SRSF1 acts as an IFN-I-regulated cellular dependency factor decisively affecting HIV-1 post-integration steps

Abstract

Efficient HIV-1 replication depends on balanced levels of host cell components including cellular splicing factors as the family of serine/arginine-rich splicing factors (SRSF, 1–10). Type I interferons (IFN-I) play a crucial role in the innate immunity against HIV-1 by inducing the expression of IFN-stimulated genes (ISGs) including potent host restriction factors. The less well known IFN-repressed genes (IRepGs) might additionally affect viral replication by downregulating host dependency factors that are essential for the viral life cycle; however, so far, the knowledge about IRepGs involved in HIV-1 infection is very limited. In this work, we could demonstrate that HIV-1 infection and the associated ISG induction correlated with low SRSF1 levels in intestinal lamina propria mononuclear cells (LPMCs) and peripheral blood mononuclear cells (PBMCs) during acute and chronic HIV-1 infection. In HIV-1-susceptible cell lines as well as primary monocyte-derived macrophages (MDMs), expression levels of SRSF1 were transiently repressed upon treatment with specific IFNα subtypes in vitro. Mechanically, 4sU labeling of newly transcribed mRNAs revealed that IFN-mediated SRSF1 repression is regulated on early RNA level. SRSF1 knockdown led to an increase in total viral RNA levels, but the relative proportion of the HIV-1 viral infectivity factor (Vif) coding transcripts, which is essential to counteract APOBEC3G-mediated host restriction, was significantly reduced. In the presence of high APOBEC3G levels, however, increased LTR activity upon SRSF1 knockdown facilitated the overall replication, despite decreased vif mRNA levels. In contrast, SRSF1 overexpression significantly impaired HIV-1 post-integration steps including LTR transcription, alternative splice site usage, and virus particle production. Since balanced SRSF1 levels are crucial for efficient viral replication, our data highlight the so far undescribed role of SRSF1 acting as an IFN-modulated cellular dependency factor decisively regulating HIV-1 post-integration steps.

Comparison of the Ct-values for genomic and subgenomic SARS-CoV-2 RNA reveals limited predictive value for the presence of replication competent virus

“…For internal control, the RNA Process Control Kit (Roche, Cat# 07099622001) was used as instructed by the manufacturer. As previously described [25] glyceraldehyde-3-phosphate dehydrogenase (GAPDH) mRNA was used as an additional housekeeping gene.…”

HIV-1 Vpr Functions in Primary CD4+ T Cells

“…Silencing, both at the transcriptional and epigenetic levels, is another antiviral mechanism that HIV-1 can override with the help of Vpr. SRSF1, an IFN-modulated splicing factor, was observed to hinder overall LTR activity in Jurkat and THP-1 cells [ 126 ]. In this context, a recent pioneering study involving direct RNA nanopore sequencing in CD4 + T cells identified the Vpr-mediated upregulation of ciTRAN, an HIV-modulating circular RNA that sequesters SRSF1 to prevent it from burdening viral gene expression [ 127 ].…”

Interferon-Regulated Expression of Cellular Splicing Factors Modulates Multiple Levels of HIV-1 Gene Expression and Replication

“…In the following sections, we describe the characteristics and functional hallmarks of these two protein families and discuss their impact on viral replication but focus on two representatives, which have recently been shown to be significantly modulated by interferons [ 46 , 47 ]. SRSF1 will be examined as the main representative of the SRSF family, and hnRNPA0 will be discussed as a representative of the hnRNP family, both selected due to their significant downregulation in gene expression upon interferon stimulation among all the examined RBPs ( Table 1 ).…”

“…SRSF1 is also a key regulator in the gene expression and RNA processing of HIV-1 [ 78 , 79 , 93 ]. The overexpression of SRSF1 has been shown to suppress viral transcription, while the knockdown increases the total viral mRNA levels [ 46 , 94 , 95 , 96 ]. As mentioned above, several HIV-1 pre-mRNA SREs are bound by SRSF1, which enhances the recruitment of the core spliceosomal components [ 92 ].…”