The hepatitis E virus polyproline region is involved in viral adaptation

PLoS ONE

Volumn 7, Issue 4, 2012, Pages

  Purdy, Michael A ^a   Lara, James ^a   Khudyakov, Yury E ^a  

^a CENTERS FOR DISEASE CONTROL AND PREVENTION   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; PEPTIDE; POLYPROLINE; VIRUS PROTEIN;

ADAPTATION; ARTICLE; CODON; CONTROLLED STUDY; CONVERGENT EVOLUTION; GENE CONTROL; GENE REPLICATION; GENE SEQUENCE; GENOTYPE; HEPATITIS E VIRUS; HOMOPLASY; HOST RANGE; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PHYLOGENY; PROTEIN PROTEIN INTERACTION; PROTEIN SECONDARY STRUCTURE; PROTEIN TERTIARY STRUCTURE; RUBELLA VIRUS; SEQUENCE ANALYSIS; AMINO ACID SEQUENCE; CHEMICAL STRUCTURE; CHEMISTRY; GENETICS; HEPATITIS E; HUMAN; MOLECULAR GENETICS; PHYSIOLOGY; SEQUENCE ALIGNMENT; VIROLOGY;

ADAPTATION, PHYSIOLOGICAL; AMINO ACID SEQUENCE; GENOTYPE; HEPATITIS E; HEPATITIS E VIRUS; HUMANS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; OPEN READING FRAMES; PEPTIDES; PHYLOGENY; SEQUENCE ALIGNMENT; VIRAL PROTEINS;

EID: 84860113261     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0035974     Document Type: Article

References (66)

