Splicing of human immunodeficiency virus RNA is position-dependent suggesting sequential removal of introns from the 5′ end

Transcription of the HIV-1 genome yields a single primary transcript, which is alternatively spliced to >30 mRNAs. Productive infection depends on inefficient and regulated splicing and appears to proceed in a tight 5′ to 3′ order. To analyse whether sequential splicing is mediated by the quality of splice sites or by the position of an intron, we inserted the efficient β-globin intron (BGI) into the 3′ region or 5′UTR of a subgenomic expression vector or an infectious proviral plasmid. RNA analysis revealed splicing of the 3′ BGI only if all upstream introns were removed, while splicing of the same intron in the 5′UTR was efficient and independent of further splicing. Furthermore, mutation of the upstream splice signal in the subgenomic vector did not eliminate the inhibition of 3′ splicing, although the BGI sequence was the only intron in this case. These results suggest that downstream splicing of HIV-1 RNAs is completely dependent on prior splicing of all upstream intron(s). This hypothesis was supported by the mutation of the major 5′ splice site in the HIV-1 genome, which completely abolished all splicing. It appears likely that the tight order of splicing is important for HIV-1 replication, which requires the stable production of intron containing RNAs, while splicing of 3′ introns on incompletely spliced RNAs would be likely to render them subject to nonsense-mediated decay

Mutation of the major 5′ splice site renders a CMV-driven HIV-1 proviral clone Tat-dependent: connections between transcription and splicing

AbstractEfficient transcription from the human immunodeficiency virus type 1 long terminal repeat (HIV-1 LTR) promoter is dependent on the viral transactivator Tat. To generate a Tat-independent proviral plasmid, we replaced the promoter in the HIV-1 LTR with the immediate early promoter of cytomegalovirus. Transfection of this plasmid yielded Tat-independent production of infectious HIV-1. Tat-independent expression was lost, however, when the major 5′ splice site in the HIV-1 genome was mutated and no HIV-1-specific RNA or protein was detected. This defect was restored when a Tat expression plasmid was cotransfected. Our results support recent reports indicating an influence of the recognition of splice sites on efficient transcriptional elongation

Limited complementarity between U1 snRNA and a retroviral 5′ splice site permits its attenuation via RNA secondary structure

Multiple types of regulation are used by cells and viruses to control alternative splicing. In murine leukemia virus, accessibility of the 5′ splice site (ss) is regulated by an upstream region, which can fold into a complex RNA stem–loop structure. The underlying sequence of the structure itself is negligible, since most of it could be functionally replaced by a simple heterologous RNA stem–loop preserving the wild-type splicing pattern. Increasing the RNA duplex formation between U1 snRNA and the 5′ss by a compensatory mutation in position +6 led to enhanced splicing. Interestingly, this mutation affects splicing only in the context of the secondary structure, arguing for a dynamic interplay between structure and primary 5′ss sequence. The reduced 5′ss accessibility could also be counteracted by recruiting a splicing enhancer domain via a modified MS2 phage coat protein to a single binding site at the tip of the simple RNA stem–loop. The mechanism of 5′ss attenuation was revealed using hyperstable U1 snRNA mutants, showing that restricted U1 snRNP access is the cause of retroviral alternative splicing

New Way of Regulating Alternative Splicing in Retroviruses: the Promoter Makes a Difference

Alternative splicing has been recognized as a major mechanism for creating proteomic diversity from a limited number of genes. However, not all determinants regulating this process have been characterized. Using subviral human immunodeficiency virus (HIV) env constructs we observed an enhanced splicing of the RNA when expression was under control of the cytomegalovirus (CMV) promoter instead of the HIV long terminal repeat (LTR). We extended these observations to LTR- or CMV-driven murine leukemia proviruses, suggesting that retroviral LTRs are adapted to inefficient alternative splicing at most sites in order to maintain balanced gene expression

Site specific target binding controls RNA cleavage efficiency by the Kaposi's sarcoma-associated herpesvirus endonuclease SOX.

