Tridimensional model structure and patterns of molecular evolution of Pepino mosaic virus TGBp3 protein

Virology Journal

Volumn 8, Issue , 2011, Pages

  Hasiów Jaroszewska, Beata ^a   Czerwoniec, Anna ^b   Pospieszny, Henryk ^a   Elena, Santiago F ^c,d  

^a INSTITUTE OF PLANT PROTECTION NATIONAL RESEARCH INSTITUTE   (Poland)

^b ADAM MICKIEWICZ UNIVERSITY   (Poland)

^c Ciudad Politécnica de la Innovación   (Spain)

^d SANTA FE INSTITUTE   (United States)

Author keywords

molecular evolution; PepMV; protein modeling; selective constraints; TGBp3; virus evolution

Indexed keywords

AMINO ACID; PROTEIN TGBP3; UNCLASSIFIED DRUG; VIRUS PROTEIN; TGBP3 PROTEIN, PEPINO MOSAIC VIRUS; VIRUS RNA;

ARTICLE; MOLECULAR EVOLUTION; MOSAIC VIRUS; NONHUMAN; PEPINO MOSAIC VIRUS; PROTEIN ANALYSIS; PROTEIN FUNCTION; PROTEIN STRUCTURE; CHEMICAL STRUCTURE; CHEMISTRY; GENETIC SELECTION; GENETICS; ISOLATION AND PURIFICATION; PLANT DISEASE; POTEXVIRUS; PROTEIN CONFORMATION; VIROLOGY;

LYCOPERSICON ESCULENTUM; PEPINO MOSAIC VIRUS; POTEXVIRUS;

EVOLUTION, MOLECULAR; MODELS, MOLECULAR; PLANT DISEASES; POTEXVIRUS; PROTEIN CONFORMATION; RNA, VIRAL; SELECTION, GENETIC; VIRAL PROTEINS;

EID: 79959463018     PISSN: None     EISSN: 1743422X     Source Type: Journal    
DOI: 10.1186/1743-422X-8-318     Document Type: Article

References (44)

