Packaging and reverse transcription of snRNAs by retroviruses may generate pseudogenes

Giles, Keith E.; Caputi, Massimo; Beemon, Karen

doi:10.1261/rna.2150604

Cited by 34 publications

(39 citation statements)

References 56 publications

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“…A recent report demonstrated that Rous sarcoma virus particles contain cellular spliceosomal RNAs, with U6 snRNA being the most abundant (22). Here, MLV Northern blots were probed for U1, U2, U4, U5, and U6 spliceosomal RNAs and for 7SK small nuclear RNA, a 330-nt-long RNA that acts as a negative regulator of the transcription factor p-TEFb (17) (Fig.…”

Section: Resultsmentioning

confidence: 96%

“…Early work on the RNA content of RSV particles demonstrated that along with the dimer of viral RNA, 7S RNA (now known as 7SL or SRP RNA, the RNA component of the signal recognition particle [29]), 4S RNA, 5S rRNA, and trace amounts of 28S and 18S ribosomal RNAs were also present (9,21,36,46). Furthermore, in RSV, the packaging of cellular mRNA has been suggested (2), and a recent report showed that cellular spliceosomal RNAs, especially U6 snRNA, are also packaged (22).…”

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confidence: 99%

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Nonrandom Packaging of Host RNAs in Moloney Murine Leukemia Virus

Onafuwa-Nuga

King

Telesnitsky

2005

J Virol

107

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Moloney murine leukemia virus (MLV) particles contain both viral genomic RNA and an assortment of host cell RNAs. Packaging of virus-encoded RNA is selective, with virions virtually devoid of spliced env mRNA and highly enriched for unspliced genome. Except for primer tRNA, it is unclear whether packaged host RNAs are randomly sampled from the cell or specifically encapsidated. To address possible biases in host RNA sampling, the relative abundances of several host RNAs in MLV particles and in producer cells were compared. Using 7SL RNA as a standard, some cellular RNAs, such as those of the Ro RNP, were found to be enriched in MLV particles in that their ratios relative to 7SL differed little, if at all, from their ratios in cells. Some RNAs were underrepresented, with ratios relative to 7SL several orders of magnitude lower in virions than in cells, while others displayed intermediate values. At least some enriched RNAs were encapsidated by genome-defective nucleocapsid mutants. Virion RNAs were not a random sample of the cytosol as a whole, since some cytoplasmic RNAs like tRNA Met were vastly underrepresented, while U6 spliceosomal RNA, which functions in the nucleus, was enriched. Real-time PCR demonstrated that env mRNA, although several orders of magnitude less abundant than unspliced viral RNA, was slightly enriched relative to actin mRNA in virions. These data demonstrate that certain host RNAs are nearly as enriched in virions as genomic RNA and suggest that ⌿ ؊ mRNAs and some other host RNAs may be specifically excluded from assembly sites.Host cell RNA packaging has been observed in several viruses, including DNA viruses such as human cytomegalovirus (54) and herpes simplex virus type 1 (50), RNA viruses such as flock house virus (49), and several retroviruses (9,11,15,16,20). In the herpesviruses, cellular mRNAs are reportedly packaged in a random fashion, most likely representative of their intracellular abundance (50, 54). For retroviruses, the primer tRNA is specifically recruited, and mRNAs are thought to a represent a random sampling (37, 41), but it is unclear whether encapsidation is random among most remaining groups of cellular RNAs.From the mixture of viral and cellular transcripts in the infected cell, two copies of genomic RNA are selected for incorporation into each retroviral particle (7, 36). Virus-encoded RNAs within a Moloney murine leukemia virus (MLV)-infected cell include the capped and polyadenylated unspliced primary transcript as well as spliced env mRNA. Unspliced MLV RNAs contain a ϳ350-nucleotide (nt) region near their 5Ј ends termed the packaging signal, or ⌿ (38), which lies downstream of the splice donor site and upstream of the gag start codon. MLV RNAs that contain ⌿ are packaged at least 100-fold more efficiently than RNAs that lack ⌿ (38). Although other viral sequences and motifs have been implicated in facilitating the specific recruitment of RNAs for packaging (6,7,42,57), the selective encapsidation of MLV and other retroviral genomes is largely attributed to the...

