TY - JOUR
T1 - A G-C-Rich Palindromic Structural Motif and a Stretch of Single-Stranded Purines Are Required for Optimal Packaging of Mason-Pfizer Monkey Virus (MPMV) Genomic RNA
AU - Jaballah, Soumeya Ali
AU - Aktar, Suriya J.
AU - Ali, Jahabar
AU - Phillip, Pretty Susan
AU - Al Dhaheri, Noura Salem
AU - Jabeen, Aayesha
AU - Rizvi, Tahir A.
N1 - Funding Information:
This research was funded primarily by a grant from Emirates Foundation ( 2009/044 to T.A.R.) and in part by new project grants ( NP 08/17 and NP 09/18 ) from the Faculty of Medicine and Health Sciences, UAE University, to T.A.R. We express our thanks to Dr. Didier Trono (Ecole Polytechnique Fédérale de Lausanne, Switzerland) for providing MD.G. and Dr. Eric Hunter (Emory University, Atlanta, GA) for providing MPMV molecular clone and MPMV Gag/Pol polyclonal serum. We also wish to thank Ms. Jaicy George, Department of Microbiology and Immunology, Faculty of Medicine and Health Sciences, UAE University, for her assistance during the course of these experiments and Ms. Akela Ghazawi, Department of Microbiology and Immunology, Faculty of Medicine and Health Sciences, UAE University, for stimulating discussions. We also wish to thank Professor Andrew Lever and Dr. Julia Kenyon, Addenbrook's Hospital, Cambridge University, Cambridge, UK, for their input on RNA structure predictions.
PY - 2010/9
Y1 - 2010/9
N2 - During retroviral RNA packaging, two copies of genomic RNA are preferentially packaged into the budding virus particles whereas the spliced viral RNAs and the cellular RNAs are excluded during this process. Specificity towards retroviral RNA packaging is dependent upon sequences at the 5' end of the viral genome, which at times extend into Gag sequences. It has earlier been suggested that the Mason-Pfizer monkey virus (MPMV) contains packaging sequences within the 5' untranslated region (UTR) and Gag. These studies have also suggested that the packaging determinants of MPMV that lie in the UTR are bipartite and are divided into two regions both upstream and downstream of the major splice donor. However, the precise boundaries of these discontinuous regions within the UTR and the role of the intervening sequences between these dipartite sequences towards MPMV packaging have not been investigated. Employing a combination of genetic and structural prediction analyses, we have shown that region "A", immediately downstream of the primer binding site, is composed of 50 nt, whereas region "B" is composed of the last 23 nt of UTR, and the intervening 55 nt between these two discontinuous regions do not contribute towards MPMV RNA packaging. In addition, we have identified a 14-nt G-C-rich palindromic sequence (with 100% autocomplementarity) within region A that has been predicted to fold into a structural motif and is essential for optimal MPMV RNA packaging. Furthermore, we have also identified a stretch of single-stranded purines (ssPurines) within the UTR and 8 nt of these ssPurines are duplicated in region B. The native ssPurines or its repeat in region B when predicted to refold as ssPurines has been shown to be essential for RNA packaging, possibly functioning as a potential nucleocapsid binding site. Findings from this study should enhance our understanding of the steps involved in MPMV replication including RNA encapsidation process.
AB - During retroviral RNA packaging, two copies of genomic RNA are preferentially packaged into the budding virus particles whereas the spliced viral RNAs and the cellular RNAs are excluded during this process. Specificity towards retroviral RNA packaging is dependent upon sequences at the 5' end of the viral genome, which at times extend into Gag sequences. It has earlier been suggested that the Mason-Pfizer monkey virus (MPMV) contains packaging sequences within the 5' untranslated region (UTR) and Gag. These studies have also suggested that the packaging determinants of MPMV that lie in the UTR are bipartite and are divided into two regions both upstream and downstream of the major splice donor. However, the precise boundaries of these discontinuous regions within the UTR and the role of the intervening sequences between these dipartite sequences towards MPMV packaging have not been investigated. Employing a combination of genetic and structural prediction analyses, we have shown that region "A", immediately downstream of the primer binding site, is composed of 50 nt, whereas region "B" is composed of the last 23 nt of UTR, and the intervening 55 nt between these two discontinuous regions do not contribute towards MPMV RNA packaging. In addition, we have identified a 14-nt G-C-rich palindromic sequence (with 100% autocomplementarity) within region A that has been predicted to fold into a structural motif and is essential for optimal MPMV RNA packaging. Furthermore, we have also identified a stretch of single-stranded purines (ssPurines) within the UTR and 8 nt of these ssPurines are duplicated in region B. The native ssPurines or its repeat in region B when predicted to refold as ssPurines has been shown to be essential for RNA packaging, possibly functioning as a potential nucleocapsid binding site. Findings from this study should enhance our understanding of the steps involved in MPMV replication including RNA encapsidation process.
KW - Mason-Pfizer Monkey Virus (MPMV)
KW - Palindromic sequence
KW - RNA secondary-structure predictions
KW - Retroviral RNA packaging
KW - Single-stranded purines
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U2 - 10.1016/j.jmb.2010.06.043
DO - 10.1016/j.jmb.2010.06.043
M3 - Article
C2 - 20600114
AN - SCOPUS:77955560291
SN - 0022-2836
VL - 401
SP - 996
EP - 1014
JO - Journal of Molecular Biology
JF - Journal of Molecular Biology
IS - 5
ER -