Structural basis of genomic RNA (gRNA) dimerization and packaging determinants of mouse mammary tumor virus (MMTV)

Retrovirology

Tahir A Rizvi²  Roland Marquet³  Farah Mustafa¹  Delphine Richer³  Rawan M Kalloush²  Ayesha Jabeen²  Lizna M Ali²  Valérie Vivet-Boudou³  Suriya J Aktar² 

[1] Department of Biochemistry, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates;Department of Microbiology & Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates;Architecture et Réactivité de l’ARN, CNRS, IBMC, Université de Strasbourg, 15 rue René Descartes, Strasbourg cedex, 67084, France

关键词: Long-range interaction (LRI);    RNA packaging signal;    RNA intermolecular interactions;    Dimerization Initiation Site (DIS);    palindromic (pal) sequence;    RNA packaging;    RNA dimerization;    Mouse mammary tumor virus (MMTV);   

Others  :  1151998
DOI  :  10.1186/s12977-014-0096-6

 received in 2014-05-08, accepted in 2014-10-23,  发布年份 2014

【 摘 要 】

Background

One of the hallmarks of retroviral life cycle is the efficient and specific packaging of two copies of retroviral gRNA in the form of a non-covalent RNA dimer by the assembling virions. It is becoming increasingly clear that the process of dimerization is closely linked with gRNA packaging, and in some retroviruses, the latter depends on the former. Earlier mutational analysis of the 5’ end of the MMTV genome indicated that MMTV gRNA packaging determinants comprise sequences both within the 5’ untranslated region (5’ UTR) and the beginning of gag.

Results

The RNA secondary structure of MMTV gRNA packaging sequences was elucidated employing selective 2’hydroxyl acylation analyzed by primer extension (SHAPE). SHAPE analyses revealed the presence of a U5/Gag long-range interaction (U5/Gag LRI), not predicted by minimum free-energy structure predictions that potentially stabilizes the global structure of this region. Structure conservation along with base-pair covariations between different strains of MMTV further supported the SHAPE-validated model. The 5’ region of the MMTV gRNA contains multiple palindromic (pal) sequences that could initiate intermolecular interaction during RNA dimerization. In vitro RNA dimerization, SHAPE analysis, and structure prediction approaches on a series of pal mutants revealed that MMTV RNA utilizes a palindromic point of contact to initiate intermolecular interactions between two gRNAs, leading to dimerization. This contact point resides within pal II (5’ CGGCCG 3’) at the 5’ UTR and contains a canonical “GC” dyad and therefore likely constitutes the MMTV RNA dimerization initiation site (DIS). Further analyses of these pal mutants employing in vivo genetic approaches indicate that pal II, as well as pal sequences located in the primer binding site (PBS) are both required for efficient MMTV gRNA packaging.

Conclusions

Employing structural prediction, biochemical, and genetic approaches, we show that pal II functions as a primary point of contact between two MMTV RNAs, leading to gRNA dimerization and its subsequent encapsidation into the assembling virus particles. The results presented here enhance our understanding of the MMTV gRNA dimerization and packaging processes and the role of structural motifs with respect to RNA-RNA and possibly RNA-protein interactions that might be taking place during MMTV life cycle.

【 授权许可】

   
2014 Aktar et al.; licensee BioMed Central Ltd.

【 图 表 】

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