1. Emerson SU, Anderson D, Arankalle A, Meng XJ, Purdy MA, et al. (2004) Hepevirus. In: Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball LA, editors. Virus Taxonomy Eigth Report of the International Committee on Taxonomy of Viruses London Elsevier/Academic Press pp. 853-857.
2. Khuroo MS, (2011) Discovery of hepatitis E: The epidemic non-A, non-B hepatitis 30 years down the memory lane. Virus Res 161: 3-14.
3. Purcell R, Emerson SU, (2010) Hidden Danger: The Raw Facts about Hepatitis E Virus. J Infect Dis 202: 819-821.
4. Teshale EH, Hu DJ, Holmberg SD, (2010) The Two Faces of Hepatitis E Virus. Clin Infect Dis 51: 328-334.
5. Meng XJ, (2011) From barnyard to food table: The omnipresence of hepatitis E virus and risk for zoonotic infection and food safety. Virus Res 161: 23-30.
6. Purdy MA, Khudyakov YE, (2011) Molecular epidemiology of hepatitis E virus infection. Virus Res 161: 31-39.
7. Liu H, Fu Y, Jiang D, Li G, Xie J, et al. (2009) A novel mycovirus that is related to the human pathogen hepatitis E virus and rubi-like viruses. J Virol 83: 1981-1991.
8. Koonin EV, Dolja VV, (1993) Evolution and taxonomy of positive-strand RNA viruses: implications of comparative analysis of amino acid sequences. Crit Rev Biochem Mol Biol 28: 375-430.
9. Batts W, Yun S, Hedrick R, Winton J, (2011) A novel member of the family Hepeviridae from cutthroat trout (Oncorhynchus clarkii). Virus Res 158: 116-123.
10. Koonin EV, Gorbalenya AE, Purdy MA, Rozanov MN, Reyes GR, et al. (1992) Computer-assisted assignment of functional domains in the nonstructural polyprotein of hepatitis E virus: Delineation of an additional group of positive-strand RNA plant and animal viruses. Proc Natl Acad Sci USA 89: 8259-8263.
11. Tsarev SA, Emerson SU, Reyes GR, Tsareva TS, Legters LJ, et al. (1992) Characterization of a prototype strain of hepatitis E virus. Proc Natl Acad Sci USA 89: 559-563.
12. Pudupakam RS, Huang YW, Opriessnig T, Halbur PG, Pierson FW, et al. (2009) Deletions of the Hypervariable Region (HVR) in Open Reading Frame 1 of Hepatitis E Virus Do Not Abolish Virus Infectivity: Evidence for Attenuation of HVR Deletion Mutants In Vivo. J Virol 83: 384-395.
13. Finn RD, Mistry J, Schuster-Bockler B, Griffiths-Jones S, Hollich V, et al. (2006) Pfam: clans, web tools and services. Nuc Acids Res 34: D247-D251.
14. Han W, Li X, Fu X, (2011) The macro domain protein family: structure, functions, and their potential therapeutic implications. Mutat Res ahead of print.
15. Dosztányi Z, Chen J, Dunker K, Simon I, Tompa P, (2006) Disorder and Sequence Repeats in Hub Proteins and Their Implications for Network Evolution. J Proteome Res 5: 2985-2995.
16. Dunker AK, Oldfield CJ, Meng J, Romero P, Yang JY, et al. (2008) The unfoldomics decade: an update on intrinsically disordered proteins. BMC Genomics 9: S1.
17. Tsai CJ, Ma B, Sham YY, Kumar S, Nussinov R, (2001) Structured Disorder and Conformational Selection. Proteins 44: 418-427.
18. Tzeng W-P, Chen M-H, Derdeyn CA, Frey TK, (2001) Rubella Virus DI RNAs and Replicons: Requirement for Nonstructural Proteins Acting in Cis for Amplification by Helper. Virus Virologt 289: 63-73.
19. Pudupakam RS, Kenney SP, Cordoba L, Huang Y-W, Dryman BA, et al. (2011) Mutational Analysis of the Hypervariable Region of Hepatitis E Virus Reveals Its Involvement in the Efficiency of Viral RNA Replication. J Virol 85: 10031-10040.
20. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, et al. (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23: 2947-2948.
21. Edgar RC, (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nuc Acids Res 32: 1792-1797.
22. Hall TA, (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nuc Acids Symp Ser 41: 95-98.
23. Pond SLK, Frost SDW, Muse SV, (2005) HyPhy: hypothesis testing using phylogenies. Bioinformatics 21: 676-679.
24. Swofford DL, (2003) PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods) Sunderland, MA Sinauer Associates.
25. Ward JJ, Sodhi JS, McGuffin LJ, Buxton BF, Jones DT, (2004) Prediction and functional analysis of native disorder in proteins from the three kingdoms of life. J Mol Biol 337: 635-645.
26. Dosztányi Z, Csizmok V, Tompa P, Simon I, (2005) IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content. Bioinformatics 21: 3433-3434.
27. Dosztányi Z, Csizmok V, Tompa P, Simon I, (2005) The Pairwise Energy Content Estimated from Amino Acid Composition Discriminates between Folded and Intrinsically Unstructured Proteins. J Mol Biol 347: 827-839.
28. Ren S, Uversky VN, Chen Z, Dunker AK, Obradovic Z, (2008) Short Linear Motifs recognized by SH2, SH3 and Ser/Thr Kinase domains are conserved in disordered protein regions. BMC Genomics 9: S26.
29. Fuxreiter M, Tompa P, Simon I, (2007) Local structural disorder imparts plasticity on linear motifs. Bioinformatics 23: 950-956.
30. Gould CM, Diella F, Via A, Puntervoll P, Gemund C, et al. (2010) ELM: the status of the 2010 eukaryotic linear motif resource. Nucl Acids Res 38: D167-D180.
