Reevaluation of the coding potential and proteomic analysis of the BAC-derived rhesus cytomegalovirus strain 68-1

Daniel Malouli, Ernesto S. Nakayasu, Kasinath Viswanathan, David G. Camp, W. L. William Chang, Peter A. Barry, Richard D. Smith, Klaus Frueh

Research output: Contribution to journalArticle

23 Citations (Scopus)

Abstract

Cytomegaloviruses are highly host restricted, resulting in cospeciation with their hosts. As a natural pathogen of rhesus macaques (RM), rhesus cytomegalovirus (RhCMV) has therefore emerged as a highly relevant experimental model for pathogenesis and vaccine development due to its close evolutionary relationship to human CMV (HCMV). Most in vivo experiments performed with RhCMV employed strain 68-1 cloned as a bacterial artificial chromosome (BAC). However, the complete genome sequence of the 68-1 BAC has not been determined. Furthermore, the gene content of the RhCMV genome is unknown, and previous open reading frame (ORF) predictions relied solely on uninterrupted ORFs with an arbitrary cutoff of 300 bp. To obtain a more precise picture of the actual proteins encoded by the most commonly used molecular clone of RhCMV, we reevaluated the RhCMV 68-1 BAC genome by whole-genome shotgun sequencing and determined the protein content of the resulting RhCMV virions by proteomics. By comparing the RhCMV genome to those of several related Old World monkey (OWM) CMVs, we were able to filter out many unlikely ORFs and obtain a simplified map of the RhCMV genome. This comparative genomics analysis suggests a high degree of ORF conservation among OWM CMVs, thus decreasing the likelihood that ORFs found only in RhCMV comprise true genes. Moreover, virion proteomics independently validated the revised ORF predictions, since only proteins that were conserved across OWM CMVs could be detected. Taken together, these data suggest a much higher conservation of genome and virion structure between CMVs of humans, apes, and OWMs than previously assumed.

Original languageEnglish (US)
Pages (from-to)8959-8973
Number of pages15
JournalJournal of Virology
Volume86
Issue number17
DOIs
StatePublished - Sep 2012

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Bacterial Artificial Chromosomes
Cytomegalovirus
bacterial artificial chromosomes
Proteomics
proteomics
Open Reading Frames
open reading frames
Genome
Cercopithecidae
genome
virion
Virion
prediction
Protein Sequence Analysis
Hominidae
Firearms
vaccine development
Pongidae
Genomics
Macaca mulatta

ASJC Scopus subject areas

  • Immunology
  • Virology

Cite this

Malouli, D., Nakayasu, E. S., Viswanathan, K., Camp, D. G., William Chang, W. L., Barry, P. A., ... Frueh, K. (2012). Reevaluation of the coding potential and proteomic analysis of the BAC-derived rhesus cytomegalovirus strain 68-1. Journal of Virology, 86(17), 8959-8973. https://doi.org/10.1128/JVI.01132-12

Reevaluation of the coding potential and proteomic analysis of the BAC-derived rhesus cytomegalovirus strain 68-1. / Malouli, Daniel; Nakayasu, Ernesto S.; Viswanathan, Kasinath; Camp, David G.; William Chang, W. L.; Barry, Peter A.; Smith, Richard D.; Frueh, Klaus.

In: Journal of Virology, Vol. 86, No. 17, 09.2012, p. 8959-8973.

Research output: Contribution to journalArticle

Malouli, D, Nakayasu, ES, Viswanathan, K, Camp, DG, William Chang, WL, Barry, PA, Smith, RD & Frueh, K 2012, 'Reevaluation of the coding potential and proteomic analysis of the BAC-derived rhesus cytomegalovirus strain 68-1', Journal of Virology, vol. 86, no. 17, pp. 8959-8973. https://doi.org/10.1128/JVI.01132-12
Malouli D, Nakayasu ES, Viswanathan K, Camp DG, William Chang WL, Barry PA et al. Reevaluation of the coding potential and proteomic analysis of the BAC-derived rhesus cytomegalovirus strain 68-1. Journal of Virology. 2012 Sep;86(17):8959-8973. https://doi.org/10.1128/JVI.01132-12
Malouli, Daniel ; Nakayasu, Ernesto S. ; Viswanathan, Kasinath ; Camp, David G. ; William Chang, W. L. ; Barry, Peter A. ; Smith, Richard D. ; Frueh, Klaus. / Reevaluation of the coding potential and proteomic analysis of the BAC-derived rhesus cytomegalovirus strain 68-1. In: Journal of Virology. 2012 ; Vol. 86, No. 17. pp. 8959-8973.
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