RNA damage in biological conflicts and the diversity of responding RNA repair systems

Abstract

RNA is targeted in biological conflicts by enzymatic toxins or effectors. A vast diversity of systems which repair or 'heal' this damage has only recently become apparent. Here, we summarize the known effectors, their modes of action, and RNA targets before surveying the diverse systems which counter this damage from a comparative genomics viewpoint. RNA-repair systems show a modular organization with extensive shuffling and displacement of the constituent domains; however, a general 'syntax' is strongly maintained whereby systems typically contain: a RNA ligase (either ATP-grasp or RtcB superfamilies), nucleotidyltransferases, enzymes modifying RNA-termini for ligation (phosphatases and kinases) or protection (methylases), and scaffold or cofactor proteins. We highlight poorly-understood or previously-uncharacterized repair systems and components, e.g. potential scaffolding cofactors (Rot/TROVE and SPFH/Band-7 modules) with their respective cognate non-coding RNAs (YRNAs and a novel tRNA-like molecule) and a novel nucleotidyltransferase associating with diverse ligases. These systems have been extensively disseminated by lateral transfer between distant prokaryotic and microbial eukaryotic lineages consistent with intense inter-organismal conflict. Components have also often been 'institutionalized' for non-conflict roles, e.g. in RNA-splicing and in RNAi systems (e.g. in kinetoplastids) which combine a distinct family of RNA-acting prim-pol domains with DICER-like proteins.

Figure 1.

Known and predicted biochemical mechanisms of biological conflict-related RNA damage and repair. The methyl group added during Hen1-mediated methylation is in red in (B). Slash in (D) separates the two RNA 3′ end phosphate group configurations the RtcB ligase accepts as substrates. Green labels provide reaction step explanation/categorization. Blue dots: predicted enzymes or reaction steps predicted for the first time.

Figure 2.

Structures of catalytic domains repairing RNA damaged in biological conflicts. Structures are grouped as appearing in the text and are labeled by protein name and Protein Databank ID; green labels provide additional domain information. Dotted lines separate domains performing similar functions but with different protein folds; dotted bracket grouping calcineurin-like and synaptojanin-like domains denotes higher-order relationship. Ligands: light green and ball-and-stick. Conserved residues involved in catalysis or substrate recognition: ball-and-stick (carbon, light blue; nitrogen, dark blue; oxygen, red; cysteine, orange), metal ions: spheres.

Figure 3.

Contextual connections of ATP-grasp ligase-based and related RNA repair systems. (A) Contextual network constructed as described in Supplementary Material. Protein domain nodes are colored according to general functional category. Phosphoesterase/phosphotransferase domains are further demarcated by dotted orange box. (B–Q) Representative depictions of conserved domain architectures and gene neighborhoods. Domain architectures are depicted as adjoining shapes, not drawn to scale. Gene neighborhoods are depicted as directed boxes, genes within neighborhood encoding multiple domains contain individually-colored boxes for each domain. All contexts are labeled with organism name and NCBI gene identifier (gi) number. Green lettering: phyletic distributions for each group of systems. Blue dots: novel predicted RNA repair systems or systems containing a previously-unrecognized component. (R–X) Representatives of conserved domain architectures and gene neighborhoods containing the MJ1316 domain. All domain and organism expansions are provided in Supplementary Material.

Figure 4.

Genome context network of RtcB ligase-based and related RNA repair systems. (A) Contextual network; domains displaying mutual exclusivity wrapped together in dotted lines. (B and C) Structures of RtcB ligase-associating domains. Despite multimerization in crystal structures, archease exists as monomer in solution (216). Swapped strand in obligate dimer archease structure colored in cyan. (D–R) Representatives of RtcB RNA ligase-centered RNA repair and related systems. The system of labeling is as in Figure 3.

Figure 5.

Structures of RtcB ligase-associating and related domains. (A) Individual domains in multi-domain proteins are labeled in green. Swapped strands in obligate Band-7 core domain are colored green. Repeat domains found N-terminal to core Band-7-like domain in MVP are colored as individual units. Interacting Band-7-like N-terminal repeat domains found in structure of the Vault complex are colored as per repeat. (B and C) Multiple sequence alignments of YRNAs (B) and b7a-tRNAs (C). Genome sequence position is provided to the left and right of sequences. Predicted secondary structure features are given on the top line of alignment in WUSS notation. Poorly-conserved regions replaced by numbers. (D) Secondary structure depictions of YRNA and b7a-tRNAs. Key features are shaded to match (B and C). Potential modification/cleavage region for YRNA described in (231) shaded in brown. All domain and organism abbreviations are provided in Supplementary Material.

Figure 6.

Alignments and evolutionary scenarios of RNA-repair enzymes. Multiple sequence alignment of prim-pol domains (A), KptA domain found in kinetoplastid DCL1 and DCL2 proteins (B). Alignments are labeled as described in Figure 5. Names of experimentally-characterized proteins: orange. Conserved positions corresponding to known substrate binding residues: ‘*’; conserved residues unique to a family, predicted to function similarly: ‘%’. Coloring scheme and abbreviations for organisms are provided in Supplementary Material. (C) Stylized phylogenetic tree depicting relationships between prim-pol families, broadly labeled at the top of the tree. Branches are collapsed at levels containing clearly-delineable and labeled monophyletic groups. Bootstrap values are shown for major branches only (complete tree available in Supplementary Material). (D and E) Major events in the evolutionary history of ATP-grasp-like ligases (D) and the CCA-adding enzyme-like polymerases of the DNA pol-β superfamily (E). Inferred functional and architectural shifts are marked/labeled with red lines/lettering. Dashed lines indicate uncertain origins for a lineage.