Identification of a new control region in the genome of the DDP strain of BK virus isolated from PBMC

Anna Marta Degener, Valeria Pietropaolo, Cristiana Di Taranto, Li Jin, Franco Ameglio, Paola Cordiali-Fei, Elisabetta Trento, Laura Sinibaldi, Nicola Orsi

Research output: Contribution to journalArticle

20 Citations (Scopus)

Abstract

The various strains of human polyomavirus BK (BKV) show a marked heterogeneity in the noncoding control region (NCCR), which includes the origin of replication and the regulatory region for early and late transcription. A new BKV strain (DDP, U91605) was identified by direct detection and sequencing of PCR products of BKV-NCCR DNA obtained from PBMC samples of HIV-positive or -negative subjects. The DDP strain NCCR sequence showed an organisation not described previously in vivo with the maximum homology with the archetypal strain (WW) (M34048), as compared with those collected in GenBank. Structurally, P68, Q39, and S68 boxes were perfectly conserved, whereas the R63 box was completely deleted. This deletion involves the loss of sequences able to bind cellular factors essential for the DNA transcription, such as NF1 binding sites, normally present twice in the R box and the modification of SP1. It is possible that these rearrangements represent a cause of the loss of the VP1 region observed in 9/22 PBMC samples and never observed in urine isolates, which are similar to the WW strain.

Original languageEnglish
Pages (from-to)413-419
Number of pages7
JournalJournal of Medical Virology
Volume58
Issue number4
DOIs
Publication statusPublished - 1999

Fingerprint

BK Virus
Genome
Replication Origin
Nucleic Acid Regulatory Sequences
DNA
Nucleic Acid Databases
Binding Sites
HIV
Urine
Polymerase Chain Reaction

Keywords

  • Binding sites
  • BKV
  • DDP strain
  • Human polyomavirus
  • NCCR
  • Transcriptional factors

ASJC Scopus subject areas

  • Virology

Cite this

Identification of a new control region in the genome of the DDP strain of BK virus isolated from PBMC. / Degener, Anna Marta; Pietropaolo, Valeria; Di Taranto, Cristiana; Jin, Li; Ameglio, Franco; Cordiali-Fei, Paola; Trento, Elisabetta; Sinibaldi, Laura; Orsi, Nicola.

In: Journal of Medical Virology, Vol. 58, No. 4, 1999, p. 413-419.

Research output: Contribution to journalArticle

Degener, AM, Pietropaolo, V, Di Taranto, C, Jin, L, Ameglio, F, Cordiali-Fei, P, Trento, E, Sinibaldi, L & Orsi, N 1999, 'Identification of a new control region in the genome of the DDP strain of BK virus isolated from PBMC', Journal of Medical Virology, vol. 58, no. 4, pp. 413-419. https://doi.org/10.1002/(SICI)1096-9071(199908)58:4<413::AID-JMV15>3.0.CO;2-W
Degener, Anna Marta ; Pietropaolo, Valeria ; Di Taranto, Cristiana ; Jin, Li ; Ameglio, Franco ; Cordiali-Fei, Paola ; Trento, Elisabetta ; Sinibaldi, Laura ; Orsi, Nicola. / Identification of a new control region in the genome of the DDP strain of BK virus isolated from PBMC. In: Journal of Medical Virology. 1999 ; Vol. 58, No. 4. pp. 413-419.
@article{d91cd739c04b469896ed3d2de1751c48,
title = "Identification of a new control region in the genome of the DDP strain of BK virus isolated from PBMC",
abstract = "The various strains of human polyomavirus BK (BKV) show a marked heterogeneity in the noncoding control region (NCCR), which includes the origin of replication and the regulatory region for early and late transcription. A new BKV strain (DDP, U91605) was identified by direct detection and sequencing of PCR products of BKV-NCCR DNA obtained from PBMC samples of HIV-positive or -negative subjects. The DDP strain NCCR sequence showed an organisation not described previously in vivo with the maximum homology with the archetypal strain (WW) (M34048), as compared with those collected in GenBank. Structurally, P68, Q39, and S68 boxes were perfectly conserved, whereas the R63 box was completely deleted. This deletion involves the loss of sequences able to bind cellular factors essential for the DNA transcription, such as NF1 binding sites, normally present twice in the R box and the modification of SP1. It is possible that these rearrangements represent a cause of the loss of the VP1 region observed in 9/22 PBMC samples and never observed in urine isolates, which are similar to the WW strain.",
keywords = "Binding sites, BKV, DDP strain, Human polyomavirus, NCCR, Transcriptional factors",
author = "Degener, {Anna Marta} and Valeria Pietropaolo and {Di Taranto}, Cristiana and Li Jin and Franco Ameglio and Paola Cordiali-Fei and Elisabetta Trento and Laura Sinibaldi and Nicola Orsi",
year = "1999",
doi = "10.1002/(SICI)1096-9071(199908)58:4<413::AID-JMV15>3.0.CO;2-W",
language = "English",
volume = "58",
pages = "413--419",
journal = "Journal of Medical Virology",
issn = "0146-6615",
publisher = "Wiley-Liss Inc.",
number = "4",

