Science Spotlight

Finding the right fit for IFIT1 and IFIT1B proteins

An ancestral IFIT1 gene (grey) duplicated to give rise to either IFIT1 (blue) or IFIT1b (green). Loss of either IFIT1 or IFIT1b in different mammalian species may influence their susceptibility to certain viruses.
Image provided by Dr. Matthew Daugherty.

A key property of our complex immune system is the ability to distinguish self from non-self. This distinction is made at the molecular level, by detecting proteins or nucleic acids (DNA or RNA). In the innate immune system, genes stimulated by a signaling protein called interferon serves as an immediate defense mechanism against invading viruses or bacteria. One group of proteins that our cells produce in response to interferon is the IFIT (interferon-induced with tetratricopeptide repeats) proteins. While previous studies suggested that some IFITs provide antiviral immunity by shutting down mRNA translation, it is unknown whether the molecular function and antiviral specificity is shared among the large number of IFITs encoded by mammalian genomes. For example, mouse IFIT1B selectively inhibits the translation of unmethylated mRNAs (cap0 structure; recognized as non-self) from viruses, while host cells are protected because their mRNAs are methylated (cap1 structure; recognized as self) by a cap1-methyltransferase (CMTR1). However, whether this mRNA cap discrimination property extends to other IFITs remains unclear. A new Fred Hutch study from the Malik (Basic Sciences Division) and Geballe's Laboratories (Clinical Research and Human Biology Divisions), led by former postdoctoral fellow Dr. Matthew Daugherty (now an Assistant Professor at UCSD) and published in eLife, charted the evolutionary history of IFITs, and showed that human IFIT1 and mouse IFIT1B differ in both their ancestry and molecular functions.

First, the authors conducted an unprecedented phylogenetic analysis of IFIT genes from 51 vertebrate species. Not only did this investigation reveal prevalent gene birth, loss, and gene conversion of IFIT genes, but also unambiguously demonstrated that human IFIT1 and mouse IFIT1B are paralogs (homologous genes that result from a duplication event) rather than orthologs (homologous genes that result from a speciation event). Next, the researchers tested whether IFIT1 and IFIT1B have distinct abilities to block translation of cap0 mRNAs. To this end, they leveraged the fact that yeast lack a CMTR and thus only have cap0 mRNAs. Thus, expression of any protein such as IFIT1B that is capable of blocking translation of cap0 mRNAs is predicted to prevent yeast growth. Indeed, while expression of either IFIT1B or IFIT1 from diverse species blocked yeast growth, expression of human CMTR1 rescued the growth of IFIT1B, but not IFIT1-expressing yeast. Finally, the authors tested their hypothesis that IFIT1 and IFIT1B have distinct antiviral specificity by infecting mammalian cell lines stably expressing either human IFIT1 or mouse IFIT1B. As expected, cells expressing IFIT1B were able to block replication of mutant vaccinia virus that lacked CMTR activity, but not wild-type vaccinia virus. Surprisingly, IFIT1-expressing cells blocked neither wild-type nor mutant vaccinia viruses. However, against a different virus that harbors cap1 mRNAs, vesicular stomatitis virus, IFIT1 but not IFIT1B-expressing cells were able to inhibit viral replication. In summary, a combination of evolutionary and functional studies revealed species-specific differences in both the molecular function and antiviral range of IFIT proteins. "There are a few cool ramifications of this work.  First, it’s a nice example of something we’ve known for a long time but sometimes forget: mice are not humans.  Especially in rapidly evolving systems like pathogen immunity, human and mouse genes that share the same name don’t necessarily perform the same function.  It also strongly suggests that there are other chemical marks on mRNAs that the immune system is leveraging to distinguish viral 'non-self' mRNAs from 'self' host mRNAs, and we are currently investigating what those marks might be.  Finally, it has the interesting implication that gene evolution, such as the loss of certain genes in certain species, could leave those species more susceptible to infection.  We are investigating whether the loss of the 'mouse' version of IFIT1 from the human lineage is one such example that opens us up to infection by certain viruses such as Chikungunya or other alphaviruses." said Dr. Daugherty.

Daugherty MD,Schaller AM,Geballe AP,Malik HS. 2016. Evolution-guided functional analyses reveal diverse antiviral specificities encoded by IFIT1 genes in mammals. Elife, 5. PMCID: PMC4887208.

Funding for this work was provided by the Cancer Research Institute, the National Institutes of Health and the Howard Hughes Medical Institute.