Genomic and bioinformatics analysis of human adenovirus type 37: New insights into corneal tropism

BMC Genomics

Volumn 9, Issue , 2008, Pages

  Robinson, Christopher M ^a,b   Shariati, Fatemeh ^a,b   Gillaspy, Allison F ^b,c   Dyer, David W ^b,c   Chodosh, James ^a,b  

^a UNIVERSITY OF OKLAHOMA HEALTH SCIENCES CENTER   (United States)

^b UNIVERSITY OF OKLAHOMA COLLEGE OF MEDICINE   (United States)

^c UNIVERSITY OF OKLAHOMA HEALTH SCIENCES CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

STRUCTURAL PROTEIN; VIRUS PROTEIN; VIRUS RNA; VIRUS DNA;

ARTICLE; CONTROLLED STUDY; CORNEA DISEASE; GENOME ANALYSIS; GENOME SIZE; HUMAN ADENOVIRUS; HUMAN ADENOVIRUS 37; HUMAN ADENOVIRUS 9; IMMUNE SYSTEM; MASTADENOVIRUS; MOLECULAR PHYLOGENY; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; STRAIN DIFFERENCE; STRUCTURAL BIOINFORMATICS; STRUCTURAL GENOMICS; TWO DIMENSIONAL GEL ELECTROPHORESIS; VIRAL GENETICS; VIRUS FIBER; VIRUS GENOME; VIRUS STRAIN; VIRUS VIRULENCE; BIOLOGY; CHEMISTRY; CLASSIFICATION; GENETICS; GENOMICS; HUMAN; KERATOCONJUNCTIVITIS; PATHOGENICITY; PHYLOGENY; VIROLOGY; VIRUS INFECTION;

ADENOVIRIDAE; HUMAN ADENOVIRUS TYPE 37; MIRIDAE;

ADENOVIRUS INFECTIONS, HUMAN; ADENOVIRUSES, HUMAN; BASE SEQUENCE; COMPUTATIONAL BIOLOGY; DNA, VIRAL; GENOME, VIRAL; GENOMICS; HUMANS; KERATOCONJUNCTIVITIS; PHYLOGENY; RNA, VIRAL; VIRAL PROTEINS;

EID: 44449152519     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-9-213     Document Type: Article

References (81)