}

TY - JOUR

T1 - Identification of a new control region in the genome of the DDP strain of BK virus isolated from PBMC

AU - Degener, Anna Marta

AU - Pietropaolo, Valeria

AU - Di Taranto, Cristiana

AU - Jin, Li

AU - Ameglio, Franco

AU - Cordiali-Fei, Paola

AU - Trento, Elisabetta

AU - Sinibaldi, Laura

AU - Orsi, Nicola

PY - 1999

Y1 - 1999

N2 - The various strains of human polyomavirus BK (BKV) show a marked heterogeneity in the noncoding control region (NCCR), which includes the origin of replication and the regulatory region for early and late transcription. A new BKV strain (DDP, U91605) was identified by direct detection and sequencing of PCR products of BKV-NCCR DNA obtained from PBMC samples of HIV-positive or -negative subjects. The DDP strain NCCR sequence showed an organisation not described previously in vivo with the maximum homology with the archetypal strain (WW) (M34048), as compared with those collected in GenBank. Structurally, P68, Q39, and S68 boxes were perfectly conserved, whereas the R63 box was completely deleted. This deletion involves the loss of sequences able to bind cellular factors essential for the DNA transcription, such as NF1 binding sites, normally present twice in the R box and the modification of SP1. It is possible that these rearrangements represent a cause of the loss of the VP1 region observed in 9/22 PBMC samples and never observed in urine isolates, which are similar to the WW strain.

AB - The various strains of human polyomavirus BK (BKV) show a marked heterogeneity in the noncoding control region (NCCR), which includes the origin of replication and the regulatory region for early and late transcription. A new BKV strain (DDP, U91605) was identified by direct detection and sequencing of PCR products of BKV-NCCR DNA obtained from PBMC samples of HIV-positive or -negative subjects. The DDP strain NCCR sequence showed an organisation not described previously in vivo with the maximum homology with the archetypal strain (WW) (M34048), as compared with those collected in GenBank. Structurally, P68, Q39, and S68 boxes were perfectly conserved, whereas the R63 box was completely deleted. This deletion involves the loss of sequences able to bind cellular factors essential for the DNA transcription, such as NF1 binding sites, normally present twice in the R box and the modification of SP1. It is possible that these rearrangements represent a cause of the loss of the VP1 region observed in 9/22 PBMC samples and never observed in urine isolates, which are similar to the WW strain.

KW - Binding sites

KW - BKV

KW - DDP strain

KW - Human polyomavirus

KW - NCCR

KW - Transcriptional factors

UR - http://www.scopus.com/inward/record.url?scp=0032770543&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0032770543&partnerID=8YFLogxK

U2 - 10.1002/(SICI)1096-9071(199908)58:4<413::AID-JMV15>3.0.CO;2-W

DO - 10.1002/(SICI)1096-9071(199908)58:4<413::AID-JMV15>3.0.CO;2-W

M3 - Article

VL - 58

SP - 413

EP - 419

JO - Journal of Medical Virology

JF - Journal of Medical Virology

SN - 0146-6615

IS - 4

ER -