Diversity and roles of (t)RNA ligases

Abstract

The discovery of discontiguous tRNA genes triggered studies dissecting the process of tRNA splicing. As a result, we have gained detailed mechanistic knowledge on enzymatic removal of tRNA introns catalyzed by endonuclease and ligase proteins. In addition to the elucidation of tRNA processing, these studies facilitated the discovery of additional functions of RNA ligases such as RNA repair and non-conventional mRNA splicing events. Recently, the identification of a new type of RNA ligases in bacteria, archaea, and humans closed a long-standing gap in the field of tRNA processing. This review summarizes past and recent findings in the field of tRNA splicing with a focus on RNA ligation as it preferentially occurs in archaea and humans. In addition to providing an integrated view of the types and phyletic distribution of RNA ligase proteins known to date, this survey also aims at highlighting known and potential accessory biological functions of RNA ligases.

Fig. 1

Position and conserved features of introns within end-matured archaeal and eukaryal pre-tRNAs [11]. A Secondary structure diagram of end-matured, intron-containing archaeal tRNAs. Schemes a and b represent end-matured tRNAs with introns in the D-arm or the T-arm, respectively. Scheme c depicts an end-matured split pre-tRNA assembled from two separate primary transcripts [25]. B Secondary structure diagram of end-matured, intron-containing eukaryotic pre-tRNAs. The accompanying scheme represents non-canonical introns and end processing sites of a permuted pre-tRNA transcript in the red alga C. merolae. The non-canonical intron in the acceptor arm is assumed to be excised by tRNA end processing enzymes rather than pre-tRNA splicing factors [19]. A, adenosine; C, cytosine; G, guanosine; U, uridine; Ψ, pseudouridine; Y, pyrimidine; R, purine; asterisks indicate positions of additional introns, 5′-exonic regions are depicted in blue, 3′-exonic regions in red and intronic regions in green. Full grey circles indicate nonconserved nucleotides in regions of variable length, full blue circles indicate the position of the anticodon

Fig. 2

Enzymatic splicing of pre-tRNA. A Splicing of introns within pre-tRNA transcripts in archaea and eukaryotes is accomplished by separate cleavage and ligation reactions catalyzed by an endonuclease and a ligase enzyme, respectively. 5′-exons are depicted in blue, 3′-exons in red, and introns in green. B RNA ligation mechanisms. Brackets in gray indicate the names of enzymes catalyzing the indicated reactions. Pase phosphatase; CPD cyclic phosphodiesterase; Appp adenosine 5′-triphosphate; App adenosine 5′-diphosphate; Ap adenosine 5′-monophosphate; Gppp guanosine 5′-triphosphate; Gpp guanosine 5′-diphosphate; Nppp unspecified nucleoside 5′-triphosphate; Np unspecified nucleoside 5′-monophosphate; pp pyrophosphate; Ap-Lig adenylated ligase protein; NT-domain nucleotidyl transferase domain; Ptase 2′-phosphotransferase; NAD ⁺ nicotinamide adenine dinucleotide; Appr>p ADP-ribose-1″,2″- cyclic phosphate

Fig. 3

Domain and polypeptide organization of archetypical RNA ligase systems from bacteriophage T4 (T4 Pnkp, T4 Rnl2, and T4 Rnl1) [70, 77, 79, 80], S. cerevisiae (ScTRL1) [74], A. thaliana (AtRNL) [52, 75], and B. floridae (BfRNL and BfKinase/CPD) [87]. Nucleotidyl transferase domains are depicted in light blue, kinase domains in green, the DxDxT Pase (aspartic acid-based phosphatase) domain in white and 2H-CPD (two conserved histidine based phosphoesterase) domains in yellow. No published domain boundaries are currently available for the A. thaliana and B. floridae Kinase/CPD modules, which is indicated by a gradual transition between the two respective colors. The positions of key motifs are drawn to scale. Pnkp polynucleotide kinase/phosphatase; Pase phosphatase; CPD cyclic phosphodiesterase

Fig. 4

Domain organization of HSPC117 complex components (listed together with frequently encountered synonyms). Pfam domains are abbreviated as follows: DEAD DEAD/DEAH box helicase domain; SPRY SPRY domain (unknown function); Hel C Helicase conserved C-terminal domain; UPF0027 Domain of unknown function; DUF2465 Domain of unknown function; RLL Putative carnitine deficiency-associated protein domain

Fig. 5

Phyletic distribution of A HSPC117-associated proteins and B RNA ligase enzymes. Numbers in brackets next to category axis labels indicate the total amount of species in the respective taxonomic group and bars represent the percentage of species with detectable homologues. Homologues of proteins (right-hand side labels) were identified within the NCBI non-redundant protein database by BLAST or Hidden Markov Model searches (see supplemental material for further details)

Fig. 6

Schematic illustration of the phyletic distribution of identified RNA ligase polypeptide sequences