1. Benko M B. Harrach, and W. C. Russell Family Adenoviridae Virus Taxonomy: Seventh Report of the International Committee on Taxonomy of Viruses San Diego, Academic Press M. H. V. van Regenmortel CMFDHLBEBCMKESMLJMMAMDJMGCRPRBW 2000:227-238.
2. Hilleman MR Werner JH Recovery of new agent from patients with acute respiratory illness Proceedings of the Society for Experimental Biology and Medicine Society for Experimental Biology and Medicine (New York, NY) 1954, 85(1):183-188.
3. Rowe WP Huebner RJ Gilmore LK Parrott RH Ward TG Isolation of a cytopathogenic agent from human adenoids undergoing spontaneous degeneration in tissue culture Proceedings of the Society for Experimental Biology and Medicine Society for Experimental Biology and Medicine (New York, NY) 1953, 84(3):570-573.
4. Dingle JH Langmuir AD Epidemiology of acute, respiratory disease in military recruits Am Rev Respir Dis 1968, 97(6 Suppl 1):65.
5. Harding SP Mutton KJ van der Avoort H Wermenbol AG An epidemic of keratoconjunctivitis due to adenovirus type 37 Eye (London, England) 1988, 2 (Pt 3):314-317. 2841171
6. Wood DJ Adenovirus gastroenteritis British medical journal (Clinical research ed) 1988, 296(6617):229-230. 2829987
7. Shenk T Adenoviridae: The Viruses and Their Replication Fields Virology Philadelphia, Lippincott - Raven Publishers B.N. Fields DMKPMH Thrid Edition 1996:2111-2148.
8. Jones MS 2nd Harrach B Ganac RD Gozum MM Dela Cruz WP Riedel B Pan C Delwart EL Schnurr DP New adenovirus species found in a patient presenting with gastroenteritis Journal of virology 2007, 81(11):5978-5984. 1900323 17360747 10.1128/JVI.02650-06
9. de Jong JC Wigand R Wadell G Keller D Muzerie CJ Wermenbol AG Schaap GJ Adenovirus 37: Identification and characterization of a medically important new adenovirus type of subgroup D Journal of medical virology 1981, 7(2):105-118. 10.1002/jmv.1890070204 7264611
10. Ariga T Shimada Y Shiratori K Ohgami K Yamazaki S Tagawa Y Kikuchi M Miyakita Y Fujita K Ishiko H Aoki K Ohno S Five new genome types of adenovirus type 37 caused epidemic keratoconjunctivitis in Sapporo, Japan, for more than 10 years Journal of clinical microbiology 2005, 43(2):726-732. 548033 15695671 10.1128/JCM.43.2.726-732.2005
11. Dhurandhar NV Contribution of pathogens in human obesity Drug news & perspectives 2004, 17(5):307-313. 10.1358/dnp.2004.17.5.829034 15334180
12. Fuzznuc: Nucleic Acid Pattern Search http://bioweb.pasteur.fr/seqanal/ interfaces/fuzznuc.html
13. Purkayastha A Ditty SE Su J McGraw J Hadfield TL Tibbetts C Seto D Genomic and bioinformatics analysis of HAdV-4, a human adenovirus causing acute respiratory disease implications for gene therapy and vaccine vector development Journal of virology 2005, 79(4):2559-2572. 546560 15681456 10.1128/JVI.79.4.2559-2572.2005
14. Temperley SM Hay RT Recognition of the adenovirus type 2 origin of DNA replication by the virally encoded DNA polymerase and preterminal proteins The EMBO journal 1992, 11(2):761-768. 556509 1537347
15. Brudno M Do CB Cooper GM Kim MF Davydov E Green ED Sidow A Batzoglou S LAGAN and Multi-LAGAN: Efficient tools for large-scale multiple alignment of genomic DNA Genome research 2003, 13(4):721-731. 430158 12654723 10.1101/gr.926603
16. Berk AJ Sharp PA Structure of the adenovirus 2 early mRNAs Cell 1978, 14(3):695-711. 10.1016/0092-8674(78)90252-0 688389
17. Frisch SM Mymryk JS Adenovirus-5 E1A: Paradox and paradigm Nature reviews 2002, 3(6):441-452. 10.1038/nrm827 12042766
18. Gallimore PH Turnell AS Adenovirus E1A: Remodelling the host cell, a life or death experience Oncogene 2001, 20(54):7824-7835. 10.1038/ sj.onc.1204913 11753665
19. Berk AJ Recent lessons in gene expression, cell cycle control, and cell biology from adenovirus Oncogene 2005, 24(52):7673-7685. 10.1038/ sj.onc.1209040 16299528
20. Martin ME Berk AJ Adenovirus E1B 55K represses p53 activation in vitro Journal of virology 1998, 72(4):3146-3154. 109770 9525640
