Chapter 1 Regulation of HIV-1 Alternative RNA Splicing and Its Role in Virus Replication

Stoltzfus, C. Martin

doi:10.1016/s0065-3527(09)74001-1

Cited by 123 publications

(201 citation statements)

References 103 publications

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“…Splicing has to be strictly regulated to allow the balanced production of all viral RNAs and proteins. The HIV-1 transcript contains several SREs to enhance or inhibit splicing at nearby positioned splice sites (Damgaard et al, 2002;Karn & Stoltzfus, 2012;Leblanc et al, 2013;Stoltzfus, 2009;Stoltzfus & Madsen, 2006;Tange et al, 2001;Zahler et al, 2004). Furthermore, usage of HIV-1 splice sites can be influenced by local RNA structure (Abbink & Berkhout, 2008;Jacquenet et al, 2001;Mueller et al, 2014;Zychlinski et al, 2009 59 ), which will allow efficient U1 snRNA annealing and splicing.…”

Section: Introductionmentioning

confidence: 99%

HIV-1 splicing is controlled by local RNA structure and binding of splicing regulatory proteins at the major 5′ splice site

Müeller

Berkhout

Das

2015

Journal of General Virology

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The 59 leader region of the human immunodeficiency virus 1 (HIV-1) RNA genome contains the major 59 splice site (ss) that is used in the production of the many spliced viral RNAs. This splice-donor (SD) region can fold into a stable stem-loop structure and the thermodynamic stability of this RNA hairpin influences splicing efficiency. In addition, splicing may be modulated by binding of splicing regulatory (SR) proteins, in particular SF2/ASF (SRSF1), SC35 (SRSF2), SRp40 (SRSF5) and SRp55 (SRSF6), to sequence elements in the SD region. The role of RNA structure and SR protein binding in splicing control was previously studied by functional analysis of mutant SD sequences. The interpretation of these studies was complicated by the fact that most mutations simultaneously affect both structure and sequence elements. We therefore tried to disentangle the contribution of these two variables by designing more precise SD region mutants with a single effect on either the sequence or the structure. The current analysis indicates that HIV-1 splicing at the major 59ss is modulated by both the stability of the local RNA structure and the binding of splicing regulatory proteins.

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Section: Introductionmentioning

confidence: 99%

HIV-1 splicing is controlled by local RNA structure and binding of splicing regulatory proteins at the major 5′ splice site

Müeller

Berkhout

Das

2015

Journal of General Virology

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“…The relatively low levels of unspliced mRNAs produced in mouse cells may impede the assembly of virions due to low levels of viral structural proteins and genomic RNA. Although this step in viral replication has been intensively investigated, the molecular mechanism has not been fully elucidated (18,50,51,57). Several host factors have been implicated in the modulation of the ratio between spliced and unspliced HIV-1 mRNA (50).…”

mentioning

confidence: 99%

“…Although this step in viral replication has been intensively investigated, the molecular mechanism has not been fully elucidated (18,50,51,57). Several host factors have been implicated in the modulation of the ratio between spliced and unspliced HIV-1 mRNA (50). Overexpression of human p32 in mouse cells decreased splicing of HIV-1 mRNA and increased virion-associated capsid (CA) by inhibiting alternative splicing factor/splicing factor 2 (ASF/SF2) (66).…”

mentioning

confidence: 99%

Human CRM1 Augments Production of Infectious Human and Feline Immunodeficiency Viruses from Murine Cells

Elinav

Coskun

et al. 2012

J Virol

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Productive replication of human immunodeficiency virus type 1 (HIV-1) occurs efficiently only in humans. The posttranscriptional stages of the HIV-1 life cycle proceed poorly in mouse cells, with a resulting defect in viral assembly and release. Previous work has shown that the presence of human chromosome 2 increases HIV-1 production in mouse cells. Recent studies have shown that human chromosome region maintenance 1 (hCRM1) stimulates Gag release from rodent cells. Here we report that expressions of hCRM1 in murine cells resulted in marked increases in the production of infectious HIV-1 and feline immunodeficiency virus (FIV). HIV-1 production was also increased by hSRp40, and a combination of hCRM1 and hSRp40 resulted in a more-than-additive effect on HIV-1 release. In contrast, the overexpression of mouse CRM1 (mCRM1) minimally affected HIV-1 and FIV production and did not antagonize hCRM1. In the presence of hCRM1 there were large increases in the amounts of released capsid, which paralleled the increases in the infectious titers. Consistent with this finding, the ratios of unspliced to spliced HIV-1 mRNAs in mouse cells expressing hCRM1 and SRp40 became similar to those of human cells. Furthermore, imaging of intron-containing FIV RNA showed that hCRM1 increased RNA export to the cytoplasm.By testing chimeras between mCRM1 and hCRM1 and comparing those sequences to feline CRM1, we mapped the functional domain to HEAT (Huntingtin, elongation factor 3, protein phosphatase 2A, and the yeast kinase TOR1) repeats 4A to 9A and a triple point mutant in repeat 9A, which showed a loss of function. Structural analysis suggested that this region of hCRM1 may serve as a binding site for viral or cellular factors to facilitate lentiviral RNA nuclear export.

