Organization and Transcription of the Simian Virus 40 Genome

Lebowitz, Paul; Weissman, S

doi:10.1007/978-3-642-67344-3_3

Cited by 82 publications

(43 citation statements)

References 487 publications

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“…Protein sequences associated with the reference genomes for 27 polyomaviruses were obtained from GenBank; these included baboon polyomavirus (NC_007611; SA12) (6), bat polyomavirus (NC_011310; BatPyV) (32), B-lymphotropic polyomavirus (NC_004763; LPyV) (34), BKPyV (NC_001538) (43), Bornean orangutan polyomavirus (NC_013439; OraV1) (17), bovine polyomavirus (NC_001442; BPyV) (41), California sea lion polyomavirus (NC_013796; SLPyV) (8), hamster polyomavirus (NC_001663; HaPyV) (9), JCPyV (NC_001699) (12), MCPyV (HM011557) (40), murine pneumotropic virus (NC_001505; MPtV) (31), murine polyomavirus (NC_001515; MPyV) (16), simian virus 40 (NC_001669; SV40) (27), squirrel monkey polyomavirus (NC_009951; SqPyV) (46), Sumatran orangutan polyomavirus (FN356901; OraV2) (17), TSPyV (NC_014361) (45), HPyV6 (NC_014406) (40), HPyV7 (NC_014407) (40), KIPyV (NC_009238) (2), WUPyV (NC_009539) (13), avian polyomavirus (NC_004764; APyV) (39), canary polyomavirus (GU345044; CaPyV) (19), crow polyomavirus (NC_007922; CPyV) (23), finch polyomavirus (NC_007923; FPyV) (23), goose hemorrhagic polyomavirus (NC_004800; GHV) (22), chimpanzee polyomavirus (NC_014743; ChPyV) (10), and HPyV9 (NC_015150) (42). The predicted open reading frames for MWPyV LTAg, VP1, and VP2 were aligned with the corresponding proteins from the 27 known polyomaviruses using Fast Statistical Alignment (FSA) software, version 1.15.2 (5).…”

Section: Methodsmentioning

confidence: 99%

Identification of MW Polyomavirus, a Novel Polyomavirus in Human Stool

Siebrasse

Reyes

Lim

et al. 2012

J Virol

172

152

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We have discovered a novel polyomavirus present in multiple human stool samples. The virus was initially identified by shotgun pyrosequencing of DNA purified from virus-like particles isolated from a stool sample collected from a healthy child from Malawi. We subsequently sequenced the virus' 4,927-bp genome, which has been provisionally named MW polyomavirus (MWPyV). The virus has genomic features characteristic of the family Polyomaviridae but is highly divergent from other members of this family. It is predicted to encode the large T antigen and small T antigen early proteins and the VP1, VP2, and VP3 structural proteins. A real-time PCR assay was designed and used to screen 514 stool samples from children with diarrhea in St. Louis, MO; 12 specimens were positive for MWPyV. Comparison of the whole-genome sequences of the index Malawi case and one St. Louis case demonstrated that the two strains of MWPyV varied by 5.3% at the nucleotide level. The number of polyomaviruses found in the human body continues to grow, raising the question of how many more species have yet to be identified and what roles they play in humans with and without manifest disease.

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Section: Methodsmentioning

confidence: 99%

Identification of MW Polyomavirus, a Novel Polyomavirus in Human Stool

Siebrasse

Reyes

Lim

et al. 2012

J Virol

172

152

View full text Add to dashboard Cite

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“…Equimolar concentrations of the two samples were ligated at a final concentration of 25 FLg/ml, and the ligation products were used to transform HB101 cells. Ampicillin-resistant colonies were screened by colony hybridization for plasmids which contained the 2,672-bp pBR322 fragment (extending from the BamHI site at 375 nucleotides [nt] [45] counterclockwise to the Sall-converted PvuII site at 2067 nt) linked to the 2,978-bp SV40 fragment (extending from the Sallconverted PvuII site at map position 0.711 to the unique BamHI site at position 0.144 [29] 25 Lg/ml. The ligation products were used to transform HB101 cells, and ampicillin-resistant colonies were screened by colony hybridization for plasmids in which the 1,729-bp SV40 fragment of pSVt extending from the Bgil site to the Sal-converted PvuII site at map position 0.330 had been replaced by the 2,702-bp SV40 fragment which extends from the BglI site at position 0.661 to the Sall-converted BamHI site, which contains the entire SV40 early region.…”

Section: Methodsmentioning

confidence: 99%

Transient expression of a mouse alpha-fetoprotein minigene: deletion analyses of promoter function.