21. Yew PR Berk AJ Inhibition of p53 transactivation required for transformation by adenovirus early 1B protein Nature 1992, 357(6373):82-85. 10.1038/357082a0 1533443
22. Horwitz MS Function of adenovirus E3 proteins and their interactions with immunoregulatory cell proteins The journal of gene medicine 2004, 6(Suppl 1):S172-83. 10.1002/jgm.495 14978760
23. Windheim M Hilgendorf A Burgert HG Immune evasion by adenovirus E3 proteins: Exploitation of intracellular trafficking pathways Curr Top Microbiol Immunol 2004, 273:29-85. 14674598
24. Burgert HG Blusch JH Immunomodulatory functions encoded by the E3 transcription unit of adenoviruses Virus genes 2000, 21(1-2):13-25. 10.1023/A:1008135928310 11022786
25. Deryckere F Burgert HG Early region 3 of adenovirus type 19 (subgroup D) encodes an HLA-binding protein distinct from that of subgroups B and C Journal of virology 1996, 70(5):2832-2841. 190140 8627757
26. Leppard KN E4 gene function in adenovirus, adenovirus vector and adeno-associated virus infections The Journal of general virology 1997, 78 (Pt 9):2131-2138. 9291998
27. Dobner T Horikoshi N Rubenwolf S Shenk T Blockage by adenovirus E4orf6 of transcriptional activation by the p53 tumor suppressor Science 1996, 272(5267):1470-1473. 8633237 10.1126/science.272.5267.1470
28. Moore M Horikoshi N Shenk T Oncogenic potential of the adenovirus E4orf6 protein Proceedings of the National Academy of Sciences of the United States of America 1996, 93(21):11295-11301. 38051 8876129 10.1073/ pnas.93.21.11295
29. Weiss RS Lee SS Prasad BV Javier RT Human adenovirus early region 4 open reading frame 1 genes encode growth-transforming proteins that may be distantly related to dUTP pyrophosphatase enzymes Journal of virology 1997, 71(3):1857-1870. 191256 9032316
30. Weiss RS Gold MO Vogel H Javier RT Mutant adenovirus type 9 E4 ORF1 genes define three protein regions required for transformation of CREF cells Journal of virology 1997, 71(6):4385-4394. 191656 9151828
31. Gustin KE Lutz P Imperiale MJ Interaction of the adenovirus L1 52/ 55-kilodalton protein with the IVa2 gene product during infection Journal of virology 1996, 70(9):6463-6467. 190681 8709283
32. Zhang W Imperiale MJ Interaction of the adenovirus IVa2 protein with viral packaging sequences Journal of virology 2000, 74(6):2687-2693. 111758 10684284 10.1128/JVI.74.6.2687-2693.2000
33. Zhang W Low JA Christensen JB Imperiale MJ Role for the adenovirus IVa2 protein in packaging of viral DNA Journal of virology 2001, 75(21):10446-10454. 114618 11581412 10.1128/JVI.75.21.10446-10454.2001
34. Alex Dong Li's SpliceSiteFinder http://www.genet.sickkids.on.ca/~ali/ splicesitefinder.html Accessed March 4th, 2008.
35. Boulanger P Lemay P Blair GE Russell WC Characterization of adenovirus protein IX The Journal of general virology 1979, 44(3):783-800. 93618
36. Lutz P Rosa-Calatrava M Kedinger C The product of the adenovirus intermediate gene IX is a transcriptional activator Journal of virology 1997, 71(7):5102-5109. 191744 9188576
37. Hasson TB Ornelles DA Shenk T Adenovirus L1 52- and 55-kilodalton proteins are present within assembling virions and colocalize with nuclear structures distinct from replication centers Journal of virology 1992, 66(10):6133-6142. 241491 1527852
38. Gustin KE Imperiale MJ Encapsidation of viral DNA requires the adenovirus L1 52/55-kilodalton protein Journal of virology 1998, 72(10):7860-7870. 110107 9733823
39. Saban SD Silvestry M Nemerow GR Stewart PL Visualization of alpha-helices in a 6-angstrom resolution cryoelectron microscopy structure of adenovirus allows refinement of capsid protein assignments Journal of virology 2006, 80(24):12049-12059. 1676273 17005667 10.1128/ JVI.01652-06
40. Wickham TJ Mathias P Cheresh DA Nemerow GR Integrins alpha v beta 3 and alpha v beta 5 promote adenovirus internalization but not virus attachment Cell 1993, 73(2):309-319. 10.1016/0092-8674(93)90231-E 8477447
