Complete Nucleotide Sequence of the Mycoplasma Virus P1 Genome

Tu, Anh-Hue Thi; Voelker, LeRoy L.; Shen, Xuejun; Dybvig, Kevin

doi:10.1006/plas.2000.1501

Cited by 34 publications

(14 citation statements)

References 20 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The smallest of the dsDNA tailed phages genomes are ~11.5 kbp [e.g. Mycoplasma phage P1 [17]], ~21kbp [e.g. Lactococcus phage c2, [18]], and ~ 30 kbp [e.g.…”

Section: Diversity Of the Bacteriophage Populationmentioning

confidence: 99%

Bacteriophages and their genomes

Hatfull

Hendrix

2011

Current Opinion in Virology

415

336

View full text Add to dashboard Cite

Bacteriophages occupy a unique position in biology, representing an absolute majority of all organisms in the biosphere. Because their genomes are relatively small, elucidating the genetic diversity of the phage population, deciphering their origins, and identifying the evolutionary mechanisms that shape the population would seem readily feasible. And yet the pace of phage genome characterization has slowed over the past three years, reflecting in part a need to transition from sequencing known and well-characterized bacteriophages to the isolation and comparative analysis of new isolates. The current state of bacteriophage genomics shows that the genetic diversity of the population is very high, that phages have been actively evolving for billions of years with active engagement of horizontal genetic exchange, and that their genomes are consequently pervasively mosaic in their architectures. But we have barely scratched the surface and the next years of phage genome exploration promise to be especially revealing.

show abstract

“…The smallest of the dsDNA tailed phages genomes are ~11.5 kbp [e.g. Mycoplasma phage P1 [17]], ~21kbp [e.g. Lactococcus phage c2, [18]], and ~ 30 kbp [e.g.…”

Section: Diversity Of the Bacteriophage Populationmentioning

confidence: 99%

Bacteriophages and their genomes

Hatfull

Hendrix

2011

Current Opinion in Virology

415

336

View full text Add to dashboard Cite

show abstract

“…However, the capsid size and, consequently, viral genome length within this supergroup vary extensively. The extreme case is the nearly 50-fold difference between the 11.6-kb genome of podovirus P1 infecting mycoplasmas (272) and the genome of the giant myovirus G (497.5 kb [110]). Protein-coding genes are generally tightly packed in viral genomes and typically occupy Ͼ90% of the genome in tailed viruses (108).…”

Section: Fig 1 Viruses Of the Ordermentioning

confidence: 99%

Genomics of Bacterial and Archaeal Viruses: Dynamics within the Prokaryotic Virosphere

Krupovìč

Prangishvili

Hendrix

et al. 2011

Microbiol Mol Biol Rev

216

176

View full text Add to dashboard Cite

SUMMARY Prokaryotes, bacteria and archaea, are the most abundant cellular organisms among those sharing the planet Earth with human beings (among others). However, numerous ecological studies have revealed that it is actually prokaryotic viruses that predominate on our planet and outnumber their hosts by at least an order of magnitude. An understanding of how this viral domain is organized and what are the mechanisms governing its evolution is therefore of great interest and importance. The vast majority of characterized prokaryotic viruses belong to the order Caudovirales, double-stranded DNA (dsDNA) bacteriophages with tails. Consequently, these viruses have been studied (and reviewed) extensively from both genomic and functional perspectives. However, albeit numerous, tailed phages represent only a minor fraction of the prokaryotic virus diversity. Therefore, the knowledge which has been generated for this viral system does not offer a comprehensive view of the prokaryotic virosphere. In this review, we discuss all families of bacterial and archaeal viruses that contain more than one characterized member and for which evolutionary conclusions can be attempted by use of comparative genomic analysis. We focus on the molecular mechanisms of their genome evolution as well as on the relationships between different viral groups and plasmids. It becomes clear that evolutionary mechanisms shaping the genomes of prokaryotic viruses vary between different families and depend on the type of the nucleic acid, characteristics of the virion structure, as well as the mode of the life cycle. We also point out that horizontal gene transfer is not equally prevalent in different virus families and is not uniformly unrestricted for diverse viral functions.