1. Two unique US isolates of Pepino mosaic virus from a limited source of pooled tomato tissue are distinct from a third (European -like) US isolate. CJ Maroon-Lango MA Guaragna RL Jordan J Hammond M Bandla SK Marquardt, Arch Virol 2005 150 1187 1201 10.1007/s00705-005-0495-z 15750864 (Pubitemid 40772029)
2. Molecular characterization of two Pepino mosaic virus variants from imported tomato seed reveals high levels of sequence identity between Chilean and US isolates. KS Ling, Virus Genes 2007 34 1 8 10.1007/s11262-006-0003-x 16927118
3. Complete genomic RNA sequence of the Polish Pepino mosaic virus isolate belonging to the US2 strain. B Hasiáw N Borodynko H Pospieszny, Virus Genes 2008 36 1 8 10.1007/s11262-007-0165-1 17922180
4. Pepino mosaic virus - a pathogen of tomato crops in Poland: biology, evolution and diagnostics. B Hasiáw-Jaroszewska N Borodynko P Jackowiak M Figlerowicz H Pospieszny, J Plant Protect Res 2010 50 477 483 10.2478/v10045-010-0079-0
5. Pepino mosaic virus: a successful pathogen that rapidly evolved from emerging to endemic in tomato crops. I Hanssen B Thomma, Mol Plant Pathol 2010 11 179 189 10.1111/j.1364-3703.2009.00600.x 20447268
6. A single mutation in TGB3 converts mild pathotype of Pepino mosaic virus into necrotic one. B Hasiáw-Jaroszewska N Borodynko P Jackowiak M Figlerowicz H Pospieszny, Virus Res 2011 159 57 61 10.1016/j.virusres.2011.04. 008 21536084
7. Statistical methods for detecting molecular adaptation. Z Yang JP Bielawski, Trends Ecol Evol 2000 15 496 503 10.1016/S0169-5347(00)01994-7 11114436
8. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. TA Hall, Nucl Acids Symp Ser 1999 41 95 98
9. MUSCLE: multiple sequence alignment with high accuracy and high throughput. RC Edgar, Nucl Acids Res 2004 32 1792 1797 10.1093/nar/gkh340 15034147 (Pubitemid 38832724)
10. PAL2NAL: robust conversion of protein sequence alignemnts into the corresponding codon alignments. M Suyama D Torrents P Bork, Nucl Acids Res 2006 34 609 612 10.1093/nar/gkl315 (Pubitemid 44529842)
11. Structure and evolution of a new avian MHC CIass II B gene in a sub-antarctic seabird, the thin-billed prion (Procellariiformes: Pachyptila belcheri). MC Silva SV Edwards, J Mol Evol 2009 68 279 291 10.1007/s00239-009- 9200-2 19209378
12. RDP3: a flexible and fast computer program for analyzing recombination. DP Martin P Lemey M Lott V Moulton D Posada P Lefeuvre, Bioinformatics 2010 26 2462 2463 10.1093/bioinformatics/btq467 20798170
13. MEGA5: molecular evolutionary genetics using maximum likelihood, evolutionary distance, and maximum parsimony methods. K Tamura D Peterson N Peterson G Stecher M Nei S Kumar, Mol Biol Evol 2011
14. Not so different after all: A comparison of methods for detecting amino acid sites under selection. SL Kosakovsky Pond SDW Frost, Mol Biol Evol 2005 22 1208 1222 10.1093/molbev/msi105 15703242 (Pubitemid 40577758)
15. HyPhy: hypothesis testing using phylogenies. S Kosakovsky Pond SDW Frost SV Muse, Bioinformatics 2005 21 676 679 10.1093/bioinformatics/bti079 15509596 (Pubitemid 40424796)
16. DATAMONKEY: rapid detection of selective pressure on individual sites of codon alignments. SL Kosakovsky Pond SDW Frost, Bioinformatics 2005 21 2531 2533 10.1093/bioinformatics/bti320 15713735 (Pubitemid 40731616)
17. Codon-substitution models for heterogeneous selection pressure at amino acid sites. Z Yang R Nielsen N Goldman AMK Pedersen, Genetics 2000 155 431 449 10790415 (Pubitemid 30257141)
18. PAML: a program package for phylogenetic analysis by maximum likelihood. Z Yang, Comput Appl Biosci 2000 13 555 556
19. SWAPSC: sliding-window analysis procedure to detect selective constraints. MA Fares, Bioinformatics 2004 20 2867 2868 10.1093/bioinformatics/ bth303 15130925 (Pubitemid 39530184)
20. ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids. H Ashkenazy E Erez E Martz T Pupko N Ben-T, Nucl Acids Res 2010 38 529 533 10.1093/nar/gkq399
21. GeneSilico protein structure prediction meta-server. MA Kurowski JM Bujnicki, Nucl Acids Res 2003 31 3305 3307 10.1093/nar/gkg557 12824313 (Pubitemid 37442145)
22. The PSIPRED protein structure prediction server. LJ McGuffin K Bryson DT Jones, Bioinformatics 2000 16 404 405 10.1093/bioinformatics/16.4.404 10869041 (Pubitemid 30417087)
23. The PredictProtein server. B Rost G Yachdav J Liu, Nucleic Acids Res 2004 32 321 326 10.1093/nar/gkh377 (Pubitemid 39004075)