41. Arnberg N Kidd AH Edlund K Olfat F Wadell G Initial interactions of subgenus D adenoviruses with A549 cellular receptors: Sialic acid versus alpha(v) integrins Journal of virology 2000, 74(16):7691-7693. 112295 10906228 10.1128/JVI.74.16.7691-7693.2000
42. Chatterjee PK Vayda ME Flint SJ Identification of proteins and protein domains that contact DNA within adenovirus nucleoprotein cores by ultraviolet light crosslinking of oligonucleotides 32P-labelled in vivo Journal of molecular biology 1986, 188(1):23-37. 10.1016/ 0022-2836(86)90477-8 3712442
43. Wodrich H Guan T Cingolani G Von Seggern D Nemerow G Gerace L Switch from capsid protein import to adenovirus assembly by cleavage of nuclear transport signals The EMBO journal 2003, 22(23):6245-6255. 291855 14633984 10.1093/emboj/cdg614
44. Honkavuori KS Pollard BD Rodriguez MS Hay RT Kemp GD Dual role of the adenovirus pVI C terminus as a nuclear localization signal and activator of the viral protease The Journal of general virology 2004, 85(Pt 11):3367-3376. 10.1099/vir.0.80203-0 15483253
45. Ebner K Pinsker W Lion T Comparative sequence analysis of the hexon gene in the entire spectrum of human adenovirus serotypes: Phylogenetic, taxonomic, and clinical implications Journal of virology 2005, 79(20):12635-12642. 1235814 16188965 10.1128/JVI.79.20.12635-12642.2005
46. Weber J Genetic analysis of adenovirus type 2 III. Temperature sensitivity of processing viral proteins Journal of virology 1976, 17(2):462-471. 515438 1255847
47. Cuesta R Xi Q Schneider RJ Structural basis for competitive inhibition of eIF4G-Mnk1 interaction by the adenovirus 100-kilodalton protein Journal of virology 2004, 78(14):7707-7716. 434077 15220445 10.1128/ JVI.78.14.7707-7716.2004
48. Hayes BW Telling GC Myat MM Williams JF Flint SJ The adenovirus L4 100-kilodalton protein is necessary for efficient translation of viral late mRNA species Journal of virology 1990, 64(6):2732-2742. 249453 2335816
49. Hong SS Szolajska E Schoehn G Franqueville L Myhre S Lindholm L Ruigrok RW Boulanger P Chroboczek J The 100K-chaperone protein from adenovirus serotype 2 (Subgroup C) assists in trimerization and nuclear localization of hexons from subgroups C and B adenoviruses Journal of molecular biology 2005, 352(1):125-138. 10.1016/j.jmb.2005.06.070 16081097
50. Liu GQ Babiss LE Volkert FC Young CS Ginsberg HS A thermolabile mutant of adenovirus 5 resulting from a substitution mutation in the protein VIII gene Journal of virology 1985, 53(3):920-925. 254727 3973969
51. Ostapchuk P Anderson ME Chandrasekhar S Hearing P The L4 22-kilodalton protein plays a role in packaging of the adenovirus genome Journal of virology 2006, 80(14):6973-6981. 1489068 16809303 10.1128/JVI.00123-06
52. Arnberg N Mei Y Wadell G Fiber genes of adenoviruses with tropism for the eye and the genital tract Virology 1997, 227(1):239-244. 10.1006/ viro.1996.8269 9007080
53. Nicol CG Graham D Miller WH White SJ Smith TA Nicklin SA Stevenson SC Baker AH Effect of adenovirus serotype 5 fiber and penton modifications on in vivo tropism in rats Mol Ther 2004, 10(2):344-354. 10.1016/ j.ymthe.2004.05.020 15294181
54. Smith TA Idamakanti N Rollence ML Marshall-Neff J Kim J Mulgrew K Nemerow GR Kaleko M Stevenson SC Adenovirus serotype 5 fiber shaft influences in vivo gene transfer in mice Human gene therapy 2003/06/14 2003, 14(8):777-787. 10.1089/104303403765255165 12804140
55. Smith TA Idamakanti N Marshall-Neff J Rollence ML Wright P Kaloss M King L Mech C Dinges L Iverson WO Sherer AD Markovits JE Lyons RM Kaleko M Stevenson SC Receptor interactions involved in adenoviral-mediated gene delivery after systemic administration in non-human primates Human gene therapy 2003/11/25 2003, 14(17):1595-1604. 10.1089/104303403322542248 14633402