A number of viruses remodel the cellular gene expression landscape by globally accelerating messenger RNA (mRNA) degradation. Unlike the mammalian basal mRNA decay enzymes, which largely target mRNA from the 5' and 3' end, viruses instead use endonucleases that cleave their targets internally. This is hypothesized to more rapidly inactivate mRNA while maintaining selective power, potentially though the use of a targeting motif(s). Yet, how mRNA endonuclease specificity is achieved in mammalian cells remains largely unresolved. Here, we reveal key features underlying the biochemical mechanism of target recognition and cleavage by the SOX endonuclease encoded by Kaposi's sarcoma-associated herpesvirus (KSHV). Using purified KSHV SOX protein, we reconstituted the cleavage reaction in vitro and reveal that SOX displays robust, sequence-specific RNA binding to residues proximal to the cleavage site, which must be presented in a particular structural context. The strength of SOX binding dictates cleavage efficiency, providing an explanation for the breadth of mRNA susceptibility observed in cells. Importantly, we establish that cleavage site specificity does not require additional cellular cofactors, as had been previously proposed. Thus, viral endonucleases may use a combination of RNA sequence and structure to capture a broad set of mRNA targets while still preserving selectivity

Mutation of the HIV-1 5′ss in pNLenv does not relieve the 3′ splice inhibition

<p><b>Copyright information:</b></p><p>Taken from "Splicing of human immunodeficiency virus RNA is position-dependent suggesting sequential removal of introns from the 5′ end"</p><p>Nucleic Acids Research 2005;33(3):825-837.</p><p>Published online 8 Feb 2005</p><p>PMCID:PMC549389.</p><p>© The Author 2005. Published by Oxford University Press. All rights reserved</p> () Schematic depiction of plasmids pNLenvM3 and pNLenvM3BGI. The sequence at the HIV-1 5′ss #4 (wt) and the complementary sequence of the U1 RNA is expanded on top. The three mutations introduced into the 5′ss are depicted below in bold and underlined (M3). () Western blot analysis of HeLa P4 cells transfected with the constructs indicated above each lane. A Tat expression plasmid was cotransfected in all cases. HIV-1 proteins are identified on the right as in . () Northern blot analysis of 10 μg of RNA obtained from the same transfection as in panel B. The upper panel was probed with an LTR-specific probe, the middle panel with a BGI-specific probe, and the bottom panel with a GAPDH-specific probe. The observed RNA species are identified as in ; numbering is according to the drawing in

U1snRNP-mediated suppression of polyadenylation in conjunction with the RNA structure controls poly (A) site selection in foamy viruses

Background During reverse transcription, retroviruses duplicate the long terminal repeats (LTRs). These identical LTRs carry both promoter regions and functional polyadenylation sites. To express full-length transcripts, retroviruses have to suppress polyadenylation in the 5′LTR and activate polyadenylation in the 3′LTR. Foamy viruses have a unique LTR structure with respect to the location of the major splice donor (MSD), which is located upstream of the polyadenylation signal. Results Here, we describe the mechanisms of foamy viruses regulating polyadenylation. We show that binding of the U1 small nuclear ribonucleoprotein (U1snRNP) to the MSD suppresses polyadenylation at the 5′LTR. In contrast, polyadenylation at the 3′LTR is achieved by adoption of a different RNA structure at the MSD region, which blocks U1snRNP binding and furthers RNA cleavage and subsequent polyadenylation. Conclusion Recently, it was shown that U1snRNP is able to suppress the usage of intronic cryptic polyadenylation sites in the cellular genome. Foamy viruses take advantage of this surveillance mechanism to suppress premature polyadenylation at the 5’end of their RNA. At the 3’end, Foamy viruses use a secondary structure to presumably block access of U1snRNP and thereby activate polyadenylation at the end of the genome. Our data reveal a contribution of U1snRNP to cellular polyadenylation site selection and to the regulation of gene expression