title: Mechanistic differences between HIV-1 and SIV nucleocapsid proteins and cross-species HIV-1 genomic RNA recognition.
abstract: BACKGROUND
  The nucleocapsid (NC) domain of HIV-1 Gag is responsible for specific recognition and packaging of genomic RNA (gRNA) into new viral particles. This occurs through specific interactions between the Gag NC domain and the Psi packaging signal in gRNA. In addition to this critical function, NC proteins are also nucleic acid (NA) chaperone proteins that facilitate NA rearrangements during reverse transcription. Although the interaction with Psi and chaperone activity of HIV-1 NC have been well characterized in vitro, little is known about simian immunodeficiency virus (SIV) NC. Non-human primates are frequently used as a platform to study retroviral infection in vivo; thus, it is important to understand underlying mechanistic differences between HIV-1 and SIV NC.
  
  
  RESULTS
  Here, we characterize SIV NC chaperone activity for the first time. Only modest differences are observed in the ability of SIV NC to facilitate reactions that mimic the minus-strand annealing and transfer steps of reverse transcription relative to HIV-1 NC, with the latter displaying slightly higher strand transfer and annealing rates. Quantitative single molecule DNA stretching studies and dynamic light scattering experiments reveal that these differences are due to significantly increased DNA compaction energy and higher aggregation capability of HIV-1 NC relative to the SIV protein. Using salt-titration binding assays, we find that both proteins are strikingly similar in their ability to specifically interact with HIV-1 Psi RNA. In contrast, they do not demonstrate specific binding to an RNA derived from the putative SIV packaging signal.
  
  
  CONCLUSIONS
  Based on these studies, we conclude that (1) HIV-1 NC is a slightly more efficient NA chaperone protein than SIV NC, (2) mechanistic differences between the NA interactions of highly similar retroviral NC proteins are revealed by quantitative single molecule DNA stretching, and (3) SIV NC demonstrates cross-species recognition of the HIV-1 Psi RNA packaging signal.
authors.affiliation: Section on Viral Gene Regulation, Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892-2780, USA.
authors.forename: Klara
authors.initials: K
authors.lastname: Post
authors.affiliation: Department of Chemistry and Biochemistry, Center for Retrovirus Research, and Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA.
authors.forename: Erik D
authors.initials: ED
authors.lastname: Olson
authors.affiliation: Department of Physics, Northeastern University, Boston, MA, 02115, USA.
authors.forename: M Nabuan
authors.initials: MN
authors.lastname: Naufer
authors.affiliation: AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, 21702-1201, USA.
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Gorelick
authors.affiliation: Department of Chemistry and Biochemistry, Center for Retrovirus Research, and Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA.
authors.forename: Ioulia
authors.initials: I
authors.lastname: Rouzina
authors.affiliation: Department of Physics, Northeastern University, Boston, MA, 02115, USA. ma.williams@northeastern.edu.
authors.forename: Mark C
authors.identifier: http://orcid.org/0000-0003-3219-376X
authors.initials: MC
authors.lastname: Williams
authors.affiliation: Department of Chemistry and Biochemistry, Center for Retrovirus Research, and Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA. musier-forsyth.1@osu.edu.
authors.forename: Karin
authors.initials: K
authors.lastname: Musier-Forsyth
authors.affiliation: Section on Viral Gene Regulation, Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892-2780, USA. levinju@mail.nih.gov.
authors.forename: Judith G
authors.identifier: http://orcid.org/0000-0002-6327-8216
authors.initials: JG
authors.lastname: Levin
mesh_terms: D016679:Genome, Viral; D015497:HIV-1 / Q000737:chemistry* / Q000235:genetics; D006801:Humans; D018832:Molecular Chaperones / Q000737:chemistry / Q000502:physiology; D009690:Nucleic Acid Conformation; D019590:Nucleocapsid Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D011485:Protein Binding; D012367:RNA, Viral / Q000235:genetics*; D048348:Reverse Transcription; D015302:Simian Immunodeficiency Virus / Q000737:chemistry* / Q000235:genetics; D054301:gag Gene Products, Human Immunodeficiency Virus / Q000737:chemistry / Q000235:genetics
chemical_list: D018832:Molecular Chaperones; D019590:Nucleocapsid Proteins; D012367:RNA, Viral; D054301:gag Gene Products, Human Immunodeficiency Virus
keywords: HIV-1; Minus-strand transfer; Nucleic acid binding; Nucleic acid chaperone activity; Nucleocapsid proteins; Psi RNA packaging signal; Reverse transcription; SIV; Single molecule DNA stretching; Small angle X-ray scattering