56. O'Malley RP Mariano TM Siekierka J Mathews MB A mechanism for the control of protein synthesis by adenovirus VA RNAI Cell 1986, 44(3):391-400. 10.1016/0092-8674(86)90460-5 3943131
57. Liao HJ Kobayashi R Mathews MB Activities of adenovirus virus-associated RNAs: Purification and characterization of RNA binding proteins Proceedings of the National Academy of Sciences of the United States of America 1998, 95(15):8514-8519. 21107 9671709 10.1073/pnas.95.15.8514
58. Andersson MG Haasnoot PC Xu N Berenjian S Berkhout B Akusjarvi G Suppression of RNA interference by adenovirus virus-associated RNA Journal of virology 2005, 79(15):9556-9565. 1181602 16014917 10.1128/ JVI.79.15.9556-9565.2005
59. Kidd AH Garwicz D Oberg M Human and simian adenoviruses: Phylogenetic inferences from analysis of VA RNA genes Virology 1995, 207(1):32-45. 10.1006/viro.1995.1049 7871747
60. Pearson WR Flexible sequence similarity searching with the FASTA3 program package Methods Mol Biol 2000, 132:185-219. 10547837
61. Hiller K Schobert M Hundertmark C Jahn D Munch R JVirGel: Calculation of virtual two-dimensional protein gels Nucleic acids research 2003, 31(13):3862-3865. 168943 12824438 10.1093/nar/gkg536
62. JVirGel v2.0 http://www.jvirgel.de/
63. Patrickios CS Yamasaki EN Polypeptide amino acid composition and isoelectric point. II. Comparison between experiment and theory Analytical biochemistry 1995, 231(1):82-91. 10.1006/abio.1995.1506 8678324
64. Skoog B Wichman A Calculation of the isoelectric points of polypeptieds from the amino acid composition Trends Anal Chem 1986:82-83. 10.1016/ 0165-9936(86)80045-0
65. Tabrizi SN Ling AE Bradshaw CS Fairley CK Garland SM Human adenoviruses types associated with non-gonococcal urethritis Sexual health 2007, 4(1):41-44. 10.1071/SH06054 17382037
66. Davison AJ Benko M Harrach B Genetic content and evolution of adenoviruses The Journal of general virology 2003, 84(Pt 11):2895-2908. 10.1099/vir.0.19497-0 14573794
67. Natarajan K Shepard LA Chodosh J The use of DNA array technology in studies of ocular viral pathogenesis DNA and cell biology 2002, 21(5-6):483-490. 10.1089/10445490260099782
68. Engelmann I Madisch I Pommer H Heim A An outbreak of epidemic keratoconjunctivitis caused by a new intermediate adenovirus 22/H8 identified by molecular typing Clin Infect Dis 2006, 43(7):e64-6. 10.1086/507533 16941356
69. Lauer KP Llorente I Blair E Seto J Krasnov V Purkayastha A Ditty SE Hadfield TL Buck C Tibbetts C Seto D Natural variation among human adenoviruses: Genome sequence and annotation of human adenovirus serotype 1 The Journal of general virology 2004, 85(Pt 9):2615-2625. 10.1099/vir.0.80118-0 15302955
70. Rozen S Skaletsky H Primer3 on the WWW for general users and for biologist programmers Methods Mol Biol 2000, 132:365-386. 10547847
71. Gordon D Abajian C Green P Consed: A graphical tool for sequence finishing Genome research 1998, 8(3):195-202. 9521923
72. Ewing B Hillier L Wendl MC Green P Base-calling of automated sequencer traces using phred. I. Accuracy assessment Genome research 1998, 8(3):175-185. 9521921
73. Ewing B Green P Base-calling of automated sequencer traces using phred. II. Error probabilities Genome research 1998, 8(3):186-194. 9521922
74. JCVI Annotation Service http://www.jcvi.org/cms/research/projects/ annotation-service/overview/
75. Manatee http://manatee.sourceforge.net/
76. GeneMark http://exon.gatech.edu/GeneMark/
77. NCBI's ORF Finder (Open Reading Frame Finder) http://www.ncbi.nlm.nih.gov/gorf/gorf.html
78. VISTA http://genome.lbl.gov/vista/index.shtml
79. EBI Tools:: FASTA and SSEARCH similarity searching against protein databases http://www.ebi.ac.uk/fasta33/
80. BLAST: Basic Local Alignment and Search Tool http://www.ncbi.nlm.nih.gov/ BLAST/Blast.cgi
81. Kumar S Tamura K Nei M MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment Briefings in bioinformatics 2004, 5(2):150-163. 10.1093/bib/5.2.150 15260895