Bipartite Signal for Genomic RNA Dimerization in Moloney Murine Leukemia Virus

Abstract

Retroviral virions each contain two identical genomic RNA strands that are stably but noncovalently joined in parallel near their 5 ends. For certain viruses, this dimerization has been shown to depend on a unique RNA stem-loop locus, called the dimer initiation site (DIS), that efficiently homodimerizes through a palindromic base sequence in its loop. Previous studies with Moloney murine leukemia virus (Mo-MuLV) identified two alternative DIS loci that can each independently support RNA dimerization in vitro but whose relative contributions are unknown. We now report that both of these loci contribute to the assembly of the Mo-MuLV dimer. Using targeted deletions, point mutagenesis, and antisense oligonucleotides, we found that each of the two stem-loops forms as predicted and contributes independently to dimerization in vitro through a mechanism involving autocomplementary interactions of its loop. Disruption of either DIS locus individually reduced both the yield and the thermal stability of the in vitro dimers, whereas disruption of both eliminated dimerization altogether. Similarly, the thermal stability of virion-derived dimers was impaired by deletion of both DIS elements, and point mutations in either element produced defects in viral replication that correlated with their effects on in vitro RNA dimerization. These findings support the view that in some retroviruses, dimer initiation and stability involve two or more closely linked DIS loci which together align the nascent dimer strands in parallel and in register.Retroviral virions each contain two copies of the singlestranded viral genomic RNA that are stably but noncovalently linked to form a homodimer (17,42). The dimeric genome is believed to promote retroviral replication and recombination by allowing reverse transcriptase to switch from one viral RNA strand to the other whenever it encounters a break in its template. Indirect evidence suggests that the dimerized chromosomes are bound together by direct RNA-RNA linkages along their entire lengths; this scenario could explain, for example, how such dimers remain intact even when both RNA strands are extensively nicked and all virion proteins have been removed (39). However, the nature and locations of the imputed dimer contacts are almost entirely unknown. Indeed, the only site of contact that has been characterized in detail is a short region, known as the dimer linkage site (DLS), that occurs near the 5Ј ends of many or all retroviral genomes (17, 42). The DLS was first defined by electron microscopic examination of dimers extracted from virions, and its appearance and location are well conserved among diverse retroviruses (2,22,28,37,47). It is typically the most stable site of linkage between strands (often the only such site that can survive denaturation in 75% formamide) and hence may be the first to form during dimer assembly in vivo. Viruses carrying mutations in the DLS have been found to contain anomalously dimerized or monomeric RNA (as judged by nondenaturing gel electrophoresis) and al...

Sequences Downstream of the 5′ Splice Donor Site Are Required for both Packaging and Dimerization of Human Immunodeficiency Virus Type 1 RNA

“…In summary, our data provide evidence for the involvement of RNA packaging signals that are located downstream of the 5Ј splice donor site in HIV-1 RNA dimerization. These findings support the notion that multiple RNA elements may be needed for RNA dimerization in retroviruses, as was recently demonstrated in murine leukemia virus (26,32). Since SL3 exhibits high affinity for NC protein, it is proposed that this RNA element may regulate HIV-1 RNA dimerization via interactions with NC.…”

“…Purine quartet structures were also proposed to play a role in RNA dimerization, as shown by in vitro studies performed with synthetic viral RNA fragments (2,26,42). However, virion-derived RNA dimers are not stabilized by potassium, which in general enhances purine quartet structures (11).…”

mRNA Molecules Containing Murine Leukemia Virus Packaging Signals Are Encapsidated as Dimers

“…Studies with transcripts have supported a role for stem-loop B in dimer formation (27); significantly, stem-loops C and D also contribute to the dimerization of MLV transcripts (16) and can independently form a remarkably stable dimer involving pairing between the CG portions of the GACG tetraloops (18,34). In addition, stem-loop BЈ has been reported to contribute to the dimerization of MLV transcripts (40,48) and, in combination with stem-loop B, to the stability of mature MLV dimers (40).…”

Identification and characterization of critical cis-acting sequences within the yeast Ty1 retrotransposon

“…HIV-1 mutants with altered dimer initiation sites also have strand-transfer defects during reverse transcription (Paillart et al 1996a;Shen et al 2000). For MoMuLV RNA, two hairpins that form intermolecular interactions and two additional stem-loops that form intermolecular kissing-loop interactions initiate dimerization, while longer self-complementary sequences are believed to stabilize the dimer (Tounekti et al 1992;Oroudjev et al 1999;Kim and Tinoco 2000;Ly and Parslow 2002). Meanwhile, the sites of dimer initiation and the detailed mechanisms of RNA dimerization and packaging remain poorly known for most retroviruses and retrotransposons.…”