Scott¹,

Tilghman²

1983

Mol. Cell. Biol.

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“…to 20 h after infection, the majority of the viral RNA and proteins are the product of the E-strand-specific transcription unit. The onset of viral DNA replication that occurs after this time interval marks the beginning of the late phase in which the L-strand-specific transcription unit is activated, resulting in the synthesis of a 20 to 100-fold excess of L-strand RNA over E-strand RNA (and a 5,000-fold excess over the L-strand RNA that can be detected early in infection) (27,39). Although no SV40 DNA replication has been detected in oocytes (17), a similar high ratio of L-strand to E-strand RNA has been observed 24 to 48 h after injection of viral DNA (29).…”

mentioning

confidence: 99%

Regulation of simian virus 40 gene expression in Xenopus laevis oocytes.

Michaeli¹,

Prives²

1985

Mol. Cell. Biol.

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Expression of the simian virus 40 (SV40) early and late regions was examined in Xenopus laevis oocytes microinjected with viral DNA. In contrast to the situation in monkey cells, both late-strand-specific (L-strand) RNA and early-strand-specific (E-strand) RNA could be detected as early as 2 h after inJection. At all time points tested thereafter, L-strand RNA was synthesized in excess over E-strand RNA. Significantly greater quantities of L-strand, relative to E-strand, RNA were detected over a 100-fold range of DNA concentrations injected. Analysis of the subcellular distribution of [35S]methionine-labeled viral proteins revealed that while the majority of the VP-1 and all detectable small t antigen were found in the oocyte cytoplasm, most of the large T antigen was located in the oocyte nucleus. The presence of the large T antigen in the nucleus led us to investigate whether this viral product influences the relative synthesis of late or early RNA in the oocyte as it does in infected monkey cells. Microinjection of either mutant C6 SV40 DNA, which encodes a large T antigen unable to bind specifically to viral regulatory sequences, or deleted viral DNA lacking part of the large T antigen coding sequences yielded ratios of L-strand to E-strand RNA that were similar to those observed with wild-type SV40 DNA. Taken together, these observations suggest that the regulation of SV40 RNA synthesis in X. laevis oocytes occurs by a fundamentally different mechanism than that observed in infected monkey cells. This notion was further supported by the observation that the major 5' ends of L-strand RNA synthesized in oocytes were different from those detected in infected cells. Furthermore, only a subset of those L-strand RNAs were polyadenylated.The permissive host cell for simian virus 40 (SV40) is the kidney cell of the African green monkey. Primary cultures and established cell lines from this tissue respond to viral infection in a temporally regulated manner. The early phase of infection is characterized by transcription of RNA from the early strand (E-strand) of the viral genome, and these RNAs are processed and translated to the large T (L-T) and small t (S-T) tumor antigens. The transition to the late phase is coincident with the onset of viral DNA replication. During the late phase, L-T and S-T antigens continue to be synthesized, but the majority of the viral RNA is transcribed from the opposite late strand (L-strand) of the viral genome. This RNA is processed and translated to the major (VP-1) and minor (VP-2 and VP-3) capsid proteins (for a review see reference 39). Although very small amounts of late RNA have been detected early in lytic (3, 23) or abortive (7) infection, the great increase in this RNA synthesized late in lytic infection is most likely due to more than one factor. First, the number of templates for transcription, arising from the L-T antigen-mediated induction of viral DNA synthesis, increases vastly late in infection. The high ratio of L-to E-strand-specific RNA, then, is most likely due to t...

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Organization and Transcription of the Simian Virus 40 Genome

Cited by 82 publications

References 487 publications

Identification of MW Polyomavirus, a Novel Polyomavirus in Human Stool

Identification of MW Polyomavirus, a Novel Polyomavirus in Human Stool

Transient expression of a mouse alpha-fetoprotein minigene: deletion analyses of promoter function.

Regulation of simian virus 40 gene expression in Xenopus laevis oocytes.

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