show abstract

“…Statistical gene prediction programs have been used previously for viral genome annotation. The GeneMark program (7a), for example, has been used to identify genes in the genomes of bovine herpesvirus 4 (65) as well as other viruses (19,32,51,53). More recent studies have used information from newly sequenced, closely related CMV genomes (17), as well as tools which derive amino acid positional patterns from protein databases to predict protein coding regions in viruses (2,35).…”

mentioning

confidence: 99%

Identification of Proteins Associated with Murine Cytomegalovirus Virions

Kattenhorn

Mills

Wagner

et al. 2004

J Virol

136

126

View full text Add to dashboard Cite

Proteins associated with the murine cytomegalovirus (MCMV) viral particle were identified by a combined approach of proteomic and genomic methods. Purified MCMV virions were dissociated by complete denaturation and subjected to either separation by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and in-gel digestion or treated directly by in-solution tryptic digestion. Peptides were separated by nanoflow liquid chromatography and analyzed by tandem mass spectrometry (LC-MS/MS). The MS/MS spectra obtained were searched against a database of MCMV open reading frames (ORFs) predicted to be protein coding by an MCMV-specific version of the gene prediction algorithm GeneMarkS. We identified 38 proteins from the capsid, tegument, glycoprotein, replication, and immunomodulatory protein families, as well as 20 genes of unknown function. Observed irregularities in coding potential suggested possible sequence errors in the 3-proximal ends of m20 and M31. These errors were experimentally confirmed by sequencing analysis. The MS data further indicated the presence of peptides derived from the unannotated ORFs ORF c225441-226898 (m166.5) and ORF 105932-106072 . Immunoblot experiments confirmed expression of m166.5 during viral infection.Murine cytomegalovirus (MCMV), a member of the betaherpesvirus family, shares 45.2% sequence identity with human CMV (HCMV) and is currently the most commonly used animal model for the study of CMV-induced disease. The MCMV genome has a size of 230 kbp and was originally estimated to encode 170 proteins (45). The MCMV virion consists of double-stranded viral DNA surrounded by an icosahedral capsid, a complex proteinaceous tegument, and a lipid membrane (34). Although the composition of HCMV particles has been addressed (3, 10), the protein composition of the MCMV virion has not been examined in detail.The majority of MCMV genes have been annotated based on their homologues in HCMV (45) and, consequently, many open reading frames (ORFs), including genes encoding some structural proteins, lack experimental confirmation. Analysis of regions unique to MCMV has been even more limited. There is, therefore, a need for characterization of the composition of MCMV particles, as well as the confirmation of putative structural and functional homologues of HCMV gene products.The traditional method of analyzing the protein composition of a virus preparation consists of denaturation in sodium dodecyl sulfate (SDS), separation of the constituent proteins by electrophoresis, and identification either by immunological methods or by sequencing of visible bands via Edman degradation or mass spectrometry (MS). This approach has been used to analyze other herpesvirus family members, such as HCMV (3), murine gammaherpesvirus 68 (9), Epstein-Barr virus (18), and Kaposi's sarcoma-associated herpesvirus (36). Direct digestion of viral particles and "shotgun" sequencing by liquid chromatography-tandem MS (LC-MS/MS) was first explored with the much simpler adenovirus type 5 proteome (13). Although adenovirus p...

show abstract

Complete Nucleotide Sequence of the Mycoplasma Virus P1 Genome

Cited by 34 publications

References 20 publications

Bacteriophages and their genomes

Bacteriophages and their genomes

Genomics of Bacterial and Archaeal Viruses: Dynamics within the Prokaryotic Virosphere

Identification of Proteins Associated with Murine Cytomegalovirus Virions

Contact Info

Product

Resources

About