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Section: Resultsmentioning

confidence: 96%

mentioning

confidence: 99%

Nonrandom Packaging of Host RNAs in Moloney Murine Leukemia Virus

Onafuwa-Nuga

King

Telesnitsky

2005

J Virol

107

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“…2C). Thus, although Y RNAs and vault RNA are both stoichiometric components of MLV virions (Garcia et al 2009;Eckwahl et al 2015) and U6 snRNA is present in 1 copy per RSV virion (Giles et al 2004), these ncRNAs do not appear to be major components of our HIV-1 virions.…”

Section: Sl Is the Major Host Cell Rna In Virionsmentioning

confidence: 94%

Analysis of the human immunodeficiency virus-1 RNA packageome

Eckwahl

Arnion

Kharytonchyk

et al. 2016

RNA

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All retroviruses package cellular RNAs into virions. Studies of murine leukemia virus (MLV) revealed that the major host cell RNAs encapsidated by this simple retrovirus were LTR retrotransposons and noncoding RNAs (ncRNAs). Several classes of ncRNAs appeared to be packaged by MLV shortly after synthesis, as precursors to tRNAs, small nuclear RNAs, and small nucleolar RNAs were all enriched in virions. To determine the extent to which the human immunodeficiency virus (HIV-1) packages similar RNAs, we used high-throughput sequencing to characterize the RNAs within infectious HIV-1 virions produced in CEM-SS T lymphoblastoid cells. We report that the most abundant cellular RNAs in HIV-1 virions are 7SL RNA and transcripts from numerous divergent and truncated members of the long interspersed element (LINE) and short interspersed element (SINE) families of retrotransposons. We also detected precursors to several tRNAs and small nuclear RNAs as well as transcripts derived from the ribosomal DNA (rDNA) intergenic spacers. We show that packaging of a pre-tRNA requires the nuclear export receptor Exportin 5, indicating that HIV-1 recruits at least some newly made ncRNAs in the cytoplasm. Together, our work identifies the set of RNAs packaged by HIV-1 and reveals that early steps in HIV-1 assembly intersect with host cell ncRNA biogenesis pathways.

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“…On vRNA binding, Gag forms a dimer or oligomer (30) that exposes the p10 NES or increases its affinity for CRM1-RanGTP, leading to export of the viral ribonucleoprotein complex through the nuclear pore. Although ψ-RNA selectively promotes Gag:CRM1 binding, considering that only two copies of vRNA are incorporated into each virion, it is possible that other RNAs in the nucleus [e.g., U6 and other small RNAs enriched in retroviral particles (31)(32)(33)(34)] might also bind Gag to stimulate nuclear export. Once in the cytoplasm, the MA and NC regions of Gag do not reassociate with importins because they are engaged in higher affinity interactions with RNA.…”

Section: Nucleic Acids Stimulate Cooperative Binding Of Gag To the Numentioning

confidence: 99%

Directionality of nucleocytoplasmic transport of the retroviral gag protein depends on sequential binding of karyopherins and viral RNA

Gudleski¹,

Flanagan²,

Ryan

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

105

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Retroviral Gag polyproteins coopt host factors to traffic from cytosolic ribosomes to the plasma membrane, where virions are released. Before membrane transport, the multidomain Gag protein of Rous sarcoma virus (RSV) undergoes importin-mediated nuclear import and CRM1-dependent nuclear export, an intrinsic step in the assembly pathway. Transient nuclear trafficking of Gag is required for efficient viral RNA (vRNA) encapsidation, suggesting that Gag: vRNA binding might occur in the nucleus. Here, we show that Gag is imported into the nucleus through direct interactions of the Gag NC domain with importin-α (imp-α) and the MA domain with importin-11 (imp-11). The vRNA packaging signal, known as ψ, inhibited imp-α binding to Gag, indicating that the NC domain does not bind to imp-α and vRNA simultaneously. Unexpectedly, vRNA binding also prevented the association of imp-11 with both the MA domain alone and with Gag, suggesting that the MA domain may bind to the vRNA genome. In contrast, direct binding of Gag to the nuclear export factor CRM1, via the CRM1-RanGTP heterodimer, was stimulated by ψRNA. These findings suggest a model whereby the genomic vRNA serves as a switch to regulate the ordered association of host import/export factors that mediate Gag nucleocytoplasmic trafficking for virion assembly. The Gag:vRNA interaction appears to serve multiple critical roles in assembly: specific selection of the vRNA genome for packaging, stimulating the formation of Gag dimers, and triggering export of viral ribonucleoprotein complexes from the nucleus.protein-RNA binding | retrovirus assembly | importin-α/β | importin-11 | CRM1

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Packaging and reverse transcription of snRNAs by retroviruses may generate pseudogenes

Cited by 34 publications

References 56 publications

Nonrandom Packaging of Host RNAs in Moloney Murine Leukemia Virus

Nonrandom Packaging of Host RNAs in Moloney Murine Leukemia Virus

Analysis of the human immunodeficiency virus-1 RNA packageome

Directionality of nucleocytoplasmic transport of the retroviral gag protein depends on sequential binding of karyopherins and viral RNA

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