Recurrent Loss of Macrodomain Activity in Host Immunity and Viral Proteins

Abstract

Protein post-translational modifications (PTMs) are an important battleground in the evolutionary arms races that are waged between the host innate immune system and viruses. One such PTM, ADP-ribosylation, has recently emerged as an important mediator of host antiviral immunity. Important for the host–virus conflict over this PTM is the addition of ADP-ribose by PARP proteins and removal of ADP-ribose by macrodomain-containing proteins. Interestingly, several host proteins, known as macroPARPs, contain macrodomains as well as a PARP domain, and these proteins are both important for the host antiviral immune response and evolving under very strong positive (diversifying) evolutionary selection. In addition, several viruses, including alphaviruses and coronaviruses, encode one or more macrodomains. Despite the presence of the conserved macrodomain fold, the enzymatic activity of many of these proteins has not been characterized. Here, we perform evolutionary and functional analyses to characterize the activity of macroPARP and viral macrodomains. We trace the evolutionary history of macroPARPs in metazoans and show that PARP9 and PARP14 contain a single active macrodomain, whereas PARP15 contains none. Interestingly, we also reveal several independent losses of macrodomain enzymatic activity within mammalian PARP14, including in the bat, ungulate, and carnivore lineages. Similar to macroPARPs, coronaviruses contain up to three macrodomains, with only the first displaying catalytic activity. Intriguingly, we also reveal the recurrent loss of macrodomain activity within the alphavirus group of viruses, including enzymatic loss in insect-specific alphaviruses as well as independent enzymatic losses in two human-infecting viruses. Together, our evolutionary and functional data reveal an unexpected turnover in macrodomain activity in both host antiviral proteins and viral proteins.

PARP14 is pro- and anti-viral host factor that promotes IFN production and affects the replication of multiple viruses

“…Its ART domain has an HYL (hydrophobic residue-tyrosine-leucine) domain as part of the catalytic triad, which restricts its ART activity to MARylation (28,29). PARP14 also has 3 tandem macrodomains (MD), of which MD1 has ADP-ribosylhydrolase (ARH) activity against MARylated protein and nucleic acid substrates, making it a rare enzyme that both adds and reverses the same post-translational modification (11,12). PARP14 also has a WWE domain that can bind to ADP-ribose subunits (30), several KH domains that facilitate protein and nucleic acid binding, and several RNA recognition motifs (RRMs) (10).…”

“…RNA was isolated from cells at 12 hpi and IFNβ mRNA was quantified by qPCR using ΔCt method. D) Parp14+/+ cells were infected with WT and N1347A at an MOI of 0.1 and then treated at 1 hpi with DMSO or increasing concentrations of PARP14 inhibitor (PARP14i) (3,11,33, 99 and 297nM). RNA was isolated from cells at 12 hpi and IFNβ mRNA levels were quantified using qPCR using ΔCt method.…”

“…PARP14 is a multidomain protein and its domain architecture was recently re-analyzed using Alphafold2 (10). This analysis determined that PARP14 contains 3 RRM domains, 7 full KH domains and 1 split KH domain that are suspected to bind to nucleic acids, 3 macrodomains (MDs) one of which has an ADP-ribose hydrolase activity (MD1) (10)(11)(12), a WWE domain that is suspected to bind ADP-ribose subunits, and the ART catalytic domain (10).…”

Wolbachia infection-responsive immune genes suppress Plasmodium falciparum infection in Anopheles stephensi

“…While the oocyst counts were increased after knockdown of either macro domain or peritrophin-44, only silencing of the peritrophin-44-like protein gene had a statistically significant effect on infection prevalence. Macro domain-containing proteins (ASTEI09413) are not well characterized in insects [ 56 , 57 ]; therefore, an association with the Wolbachia -induced anti- Plasmodium defense could be an interesting new field to explore. Similarly, little information is available about the peritrophin-44-like gene in insect–parasite interactions.…”

Regulation of ADP-ribosyltransferase activity by ART domain dimerization in PARP15

“…The subfamily of macrodomain containing PARP enzymes (PARP9, PARP14 and PARP15) was originally identified as B-aggressive lymphoma (BAL) proteins 1-3 [11]. PARP9 and PARP14 contain a macrodomain with ADP-ribosyl glycohydrolase activity [12][13][14] as well as one and two ADP-ribosyl binding macrodomains, respectively [15][16][17]. PARP15, the third member of the subfamily, originated by partial duplication of the structurally more complex PARP14 early during mammalian evolution.…”