Comparative Analysis of Individual Domains of Hoc Proteins in Subfamily Teequatrovirinae Bacteriophages

Mathematical Biology & Bioinformatics. 2012;7(2):611-631.

doi: 10.17537/2012.7.611.

1. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25:3389-3402. doi: 10.1093/nar/25.17.3389
2. Basic Local Alignment Search Tool. http://blast.ncbi.nlm.nih.gov/Blast.cgi (accessed 12 November 2012).
3. Balter M. Virology. Evolution on life’s fringes. Science. 2000;289:1866-1867. doi: 10.1126/science.289.5486.1866
4. Bateman A, Eddy SR, Chothia C. Members of the immunoglobulin superfamily in bacteria. Protein Sci. 1996;5(9):1939-1941. doi: 10.1002/pro.5560050923
5. Bateman A, Eddy SR, Mesyanzhinov VV. A member of the immunoglobulin superfamily in bacteriophage T4. Virus Genes. 1997;14:163-165. doi: 10.1023/A:1007977503658
6. Bork P, Holm L, Sander C. The immunoglobulin fold. Structural classification, sequence patterns and common core. J. Mol. Biol. 1994;242:309-320.
7. Dabrowska K, Zembala M, Boratynski J, Switala-Jelen K, Wietrzyk J, Opolski A, Szczaurska K, Kujawa M, Godlewska J, Gorski A. Hoc protein regulates the biological effects of T4 phage in mammals. Arch. Microbiol. 2007;187(6):489-498.
8. De Bono B, Chothia C. Exegesis: a procedure to improve gene predictions and its use to find immunoglobulin superfamily proteins in the human and mouse genomes. Nucleic Acids Res. 2003;31(21):6096-6103. doi: 10.1093/nar/gkg828
9. Fokine A, Islam MZ, Zhang Z, Bowman VD, Rao VB, Rossmann MG. Structure of the three N-terminal immunoglobulin domains of the highly immunogenic outer capsid protein from a T4-like bacteriophage. J. Virol. 2011;85(16):8141-8148. doi: 10.1128/JVI.00847-11
10. Fokine A, Leiman PG, Shneider MM, Ahvazi B, Boeshans KM, Steven AC, Black LW, Mesyanzhinov VV, Rossmann MG. Structural and functional similarities between the capsid proteins of bacteriophages T4 and HK97 point to a common ancestry. Proc Nat. Acad. Sci. USA. 2005;102:7163-7168. doi: 10.1073/pnas.0502164102
11. Fong S, Hamill SJ, Proctor M, Freund SM, Benian GM, Chothia C, Bycroft M, Clarke J. Structure and stability of an immunoglobulin superfamily domain from twitchin, a muscle protein of the nematode Caenorhabditis elegans. J. Mol. Biol. 1996;264(3):624-639.
12. Halaby DM, Poupon A, Mornon J. The immunoglobulin fold family: sequence analysis and 3D structure comparisons. Protein Eng. 1999;12:563-571. doi: 10.1093/protein/12.7.563
13. Jeanmougin F, Thompson JD, Gouy M, Higgins DG, Gibson TJ. Multiple sequence alignment with Clustal X. Trends Biochem. Sci. 1998;23:403-405.
14. Jing H, Takagi J, Liu JH, Lindgren S, Zhang RG, Joachimiak A, Wang JH, Springer TA. Archaeal surface layer proteins contain beta propeller, PKD, and beta helix domains and are related to metazoan cell surface proteins. Structure. 2002;10:1453-1464. doi: 10.1016/S0969-2126(02)00840-7
15. ICTV Virus Taxonomy: 2011 Release (current). http://ictvonline.org/virusTaxonomy.asp?version=2011 (accessed 12 November 2012).
16. Ishii T, Yamaguchi Y, Yanagida M. Binding of the structural protein Soc to the head shell of bacteriophage T4. J. Mol. Biol. 1978;120:533-544.
17. Ishii T, Yanagida M. Molecular organization of the shell of the T-even bacteriophage head. J. Mol. Biol. 1975;97:655-660.
18. Ishii T, Yanagida M. The two dispensable structural proteins (Soc and Hoc) of the T4 phage capsid; their purification and properties, isolation and characterization of the defective mutants, and their binding with the defective heads in vitro. J. Mol. Biol. 1977;109:487-514.
19. Kadyrov FA, Shlyapnikov MG, Kryukov VM. A phage T4 site-specific endonuclease, SegE, is responsible for a non-reciprocal genetic exchange between T-even-related phages. FEBS Lett. 1997;415(1):75-80. doi: 10.1016/S0014-5793(97)01098-3
20. Lavigne R, Darius P, Summer EJ, Seto D, Mahadevan P, Nilsson AS, Ackermann HW, Kropinski AM. Classification of Myoviridae bacteriophages using protein sequence similarity. BMC Microbiol. 2009;9:Article No. 224. doi: 10.1186/1471-2180-9-224
21. Lawrence JG, Hatfull GF, Hendrix RW. Imbroglios of viral taxonomy: genetic exchange and failings of phenetic approaches. J. Bacteriol. 2002;184:4891-4905. doi: 10.1128/JB.184.17.4891-4905.2002
22. Rohwer F, Edwards R. The phage proteomic tree: a genome-based taxonomy for phage. J. Bacteriol. 2002;184(16):4529-4535. doi: 10.1128/JB.184.16.4529-4535.2002
23. Ross PD, Black LW, Bisher ME, Steven AC. Assembly-dependent conformational changes in a viral capsid protein. Calorimetric comparison of successive conformational states of the gp23 surface lattice of bacteriophage T4. J. Mol. Biol. 1985;183:353-364.
24. Sathaliyawala T, Islam MZ, Li Q, Fokine A, Rossmann MG, Rao VB. Functional analysis of the highly antigenic outer capsid protein, Hoc, a virus decoration protein from T4-like bacteriophages. Mol. Microbiol. 2010;77(2):444-455.
25. Susskind MM, Botstein D. Molecular genetics of bacteriophage. Microbiol. Rev. 1978;42:385-413.
26. Tamura K, Dudley J, Nei M, Kumar S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol. Biol. Evol. 2007;24:1596-1599.
27. Teichmann SA, Chothia C. Immunoglobulin superfamily proteins in Caenorhabditis elegans. J. Mol. Biol. 2000;296(5):1367-1383.
28. Vogel C, Teichmann SA, Chothia C. The immunoglobulin superfamily in Drosophila melanogaster and Caenorhabditis elegans and the evolution of complexity. Development. 2003;130(25):6317-6328. doi: 10.1242/dev.00848
29. Yamaguchi Y, Yanagida M. Head shell protein hoc alters the surface charge of bacteriophage T4. Composite slab gel electrophoresis of phage T4 and related particles. J. Mol. Biol. 1980;141:175-193.