A second eukaryotic group with mitochondrion-encoded tmRNA In silico identification and experimental confirmation

• Published in: RNA biology Vol. 10; no. 7; pp. 1117 - 1124
• Main Authors: Hafez, Mohamed, Burger, Gertraud, Steinberg, Sergey V., Lang, Franz
• Format: Journal Article
• Language: English
• Published: United States Taylor & Francis 01.07.2013; Landes Bioscience
• Subjects: Base Sequence; Conserved Sequence; covariance model; Genes, Mitochondrial; Genome, Mitochondrial; Molecular Sequence Data; Nucleic Acid Conformation; oomycetes; Oomycetes - genetics; Oomycetes - metabolism; Phytophthora; post-transcriptional modification; Research Paper; RNA - chemistry; RNA - genetics; RNA - metabolism; RNA Processing, Post-Transcriptional; RNA, Bacterial - chemistry; RNA, Bacterial - genetics; RNA, Bacterial - metabolism; RNA, Messenger - chemistry; RNA, Messenger - genetics; RNA, Messenger - metabolism; RNA, Transfer - chemistry; RNA, Transfer - genetics; RNA, Transfer - metabolism; RNA-Seq analysis; Sequence Alignment; tmRNA processing; tmRNA tertiary structure; Transcription, Genetic; tmRNA processing; RNA-Seq analysis; oomycetes; tmRNA tertiary structure; Phytophthora; post-transcriptional modification; covariance model
• ISSN: 1547-6286; 1555-8584
• DOI: 10.4161/rna.25376

In bacteria, stalled ribosomes are rescued by transfer-mRNA (tmRNA) that catalyzes two steps. First, a non-encoded alanine is added to the incomplete polypeptide chain by the tRNA Ala -like portion of tmRNA, and second, the ribosome switches to the mRNA-like domain of tmRNA, thus resuming protein synthesis. Mitochondrial DNA (mtDNA)-encoded mt-tmRNA is so far only known from jakobid protists, but we posit that the corresponding ssrA gene may also reside in other mtDNAs. Here we present a highly sensitive covariance model built from jakobid ssrA genes that identifies previously unrecognized ssrA homologs in mtDNAs of oomycetes. These genes, located in previously unassigned genomic regions, are circular permuted as in α-Protobacteria, implying that pre-tmRNA is processed and the two pieces are held together by non-covalent interactions. RNA-Seq data from Phytophthora sojae confirm predicted processing sites as well as post-transcriptional addition of 3′ CCA, a prerequisite for tmRNAs to be charged with alanine by alanyl-tRNA synthetase. Structure modeling of oomycete tmRNAs infers that the mRNA-like domain is lacking as in jakobids. Features of mitochondrial tmRNAs include the G-U pair at position three of the acceptor stem, a hallmark of bacterial tmRNAs, and a T-loop sequence that differs from that of standard tRNAs and most bacterial tmRNAs, forming alternative, virtually isosteric tertiary interactions with the D-loop. The anticodon stem has two additional G-A base pairs formed between the D-loop and the variable region, shortening the length of the variable region to a single nucleotide.