phages. The RBP structure of the temperate phage TP901-1. J Biol Chem 281 (2006) 14256-14262
28. Tremblay D.M., Tegoni M., Spinelli S., Campanacci V., Blangy S., Huyghe C., Desmyter A., Labrie S., Moineau S., and Cambillau C. Receptor-binding protein of Lactococcus lactis phages: identification and characterization of the saccharide receptor-binding site. J Bacteriol 188 (2006) 2400-2410
29. Fortier L.C., Bransi A., and Moineau S. Genome sequence and global gene expression of Q54, a new phage species linking the 936 and c2 phage species of Lactococcus lactis. J Bacteriol 188 (2006) 6101-6114. The authors analyze the newly sequenced genome of phage Q54 and discover that the major tail protein is fused, via a -1 programmed ribosomal frameshift, to the receptor-binding protein. This demonstrates a functional role for frameshifted fusion domains attached to structural proteins.
30. Weitz J.S., Hartman H., and Levin S.A. Coevolutionary arms races between bacteria and bacteriophage. Proc Natl Acad Sci USA 102 (2005) 9535-9540
31. Boulanger P., and Letellier L. Characterization of ion channels involved in the penetration of phage T4 DNA into Escherichia coli cells. J Biol Chem 263 (1988) 9767-9775
32. Nakayama K., Takashima K., Ishihara H., Shinomiya T., Kageyama M., Kanaya S., Ohnishi M., Murata T., Mori H., and Hayashi T. The R-type pyocin of Pseudomonas aeruginosa is related to P2 phage, and the F-type is related to lambda phage. Mol Microbiol 38 (2000) 213-231
33. Finn R.D., Mistry J., Schuster-Bockler B., Griffiths-Jones S., Hollich V., Lassmann T., Moxon S., Marshall M., Khanna A., Durbin R., et al. Pfam: clans, web tools and services. Nucleic Acids Res 34 (2006) D247-D251
34. Roessner C.A., and Ihler G.M. Proteinase sensitivity of bacteriophage lambda tail proteins gpJ and pH in complexes with the lambda receptor. J Bacteriol 157 (1984) 165-170
35. Piuri M., and Hatfull G.F. A peptidoglycan hydrolase motif within the mycobacteriophage TM4 tape measure protein promotes efficient infection of stationary phase cells. Mol Microbiol (2006). They demonstrate that the TMP of a mycobacteriophage has novel carbohydrate binding and degradation functions. Experiments point to a role for this motif in the infection of stationary phase hosts. This suggests that bacteriophage adapt different strategies of infection depending on the host growth phase.
36. Lai X., Weng J., Zhang X., Shi W., Zhao J., Wang H., and Wang H. MSTF: a domain involved in bacterial metallopeptidases and surface proteins, mycobacteriophage tape-measure proteins and fungal proteins. FEMS Microbiol Lett 258 (2006) 78-82
37. Nakamura Y., Itoh T., Matsuda H., and Gojobori T. Biased biological functions of horizontally transferred genes in prokaryotic genomes. Nat Genet 36 (2004) 760-766
38. Eyer L., Pantucek R., Zdrahal Z., Konecna H., Kasparek P., Ruzickova V., Hernychova L., Preisler J., and Doskar J. Structural protein analysis of the polyvalent staphylococcal bacteriophage 812. Proteomics 7 (2007) 64-72
39. Anantharaman V., and Aravind L. Evolutionary history, structural features and biochemical diversity of the NlpC/P60 superfamily of enzymes. Genome Biol 4 (2003) R11
40. Rigden D.J., Jedrzejas M.J., and Galperin M.Y. Amidase domains from bacterial and phage autolysins define a family of gamma-d,l-glutamate-specific amidohydrolases. Trends Biochem Sci 28 (2003) 230-234
41. Bateman A., and Rawlings N.D. The CHAP domain: a large family of amidases including GSP amidase and peptidoglycan hydrolases. Trends Biochem Sci 28 (2003) 234-237
42. Blackburn N.T., and Clarke A.J. Identification of four families of peptidoglycan lytic transglycosylases. J Mol Evol 52 (2001) 78-84