31. Takahashi M, Nishizawa T, Sato H, Sato Y, Jirintai D, et al. (2011) Analysis of the full-length genome of a hepatitis E virus isolate obtained from a wild boar in Japan that is classifiable into a novel genotype. J Gen Virol 92: 902-908.
32. Felsenstein J, (1989) PHYLIP- Phylogeny Inference Package (Version 3.2). Cladistics 5: 164-166.
33. Puigbò P, Garcia-Vallvé S, McInerney JO, (2007) TOPD/FMTS: a new software to compare phylogenetic trees. 23: 1556-1558.
34. Roy A, Kucukural A, Zhang Y, (2010) I-TASSER: a unified platform for automated protein structure and function prediction. Nat Protoc 5: 725-738.
35. Wu S, Skolnick J, Zhang Y, (2007) Ab initio modeling of small proteins by iterative TASSER simulations. BMC Biol 5: 17.
36. Laskowski RA, (2001) PDBsum: summaries and analyses of PDB structures. Nucleic Acids Res 29: 221-222.
37. Willard L, Ranjan A, Zhang H, Monzavi H, Boyko RF, et al. (2003) VADAR: a web server for quantitative evaluation of protein structure quality. Nucleic Acids Res 31: 3316-3319.
38. Vriend G, (1990) WHAT IF: a molecular modeling and drug design program. J Mol Graph 8: 52-56.
39. Jones DT, (1999) Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 292: 195-202.
40. Kabsch W, Sander C, (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22: 2577-2637.
41. Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA, (2001) Electrostatics of nanosystems: application to microtubules and the ribosome. Proc Natl Acad Sci U S A 98: 10037-10041.
42. DeLano WL, (2002) The PyMOL Molecular Graphics System User's Manual San Carlos DeLano Scientific, LLC.
43. Roy A, Xu D, Poisson J, Zhang Y, (2011) A protocol for computer-based protein structure and function prediction. J Vis Exp pp. e3259.
44. Roy A, Zhang Y, (2011) Recognizing protein-ligand binding sites by global structural alignment and local geometry refinement. Submitted.
45. Dyson HJ, Wright PE, (2005) Intrinsically unstructured proteins and their functions. Nature Reviews Molec Cell Biol 6: 197-208.
46. Dyson HJ, Wright PE, (2002) Coupling of folding and binding for unstructured proteins. Curr Opin Struct Biol 12: 54-60.
47. Uversky VN, (2002) Natively unfolded proteins: a point where biology waits for physics. Protein Sci 11: 739-756.
48. Vucetic S, Brown CJ, Dunker AK, Obradovic Z, (2003) Flavors of protein disorder. Proteins 52: 573-584.
49. Schlessinger A, Punta M, Rost B, (2007) Natively unstructured regions in proteins identified from contact predictions. Bioinformatics 23: 2376-2384.
50. Mohan A, Oldfield CJ, Radivojac P, Vacic V, Cortese MS, et al. (2006) Analysis of molecular recognition features (MoRFs). J Mol Biol 362: 1043-1059.
51. Vacic V, Oldfield CJ, Mohan A, Radivojac P, Cortese MS, et al. (2007) Characterization of molecular recognition features, MoRFs, and their binding partners. J Proteome Res 6: 2351-2366.
52. Meszaros B, Simon I, Dosztanyi Z, (2009) Prediction of protein binding regions in disordered proteins. PLoS Comput Biol 5: e1000376.
53. Dosztanyi Z, Meszaros B, Simon I, (2009) ANCHOR: web server for predicting protein binding regions in disordered proteins. Bioinformatics 25: 2745-2746.
54. Tompa P, (2003) Intrinsically unstructured proteins evolve by repeat expansion. BioEssays 25: 847-855.
55. NCBI (2011) pfam12526: DUF3729. Conserved Domains.
56. Arankalle VA, Paranjape S, Emerson SU, Purcell RH, Walimbe AM, (1999) Phylogenetic analysis of hepatitis E virus isolates from India (1976-1993). Journal of General Virology 80: 1691-1700.
57. Arankalle VA, Chobe LP, Chadha MS, (2006) Type-IV Indian swine HEV infects rhesus monkeys. J Viral Hep 13: 742-745.
58. Chatterjee R, Tsarev SA, Pillot J, Coursaget P, Emerson SU, et al. (1997) African Strains of Hepatitis E Virus That Are Distinct From Asian Strains.
59. Legrand-Abravanel F, Mansuy J-M, Dubois M, Kamar N, Peron J-M, et al. (2009) Hepatitis E Virus Genotype 3 Diversity, France. Emerg Infect Dis 15: 110-114.
60. Tettamanzi MC, Yu C, Bogan JS, Hodsdon ME, (2006) Solution structure and backbone dynamics of an N-terminal ubiquitin-like domain in the GLUT4-regulating protein, TUG. Protein Sci 15: 498-508.
61. Nguyen HT, Torian U, Faulk K, Mather K, Engle RE, et al. (2011) A naturally-occurring human/hepatitis E recombinant virus predominates in serum but not in feces of a chronic hepatitis E patient and has a growth advantage in cell culture. J Gen Virol doi:10.1099/vir.1090.037259-037250.
62. Ropp SL, Tam AW, Beames B, Purdy M, Frey TK, (2000) Expression of the hepatitis E virus ORF1. Arch Virol 145: 1321-1337.
63. Shukla P, Nguyen HT, Torian U, Engle RE, Faulk K, et al. (2011) Cross-species infections of cultured cells by hepatitis E virus and discovery of an infectious virus-host recombinant. PNAS 108: 2438-2443.
64. Eisenberg D, Schwarz E, Komaromy M, Wall R, (1984) Analysis of membrane and surface protein sequences with the hydrophobic moment plot. J Mol Biol 179: 125-142.
65. Karplus PA, Schulz GE, (1985) Prediction of chain flexibility in proteins: A tool for the selection of peptide antigens. Naturwissenschaften 72: 212-213.
66. Zhang Y, Skolnick J, (2005) TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res 33: 2302-2309.