Modified base-binding EVE and DCD domains: striking diversity of genomic contexts in prokaryotes and predicted involvement in a variety of cellular processes

Abstract

Background DNA and RNA of all cellular life forms and many viruses contain an expansive repertoire of modified bases. The modified bases play diverse biological roles that include both regulation of transcription and translation, and protection against restriction endonucleases and antibiotics. Modified bases are often recognized by dedicated protein domains. However, the elaborate networks of interactions and processes mediated by modified bases are far from being completely understood. Results We present a comprehensive census and classification of EVE domains that belong to the PUA/ASCH domain superfamily and bind various modified bases in DNA and RNA. We employ the “guilt by association” approach to make functional inferences from comparative analysis of bacterial and archaeal genomes, based on the distribution and associations of EVE domains in (predicted) operons and functional networks of genes. Prokaryotes encode two classes of EVE domain proteins, slow-evolving and fast-evolving ones. Slow-evolving EVE domains in α-proteobacteria are embedded in conserved operons, potentially involved in coupling between translation and respiration, cytochrome c biogenesis in particular, via binding 5-methylcytosine in tRNAs. In β- and γ-proteobacteria, the conserved associations implicate the EVE domains in the coordination of cell division, biofilm formation, and global transcriptional regulation by non-coding 6S small RNAs, which are potentially modified and bound by the EVE domains. In eukaryotes, the EVE domain-containing THYN1-like proteins have been reported to inhibit PCD and regulate the cell cycle, potentially, via binding 5-methylcytosine and its derivatives in DNA and/or RNA. We hypothesize that the link between PCD and cytochrome c was inherited from the α-proteobacterial and proto-mitochondrial endosymbiont and, unexpectedly, could involve modified base recognition by EVE domains. Fast-evolving EVE domains are typically embedded in defense contexts, including toxin-antitoxin modules and type IV restriction systems, suggesting roles in the recognition of modified bases in invading DNA molecules and targeting them for restriction. We additionally identified EVE-like prokaryotic Development and Cell Death (DCD) domains that are also implicated in defense functions including PCD. This function was inherited by eukaryotes, but in animals, the DCD proteins apparently were displaced by the extended Tudor family proteins, whose partnership with Piwi-related Argonautes became the centerpiece of the Piwi-interacting RNA (piRNA) system. Conclusions Recognition of modified bases in DNA and RNA by EVE-like domains appears to be an important, but until now, under-appreciated, common denominator in a variety of processes including PCD, cell cycle control, antivirus immunity, stress response, and germline development in animals.

Major episodes of horizontal gene transfer drove the evolution of land plants

“…The pollen-pistil interaction 2 gene (POP2), involved in fertilization regulation in angiosperms (Renault et al, 2011), was acquired from bacteria during episode 1 (Figure 4E). EVE domain-containing proteins (or thymocyte nuclear-like proteins), widely distributed in streptophytes and bacteria, are thought to be functionally related to programmed cell death (Bell et al, 2020). Consistent with an earlier finding (Bell et al, 2020), our data show that plant EVE domaincontaining protein genes are derived from bacteria (Supplemental Figure 14).…”

“…EVE domain-containing proteins (or thymocyte nuclear-like proteins), widely distributed in streptophytes and bacteria, are thought to be functionally related to programmed cell death (Bell et al, 2020). Consistent with an earlier finding (Bell et al, 2020), our data show that plant EVE domaincontaining protein genes are derived from bacteria (Supplemental Figure 14). At least three acquired genes have been shown experimentally to modulate vascular development (Jun et al, 2002;Yang et al, 2015;Ribeiro et al, 2020) (Supplemental Table 5).…”

CoCoNuTs: A diverse subclass of Type IV restriction systems predicted to target RNA

“…In contrast to Type II and Type III CnuB homologs, which contain only coiled-coils fused at their N-termini (Figure 6), cold-shock domain (CSD)-like OB-folds are usually fused at the N-termini of Type I CoCoNuT CnuB/McrB proteins, in addition to the coiled-coils (except for the majority of Type I-B, where the coiled-coils are encoded separately) (Figure 5, Supplementary Table S1) (Amir et al, 2018). Often, in Type I-B and I-C, but not Type I-A, a YTH-like domain, a member of the modified base-binding EVE superfamily, is present in CnuB as well, between the CSD and coiled-coil, or in Type I-B, between the CSD and the GTPase domain (Figure 5, Supplementary Table S1) (Bell et al, 2020, Hazra et al, 2019, Liao et al, 2018).…”

“…In recent years, systematic searches for defense systems in prokaryotes, primarily by analysis of defense islands, revealed enormous, previously unsuspected diversity of such systems that function through a remarkable variety of molecular mechanisms. In this work, we (Bell et al, 2020). All alignments were clustered, and each sub-alignment or individual query sequence was used to produce a position-specific scoring matrix (PSSM).…”

Characterization of BisI Homologs

“…More recently, the EVE protein domain in the PUA superfamily has been found in fusion with the HNH nuclease domain to provide restriction of hm5C/m5C-modified DNA ( Lutz et al, 2019 ). EVE domain can be fused with PD-D/E xK nuclease and other nuclease domains such as Pin nuclease, PLD nuclease, and GIY-YIG family nucleases ( Bell et al, 2020 ). SauUSI is another example of Type IV REases with PLD nuclease-DNA helicase (ATPase)-Sra domain fusion that restricts hm5C/m5C modified DNA ( Xu et al, 2011 ; Tumuluri et al, 2021 ).…”