Eukaryotic CD-NTase, STING, and viperin proteins evolved via domain shuffling, horizontal transfer, and ancient inheritance from prokaryotes

Abstract

Animals use a variety of cell-autonomous innate immune proteins to detect viral infections and prevent replication. Recent studies have discovered that a subset of mammalian antiviral proteins have homology to antiphage defense proteins in bacteria, implying that there are aspects of innate immunity that are shared across the Tree of Life. While the majority of these studies have focused on characterizing the diversity and biochemical functions of the bacterial proteins, the evolutionary relationships between animal and bacterial proteins are less clear. This ambiguity is partly due to the long evolutionary distances separating animal and bacterial proteins, which obscures their relationships. Here, we tackle this problem for 3 innate immune families (CD-NTases [including cGAS], STINGs, and viperins) by deeply sampling protein diversity across eukaryotes. We find that viperins and OAS family CD-NTases are ancient immune proteins, likely inherited since the earliest eukaryotes first arose. In contrast, we find other immune proteins that were acquired via at least 4 independent events of horizontal gene transfer (HGT) from bacteria. Two of these events allowed algae to acquire new bacterial viperins, while 2 more HGT events gave rise to distinct superfamilies of eukaryotic CD-NTases: the cGLR superfamily (containing cGAS) that has since diversified via a series of animal-specific duplications and a previously undefined eSMODS superfamily, which more closely resembles bacterial CD-NTases. Finally, we found that cGAS and STING proteins have substantially different histories, with STING protein domains undergoing convergent domain shuffling in bacteria and eukaryotes. Overall, our findings paint a picture of eukaryotic innate immunity as highly dynamic, where eukaryotes build upon their ancient antiviral repertoires through the reuse of protein domains and by repeatedly sampling a rich reservoir of bacterial antiphage genes.

cGLRs Join Their Cousins of Pattern Recognition Receptor Family to Regulate Immune Homeostasis

“…The first enzyme responsible for synthesizing cyclic guanosine monophosphate (GMP)-adenosine monophosphate (AMP) (cGAMP) or cyclicdinucleotides (CDNs), dinucleotide cyclase (DncV), or cGAS-DncV-like nucleotidyltransferase (CD-NTase), evolved in bacteria and has been reported in Vibrio cholerae. CD-NTases generating CDNs, like animal cGASs, are very diverse proteins numbering over 6000 to date [18]. In addition to producing CDNs, bacterial CD-NTases can also produce cyclic trinucleotides (CTNs) and linear oligonucleotides [19,20].…”

“…Phylogenetic studies have indicated that animal cGAS, or chromosome 6 open reading frame 150 (C6orf150), and STING date back to the origin of choanoflagellate (nearest freeliving unicellular and colonial flagellates related to metazoans) called Monosiga brevicollis [22]. However, cGAS and STING proteins have substantially different origins, as STINGs arose via convergent domain shuffling in bacteria and eukaryotes, while cGAS homologs or eukaryotic CD-NTases arose due to multiple horizontal gene transfer (HGT) events from bacteria to eukaryotes [18]. Notably, cGAS homologs of invertebrates may not always recognize ds-DNA as a PAMP/MAMP and DAMP.…”

“…Notably, h-cGAS structurally and enzymatically resembles human OAS1, a template-independent nucleotidyl transferase that activates antiviral innate immunity upon recognizing cytosolic short dsRNA (>18 bp) [33][34][35]. Notably, OAS-like proteins also have an evolutionary prokaryotic or bacterial origin through the development of antiviral defense and are independently acquired by eukaryotes [18]. Furthermore, the Zn 2+ -ribbon domain of vertebrate cGAS is absent in OAS1, nematode Mab-21, and mammalian Mab-21-like proteins [22].…”

“…Furthermore, cGLR sequence analysis has delineated specific evolutionary patterns in animal immunity and protein features that are distinct from bacterial CD-NTase anti-phage defense enzymes [24]. Animal cGLRs form a single family of signaling proteins that share more distantly related homologies with bacterial CD-NTase anti-phage defense enzymes and animal OAS1-like proteins [18,24]. Furthermore, the interaction between STING and CDNs is universally conserved.…”

Tracing the evolutionary origins of antiviral immunity

“…With the realization that central aspects of human immunity are shared with bacteria, a key question is how did this come to be? In this issue of PLOS Biology , Culbertson and Levin provide a comprehensive bioinformatic analysis of eukaryotic cGLR, STING, and viperin proteins, revealing strikingly different evolutionary histories and providing insight into the early emergence of metazoan antiviral immunity ( Fig 1 ) [ 8 ].…”