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“…Accumulation of unspliced and 4-kb transcripts coincides with the transition to late phase replication and expression of Gag, Gag/Pol, Vpr, Vif, and Env/Vpu. Thus, HIV-1 splicing pathways are essential components of the viral replication cycle and represent new targets for therapeutic intervention (3,4).…”

Section: Human Immunodeficiency Virus Type 1 (Hiv-1)mentioning

confidence: 99%

“…Efforts to understand mechanisms of HIV-1 splicing reveal that all of the acceptor sites and splice donors D2-D4 are suboptimal due to non-consensus core splicing signals (4,5). Proper spliced ratios are therefore established via auxiliary cis RNA features, collectively known as splicing regulatory elements.…”

Section: Human Immunodeficiency Virus Type 1 (Hiv-1)mentioning

confidence: 99%

Solution Structure of the HIV-1 Intron Splicing Silencer and Its Interactions with the UP1 Domain of Heterogeneous Nuclear Ribonucleoprotein (hnRNP) A1

Jain

Morgan

Rife

et al. 2016

Journal of Biological Chemistry

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Splicing patterns in human immunodeficiency virus type 1 (HIV-1) are maintained through cis regulatory elements that recruit antagonistic host RNA-binding proteins. The activity of the 3 acceptor site A7 is tightly regulated through a complex network of an intronic splicing silencer (ISS), a bipartite exonic splicing silencer (ESS3a/b), and an exonic splicing enhancer (ESE3). Because HIV-1 splicing depends on protein-RNA interactions, it is important to know the tertiary structures surrounding the splice sites. Herein, we present the NMR solution structure of the phylogenetically conserved ISS stem loop. ISS adopts a stable structure consisting of conserved UG wobble pairs, a folded 2X2 (GU/UA) internal loop, a UU bulge, and a flexible AGUGA apical loop. Calorimetric and biochemical titrations indicate that the UP1 domain of heterogeneous nuclear ribonucleoprotein A1 binds the ISS apical loop site-specifically and with nanomolar affinity. Collectively, this work provides additional insights into how HIV-1 uses a conserved RNA structure to commandeer a host RNA-binding protein.Human immunodeficiency virus type 1 (HIV-1) 2 requires controlled synthesis of its protein complement for persistent infection and successful virion production. Genome expression is tightly regulated at the levels of transcription, splicing, mRNA nuclear export, and translation (1). RNA polymerase II-dependent transcription yields a 9-kilobase (kb) polycistronic transcript that undergoes multiple rounds of alternative splicing to produce upward of 100 different viral mRNAs that are classified by their intron composition: unspliced, incompletely spliced (4 kb), and completely spliced (2 kb) (2, 3). During early phase HIV-1 replication, cytoplasmic levels of the 2-kb transcripts predominate to encode Tat, Rev, and Nef. Accumulation of unspliced and 4-kb transcripts coincides with the transition to late phase replication and expression of Gag, Gag/Pol, Vpr, Vif, and Env/Vpu. Thus, HIV-1 splicing pathways are essential components of the viral replication cycle and represent new targets for therapeutic intervention (3, 4).The identities of HIV-1 transcripts are determined by the combinatorial use of several 5Ј donor and 3Ј acceptor splice sites. Efforts to understand mechanisms of HIV-1 splicing reveal that all of the acceptor sites and splice donors D2-D4 are suboptimal due to non-consensus core splicing signals (4, 5). Proper spliced ratios are therefore established via auxiliary cis RNA features, collectively known as splicing regulatory elements. Splicing regulatory elements function either as enhancers or silencers of splicing by recruiting host proteins belonging to the serine-arginine-rich (SR) and hnRNP families, respectively. Splicing regulatory element location (intronic or exonic) influences how frequently a given splice site is utilized, thereby making it difficult to determine general rules of the mechanisms that regulate alternative splicing (6).Splicing from site D4 to A7 removes the Rev-responsive element, which leads to the accu...

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Chapter 1 Regulation of HIV-1 Alternative RNA Splicing and Its Role in Virus Replication

Cited by 123 publications

References 103 publications

HIV-1 splicing is controlled by local RNA structure and binding of splicing regulatory proteins at the major 5′ splice site

HIV-1 splicing is controlled by local RNA structure and binding of splicing regulatory proteins at the major 5′ splice site

Human CRM1 Augments Production of Infectious Human and Feline Immunodeficiency Viruses from Murine Cells

Solution Structure of the HIV-1 Intron Splicing Silencer and Its Interactions with the UP1 Domain of Heterogeneous Nuclear Ribonucleoprotein (hnRNP) A1

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