24. Cascaded multiple classifiers for secondary structure prediction. M Ouali RD King, Protein Sci 2000 9 1162 1176 10.1110/ps.9.6.1162 10892809 (Pubitemid 30419151)
25. Accurate prediction of solvent accessibility using neural networks-based regression. R Adamczak A Porollo J Meller, Proteins 2004 56 753 767 10.1002/prot.20176 15281128 (Pubitemid 39063318)
26. Application of multiple sequence alignment profiles to improve protein secondary structure prediction. JA Cuff GJ Barton, Proteins 2000 40 502 511 10.1002/1097-0134(20000815)40:3<502::AID-PROT1703.0.CO;2-Q 10861942 (Pubitemid 30624459)
27. Assembly of protein tertiary structure from fragments with similar local sequences using simulated annealing and bayesian scoring function. KT Simons C Kooperberg E Huang D Baker, J Mol Biol 1997 268 209 225 10.1006/jmbi.1997.0959 9149153 (Pubitemid 27192690)
28. MaxSub: An automated measure to assess the quality of protein structure predictions. N Siew A Elofsson L Rychlewski D Fischer, Bioinformatics 2000 16 776 785 10.1093/bioinformatics/16.9.776 11108700
29. Can correct protein models be identified. B Wallner A Elofsson, Protein Sci 2003 12 1073 1086 10.1110/ps.0236803 12717029 (Pubitemid 36505441)
30. MetaMQAP: a meta-server for the quality assessment of protein models. M Pawlowski MJ Gajda R Matlak JM Bujnicki, BMC Bioinformatics 2008 9 403 10.1186/1471-2105-9-403 18823532
31. Electrostatics of cellular components: Application to microtubules and the ribosome. NA Baker D Sept MJ Holst JA McCammon, Proc Natl Acad Sci USA 2001 98 10037 10041 10.1073/pnas.181342398 11517324 (Pubitemid 32802969)
32. The rate and spectrum of spontaneous mutations in a plant RNA virus. N Tromas SF Elena, Genetics 2010 185 983 989 10.1534/genetics.110.115915 20439778
33. A 'Frankenstein's monster' approach to comparative modeling: merging the finest fragments of fold-recognition models and iterative model refinement aided by 3D structure evaluation. J Kosinski IA Cymerman M Feder MA Kurowski JM Sasin JM Bujnicki, Proteins 2003 53 369 79 10.1002/prot.10545 14579325 (Pubitemid 37352195)
34. Triple gene block: modular design of a multifunctional machine for plant virus movement. SY Morozov AG Solovyev, J Gen Virol 2003 84 1351 1366 10.1099/vir.0.18922-0 12771402 (Pubitemid 36675503)
35. Triple gene block proteins of White clover mosaic potexvirus are required for transport. DL Beck PJ Guilford DM Voot MT Andersen RLS Forster, Virology 1991 83 695 702
36. Variability in the level of RNA silencing suppression caused by triple gene block protein 1 (TGBp1) from various potexviruses during infection. H Senshu J Ozeki K Komatsu M Hashimoto K Hatada M Aoyama S Kagiwada Y Yamaji S Namba, J Gen Virol 2009 90 1014 24 10.1099/vir.0.008243-0 19264652
37. In vitro membrane binding of the translation products of the carlavirus 7-kDa protein genes. SY Morozov NA Miroshnichenko AG Solovyev DA Zelenina ON Fedorkin LI Lukasheva SA Grachev BK Chernov, Virology 1991 183 782 785 10.1016/0042-6822(91)91011-5 1853576
38. Subcellular localisation, protein interactions, and RNA binding of potato mop-top virus triple gene block proteins. GH Cowan F Lioliopoulou A Ziegler L Torrance, Virology 2002 298 106 115 10.1006/viro.2002.1435 12093178 (Pubitemid 34734884)
39. Immunodetection and fluorescent microscopy of transgenically expressed hordeivirus TGBp3 movement protein reveals its association with endoplasmic reticulum elements in close proximity to plasmodesmata. EN Gorshkova TN Erokhina TA Stroganova NE Yelina AA Zamyatnin Jr NO Kalinina J Schiemann AG Solovyev SYu Morozov, J Gen Virol 2003 84 985 994 10.1099/vir.0.18885-0 12655101 (Pubitemid 36432231)
40. Selective constraints, amino acid composition, and the rate of protein evolution. NJ Tourasse WH Li, Mol Biol Evol 2000 17 656 664 10742056 (Pubitemid 30210710)
41. Divergent evolution and purifying selection of the flaA gene sequences in Aeromas. M Farfan D Minana-Galbis M Carmenn Fuste G Loren, Biol Direct 2009 4 23 39 10.1186/1745-6150-4-23 19622168
42. Quasispecies nature of Pepino mosaic virus and its evolutionary dynamics. B Hasiáw-Jaroszewska P Jackowiak N Borodynko M Figlerowicz H Pospieszny, Virus Genes 2010 41 260 267 10.1007/s11262-010-0497-0 20549323
43. Mixed infections of Pepino mosaic virus strains modulate the evolutionary dynamics of this emergent virus. P Gámez RN Sempere SF Elena MA Aranda, J Virol 2009 83 12378 12387 10.1128/JVI.01486-09 19759144
44. The PyMOL User's Manual. WL DeLano, DeLano Scientific, San Carlos, CA, USA 2002