title: Sp1 sites in the noncoding control region of BK polyomavirus are key regulators of bidirectional viral early and late gene expression.
abstract: In kidney transplant patients with BK polyomavirus (BKPyV) nephropathy, viral variants arise bearing rearranged noncoding control regions (rr-NCCRs) that increase viral early gene expression, replicative fitness, and cytopathology. rr-NCCRs result from various deletions and duplications of archetype NCCR (ww-NCCR) sequences, which alter transcription factor binding sites (TFBS). However, the role of specific TFBS is unclear. We inactivated 28 TFBS in the archetype NCCR by selective point mutations and examined viral gene expression in bidirectional reporter constructs. Compared to the archetype, group 1 mutations increased viral early gene expression similar to rr-NCCR and resulted from inactivating one Sp1 or one Ets1 TFBS near the late transcription start site (TSS). Group 2 mutations conferred intermediate early gene activation and affected NF1, YY1, and p53 sites between early and late TSS. Group 3 mutations decreased early and late gene expression and included two other Sp1 sites near the early TSS. Recombinant viruses bearing group 1 NCCRs showed increased replication in human renal epithelial cells similar to clinical rr-NCCR variants. Group 2 and 3 viruses showed intermediate or no replication, respectively. A literature search revealed unnoticed group 1 mutations in BKPyV nephropathy, hemorrhagic cystitis, and disseminated disease.
  
  
  OBJECTIVE
  The NCCRs of polyomaviruses mediate silent persistence of the viral genome as well as the appropriately timed (re)activation of the viral life cycle. This study indicates that the basal BKPyV NCCR is critically controlled by a hierarchy of single TFBS in the archetype NCCR that direct, modulate, and execute the bidirectional early and late viral gene expression. The results provide new insights into how BKPyV NCCR functions as a viral sensor of host cell signals and shed new light on how transcription factors like Sp1 control bidirectional viral gene expression and contribute to replication and pathology.
authors.affiliation: Transplantation & Clinical Virology, Department Biomedicine (Haus Petersplatz), University of Basel, Basel, Switzerland.
authors.forename: Tobias
authors.initials: T
authors.lastname: Bethge
authors.affiliation: Transplantation & Clinical Virology, Department Biomedicine (Haus Petersplatz), University of Basel, Basel, Switzerland.
authors.forename: Helen A
authors.initials: HA
authors.lastname: Hachemi
authors.affiliation: Transplantation & Clinical Virology, Department Biomedicine (Haus Petersplatz), University of Basel, Basel, Switzerland.
authors.forename: Julia
authors.initials: J
authors.lastname: Manzetti
authors.affiliation: Transplantation & Clinical Virology, Department Biomedicine (Haus Petersplatz), University of Basel, Basel, Switzerland Division Infection Diagnostics, Department Biomedicine (Haus Petersplatz), University of Basel, Basel, Switzerland.
authors.forename: Rainer
authors.initials: R
authors.lastname: Gosert
authors.affiliation: Institute of Molecular Life Sciences, University of Zürich, Zürich, Switzerland.
authors.forename: Walter
authors.initials: W
authors.lastname: Schaffner
authors.affiliation: Transplantation & Clinical Virology, Department Biomedicine (Haus Petersplatz), University of Basel, Basel, Switzerland Division Infection Diagnostics, Department Biomedicine (Haus Petersplatz), University of Basel, Basel, Switzerland Infectious Diseases & Hospital Epidemiology, University Hospital Basel, Basel, Switzerland hans.hirsch@unibas.ch.
authors.forename: Hans H
authors.initials: HH
authors.lastname: Hirsch
mesh_terms: D001739:BK Virus / Q000235:genetics* / Q000378:metabolism; D004279:DNA, Viral / Q000378:metabolism; D015967:Gene Expression Regulation, Viral; D006801:Humans; D027601:Polyomavirus Infections / Q000821:virology*; D011485:Protein Binding; D016329:Sp1 Transcription Factor / Q000378:metabolism*; D014158:Transcription, Genetic; D014764:Viral Proteins / Q000235:genetics* / Q000378:metabolism
chemical_list: D004279:DNA, Viral; D016329:Sp1 Transcription Factor; D014764:Viral Proteins