Both kinds of RNase P in all domains of life: surprises galore

Abstract

RNase P, an essential housekeeping endonuclease needed for 5 ′ ′ ′ ′ ′-processing of tRNAs, exists in two distinct forms: one with an RNA-and the other with a protein-based active site. The notion that the protein form of RNase P exists only in eukaryotes has been upended by the recent discovery of a protein-only variant in Bacteria and Archaea. The use of these two divergent scaffolds, shaped by convergent evolution, in all three domains of life inspires questions relating to the ancestral form of RNase P, as well as their origins and function(s) in vivo. Results from our analysis of publicly available bacterial and archaeal genomes suggest that the widespread RNA-based ribonucleoprotein variant is likely the ancient form. We also discuss the possible genetic origins and function of RNase P, including how the simultaneous presence of its variants may contribute to the fitness of their host organisms.

Involvement of PIN‐like domain nucleases in tRNA processing and translation regulation

“…). Bioinformatic analyses have shown that HARP proteins are present in 2 of the 4 Archaea superphyla, however in only 6 of the 36 bacteria phyla; and in most cases in only a small subset of the genera within each of these phyla . Moreover, in bacteria and archaea, HARP is rarely found as the sole putative RNase P but most often coexist with the ribozyme form of RNase P. As such, it is still unclear if HARP enzymes all have RNase P activity in vivo or whether they function as RNase P enzymes only in specific cases.…”

Structure and mechanistic features of the prokaryotic minimal RNase P

“…This prokaryotic type of minimal RNase P system was named HARP (for: H omolog of A quifex R Nase P ) and identified in 5 other of the 36 bacterial phyla beyond Aquificae ( Nickel et al, 2017 ). Among HARP-encoding bacteria, only some lack the genes for RNA-based RNase P (i.e., Aquificae, Nitrospirae), while others harbor rnpA and rnpB genes as well ( Daniels et al, 2019 ; Nickel et al, 2017 ). Overall, HARP genes are more abundant in archaea than bacteria.…”

“…Overall, HARP genes are more abundant in archaea than bacteria. However, all of these HARP-positive archaea also encode the RNA and protein subunits of the RNA-based RNase P ( Nickel et al, 2017 ; Daniels et al, 2019 ). Remarkably, HARP gene knockouts in two Euryarchaeota, Haloferax volcanii and Methanosarcina mazei , showed no growth phenotypes under standard conditions, temperature, and salt stress ( H. volcanii ) or nitrogen deficiency ( M. mazei ) ( Schwarz et al, 2019 ).…”

“…The findings suggest that HARP is neither essential nor represents the housekeeping RNase P function in archaea, explaining its sporadic loss in archaea. HARPs are evolutionarily linked to toxin-antitoxin systems ( Daniels et al, 2019 ; Schwarz et al, 2019 ; Gobert et al, 2019 ). Frequently, the toxin proteins are endoribonucleases that cleave mRNA, rRNA, tmRNA, or tRNA to inhibit protein biosynthesis in response to certain stresses ( Masuda and Inouye, 2017 ).…”

Minimal protein-only RNase P structure reveals insights into tRNA precursor recognition and catalysis

“…A previous study reported that Aq880 comprises only the nuclease domain, which also belongs to the PIN superfamily (12). Bioinformatics analysis has shown that homologs of Aq880 are widely present in some phyla of bacteria and archaea (termed HARPs for homologs of Aquifex RNase P) (11,13).…”