IFIT1 is an antiviral protein that recognizes 5′-triphosphate RNA

Abstract

Antiviral innate immunity relies on the recognition of microbial structures. One such structure is viral RNA that carries a triphosphate group on its 5' terminus (PPP-RNA). By an affinity proteomics approach with PPP-RNA as the 'bait', we found that the antiviral protein IFIT1 (interferon-induced protein with tetratricopeptide repeats 1) mediated binding of a larger protein complex containing other IFIT family members. IFIT1 bound PPP-RNA with nanomolar affinity and required the arginine at position 187 in a highly charged carboxy-terminal groove of the protein. In the absence of IFIT1, the growth and pathogenicity of viruses containing PPP-RNA was much greater. In contrast, IFIT proteins were dispensable for the clearance of pathogens that did not generate PPP-RNA. On the basis of this specificity and the great abundance of IFIT proteins after infection, we propose that the IFIT complex antagonizes viruses by sequestering specific viral nucleic acids.

Crystal structure of IFIT2 (ISG54) predicts functional properties of IFITs

“…Moreover, there is a strong preference for binding to AU-rich dsRNA and AU-rich ARE sequence present in the 3′ UTRs of many unstable mRNAs. These findings are in contrast with those of Pichlmair et al [3] which reported that IFIT2 can bind to RNA only indirectly by complexing with IFIT1 and the complex binds to 5′-triphosphorylated RNA only. The above studies were done in vitro, whereas in vivo studies by Daffis et al [4] demonstrated that mouse Ifit1 can functionally distinguish mRNAs, which have 2′-O methylation, from those that do not.…”

Crystal structure and nucleotide selectivity of human IFIT5/ISG58

“…ISG58 expression can be induced strongly upon viral infection [4], therefore, we sought to examine the potential inhibitory effect of ISG58 on viral replication by using a model of vesicular stomatitis virus expressing GFP (VSV-GFP). Earlier work reported that both ISG54 and ISG56 inhibited VSV replication when they were overexpressed in HEK293T cells [1,7]. Similarly, ISG58 reduced VSV replication by more than 60% ( Figure 1G).…”

“…Recent studies have shown that ISG56 specifically recognizes viral 5′-pppRNA [1]. Using structural biology methods, we found that ISG54 possesses a right-handed helical channel in its C-terminal region, which recognizes AU-rich RNAs [2].…”

“…To explore why ISG58 binds to both ssRNA and ds-DNA, we next compared its structure with that of ISG54 that recognizes dsRNA. First, in contrast to the dimerforming ISG54 [1,2], ISG58 is stably monomeric in the solution state ( Figure 1H). We found that helices 1-6 and helices 10-16 of ISG58 superimpose well with the corresponding regions of one monomer (monomer A) of the ISG54 dimer, while helices 7-9 of ISG58 overlap with helices 7-9 from the other ISG54 monomer (monomer B) (Supplementary information, Figure S3A).…”

Cellular and molecular regulation of innate inflammatory responses

“…RIG-I 11 and melanoma differentiation-associated protein 5 (MDA5) 12 can recognize viral dsRNA and recruit the CARD containing adaptor protein MAVS (also known as IPS-1, CARDIF or VISA), leading to IRF activation and the production of type I IFN. In addition to RLRs, a group of cytosolic DNA sensors such as cyclic GMP-AMP synthase (cGAS), [13][14][15] absent in melanoma 2 (AIM2), 16,17 DDX41, 18,19 Rad50, 20,21 LRRFIP1, 22 DNA-dependent activator of IRFs (DAI), 23 as well as various RNA sensors such as IFN-induced protein with tetratricopeptide repeats 1 (IFIT1) 24 also play potent roles in inducing antiviral immune response, respectively via the adaptor protein stimulator of interferon genes (STING, also known as MITA, ERIS or MPYS) or the MAVS pathway. cGAS, which was previously thought to recognize cytoplasmic dsDNA over 40 bp in a sequence-independent manner, is recently shown to recognize unpaired guanosines flanking short (12-20 bp) dsDNA (Y-form DNA) found in human immunodeficiency virus type 1 to induce type I IFN production.…”