title: Naturally arising strains of polyomaviruses with severely attenuated microRNA expression.
abstract: Several different polyomaviruses (PyVs) encode microRNAs (miRNAs) that regulate viral as well as host gene expression. However, the functions of polyomaviral miRNAs, particularly during in vivo infection, remain poorly understood. Here we identify rare naturally arising PyVs that are severely attenuated or null for miRNA expression. We identify hypomorphic or null strains for miRNA expression from rhesus macaque simian virus 40 (SV40) and human JC virus. These strains were isolated from immunocompromised hosts and derive from insertions or deletions in the viral DNA that preserve the amino acid reading frame of opposing-strand large T antigen gene. Characterization of the SV40 miRNA hypomorph, K661, shows that it is inhibited at the early miRNA biogenesis step of Drosha-mediated processing. Despite having a nonrearranged enhancer, which a previous study has shown renders some PyVs more susceptible to the autoregulatory activities of the miRNA, restoring miRNA expression to K661 has little effect on virus growth in either immortalized or primary monkey kidney cells. Thus, in addition to any effect of accompanying genomic elements, these results suggest that the cellular context also determines susceptibility to PyV miRNA-mediated effects. Combined, these results demonstrate that polyomaviruses lacking miRNAs can arise infrequently and that the functional importance of polyomaviral miRNAs is context dependent, consistent with an activity connected to the immune status of the host.
  
  
  OBJECTIVE
  Diverse virus families encode miRNAs, yet much remains unknown about viral miRNA function and contribution to the infectious cycle. Polyomaviruses (PyVs) are small DNA viruses, long known to be important as etiological agents of rare diseases and valuable models of DNA virus infection. Here, in immunosuppressed hosts, we uncover rare naturally arising variants of different PyVs that have lost the ability to express miRNAs. This represents some of the only known natural viruses to have lost miRNA expression. By probing the biogenesis pathways of these variants, we uncover that miRNA expression is lost via small insertions or deletions that render the transcripts resistant to early steps of miRNA biogenesis while preserving the reading frame of the opposing T antigen transcripts. Overall, our study informs how miRNA genes evolve/devolve in viruses and suggests that miRNA function is exquisitely dependent not only on viral genomic context but also on the cellular and host environment.
authors.affiliation: The University of Texas at Austin, Institute for Cellular and Molecular Biology, Department of Molecular Biosciences, Center for Systems and Synthetic Biology, Center for Infectious Disease, Austin, Texas, USA.
authors.forename: Chun Jung
authors.initials: CJ
authors.lastname: Chen
authors.affiliation: The University of Texas at Austin, Institute for Cellular and Molecular Biology, Department of Molecular Biosciences, Center for Systems and Synthetic Biology, Center for Infectious Disease, Austin, Texas, USA.
authors.forename: James M
authors.initials: JM
authors.lastname: Burke
authors.affiliation: The University of Texas at Austin, Institute for Cellular and Molecular Biology, Department of Molecular Biosciences, Center for Systems and Synthetic Biology, Center for Infectious Disease, Austin, Texas, USA.
authors.forename: Rodney P
authors.initials: RP
authors.lastname: Kincaid
authors.affiliation: The University of Texas at Austin, Institute for Cellular and Molecular Biology, Department of Molecular Biosciences, Center for Systems and Synthetic Biology, Center for Infectious Disease, Austin, Texas, USA.
authors.forename: Kristopher D
authors.initials: KD
authors.lastname: Azarm
authors.affiliation: American Chemical Society Project SEED Summer Internship Program, James Bowie High School, Austin, Texas, USA.
authors.forename: Noel
authors.initials: N
authors.lastname: Mireles
authors.affiliation: Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA.
authors.forename: Janet S
authors.initials: JS
authors.lastname: Butel
authors.affiliation: The University of Texas at Austin, Institute for Cellular and Molecular Biology, Department of Molecular Biosciences, Center for Systems and Synthetic Biology, Center for Infectious Disease, Austin, Texas, USA Chris_sullivan@austin.utexas.edu.
authors.forename: Christopher S
authors.initials: CS
authors.lastname: Sullivan
mesh_terms: D000818:Animals; D002460:Cell Line; D015967:Gene Expression Regulation, Viral; D006801:Humans; D016867:Immunocompromised Host; D007577:JC Virus / Q000235:genetics* / Q000302:isolation & purification / Q000502:physiology; D008253:Macaca mulatta; D035683:MicroRNAs / Q000096:biosynthesis* / Q000235:genetics; D016254:Mutagenesis, Insertional; D027601:Polyomavirus Infections / Q000662:veterinary* / Q000821:virology*; D017384:Sequence Deletion; D013539:Simian virus 40 / Q000235:genetics* / Q000302:isolation & purification / Q000502:physiology; D014779:Virus Replication
chemical_list: D035683:MicroRNAs