Of P and Z: mitochondrial tRNA processing enzymes

Abstract

Mitochondrial tRNAs are generally synthesized as part of polycistronic transcripts. Release of tRNAs from these precursors is thus not only required to produce functional adaptors for translation, but also responsible for the maturation of other mitochondrial RNA species. Cleavage of mitochondrial tRNAs appears to be exclusively accomplished by endonucleases. 5'-end maturation in the mitochondria of different Eukarya is achieved by various kinds of RNase P, representing the full range of diversity found in this enzyme family. While ribonucleoprotein enzymes with RNA components of bacterial-like appearance are found in a few unrelated protists, algae, and fungi, highly degenerate RNAs of dramatic size variability are found in the mitochondria of many fungi. The majority of mitochondrial RNase P enzymes, however, appear to be pure protein enzymes. Human mitochondrial RNase P, the first to be identified and possibly the prototype of all animal mitochondrial RNases P, is composed of three proteins. Homologs of its nuclease subunit MRPP3/PRORP, are also found in plants, algae and several protists, where they are apparently responsible for RNase P activity in mitochondria (and beyond) without the help of extra subunits. The diversity of RNase P enzymes is contrasted by the uniformity of mitochondrial RNases Z, which are responsible for 3'-end processing. Only the long form of RNase Z, which is restricted to eukarya, is found in mitochondria, even when an additional short form is present in the same organism. Mitochondrial tRNA processing thus appears dominated by new, eukaryal inventions rather than bacterial heritage. This article is part of a Special Issue entitled: Mitochondrial Gene Expression.

Fig. 1

Schematic structures of RNase P RNAs. (A) Universal consensus secondary structure of bacterial, archaeal, and eukaryal nuclear RNase P RNAs . Gray indicates variable structures connecting conserved regions. Helices P1–P12 and conserved sequence regions CR I–V are indicated. Structural elements absent only in single, minor phylogenetic groups are included: P12, absent in M. genitalium; P11, P12, CR II, and CR III, absent in P. aerophilum. (B) Secondary structure of S. cerevisiae mtRNase P RNA (Rpm1r) .

Fig. 2

Structure of proteinaceous RNase P (PRORP). MTS, mitochondrial targeting sequence (facultative); PPR, pentatricopeptide repeat; CXXC, zinc-finger-like motif; NYN domain, N4BP1-YacP-like metallonuclease domain . Sequence logos were generated using WebLogo and are based on a ClustalW alignment of PRORP sequences from the following species (number of PRORPs if more than one indicated in parentheses): man, macaque, dog, cow, mouse, platypus, chicken, Xenopus tropicalis, zebrafish, Tribolium castaneum, fruit fly, Aedes aegypti, Anopheles gambiae, Culex pipiens, Nasonia vitripennis, A. thaliana (3), Oryza sativa (3), Physcomitrella patens (3), T. brucei (2), Leishmania major (2).