FTSJ3 is an RNA 2′-O-methyltransferase recruited by HIV to avoid innate immune sensing

Abstract

In mammals, RNA 2'-O-methylation is a molecular signature for the discrimination of endogenous from exogenous mRNA by the cellular innate immune system 1-3 . Here we purified TRBP and its interacting partners to identify a DICERindependent TRBP complex containing FTSJ3, a putative 2'-O-methyltransferase (2'O-MTase). In vitro and ex-vivo experiments show that FTSJ3 is a 2'O-MTase that is recruited to HIV RNA through TRBP. Using RiboMethSeq analysis 4 , we identified 2'-Omethylated residues on viral genome, and found that FTSJ3 modifies HIV RNA at specific sites. HIV-1 viruses produced in FTSJ3 knock-down cells show reduced 2'-Omethylation and trigger type 1-interferons (IFN) expression in human dendritic cells through the RNA sensor MDA5. This IFN-α and IFN-β induction leads to a reduced HIV expression. Altogether, our study revealed an unexpected mechanism used by HIV to evade innate immune recognition involving the recruitment of TRBP/FTSJ3 complex to viral RNA and its 2'-O-methylation.Among post-transcriptional modifications of RNA, called epitranscriptome, 2'-Omethylation is present at the 5'-extremity of all mRNAs in mammals and internally at specific residues of tRNA, rRNA, snRNA and cellular mRNA 5 , 6 . Known for decades for its role in RNA stabilization, its key function in innate immunity has been uncovered recently 1,2 .Cellular mRNAs are capped with a 7-methyl-guanosine ( m7 G), a 5'-modification crucial for mRNA splicing, export to the cytoplasm, and efficient translation into proteins 7 . In addition, mRNAs in higher Eucaryotes acquire a second modification: a 2'-O-ribose methylation on the first (cap1) and the second transcribed nucleotide (cap2). This modification provides a molecular signature for discrimination of self from non-self mRNA. In the cell, cytoplasmic sensors, such as MDA5 and RIG-I, recognize exogenous unmodified RNAs and activate type-1 interferon production to establish an antiviral state 8,9 . To evade innate immune response, some viruses, including Flaviviruses, encode for their own viral 2'O-MTase that can add a cap1/2 on viral transcripts 10 and in the case of West Nile, Dengue and Ebola viruses can also methylate internal adenosine residues of viral genome in vitro 11,12 . In addition, in other pathogens, such as E.coli strains, tRNA 2'-O-methylation also plays an important role in immunostimulation of human dendritic cells since the loss of unique Gm18 residue in mutant TrmH E.coli strain abolishes immunosuppression 13,14 . This is due to the G18 residue of tRNA Tyr that has to be 2'-O-methylated to avoid innate sensing in human cells. In contrast to Flaviviruses, HIV does not encode a 2'O-MTase. However, FTSJ3, a putative host 2'O-MTase, was purified as a partner of TAR RNA binding protein (TRBP), a dsRNA binding

tRNA 2’-O-methylation modulates small RNA silencing and life span in Drosophila

“…Interestingly, both WDR6 and FTSJ1 were identified as principal human host restriction factors against vaccinia virus indicating that this Nm-MTase complex functions at the interface of host-virus interactions (76) . In support of the notion that Nm modifications modulate mobile element control, human Nm-MTase FTSJ3 can be hijacked by HIV-1 to methylate viral mRNAs resulting in avoidance of being sensed by the host innate immune system (17) .…”

“…Interestingly, it was recently proposed that TRM7 methylates substrates different than tRNAs including mRNAs in yeast (16,17) suggesting that TRM7 family members can act as multi-substrate Nm-MTases, which modulate translation by methylating mRNA codons and tRNA anticodons. Importantly, loss of Nm at tRNA positions 32 and 34 in trm7 mutant yeast affected translation rates and, consecutively, cell growth (36,38) .…”

“…Importantly, Nm deposition was also reported at 3'-terminal nucleotides in small non-coding RNAs (sncRNAs) such as microRNAs (miRNAs) and small-interfering RNAs (siRNAs) in plants (10)(11)(12) , in Argonaute-2 (Ago2) loaded siRNAs and miRNAs in flies and in PIWI-interacting RNAs (piRNAs) in animals (13)(14)(15) . More recently Nm was also reported to be present in messenger RNA (mRNA) (16,17) .…”

A novel platform of RNA 2′-O-methylation high-throughput and site-specific quantification tools revealed its broad distribution on mRNA

“…The Nm sites may be methylated in two ways, one is a group of methyltransferases recognizing targeted sites with the specific feature of secondary structures such as 5' cap or the 3' end of small RNAs, the other is a group of methyltransferases recognizing targeted sites by the guidance of an RNA partially complementary to the target sequence around such as snoRNA and other unknown RNAs [5,17,22,23]. Because we found most of Nm sites were not correlated with snoRNA regulation, our study strongly implies the involvement of other major Nm sites methylation unknown mechanisms.…”

Persistent DNA Hyper-methylation Dampens Host Anti-Mycobacterial Immunity

“…Given that chronic antigen stimulation from HIV, schistosomiasis, or LCMV induces long-lasting epigenetic-mediated immune exhaustion, we were concerned that TB disease may also result in persistent detrimental epigenetic changes 8,10,[13][14][15] . We hypothesized that TB patients would have a DNA methylation landscape similar to chronic LCMV.…”