The phylogenetic distribution of bacterial ribonucleases

Abstract

Ribonucleases play key, often essential, roles in cellular metabolism. Nineteen ribonuclease activities, from 22 different proteins, have so far been described in bacteria, the majority of them from either Escherichia coli or Bacillus subtilis. Here we examine the phylogenetic distribution of all of these ribonucleases in 50 eubacterial and archaeal species whose genomes have been completely sequenced, with particular emphasis on the endoribonucleases. Although some enzymes are very highly conserved throughout evolution, there appears to be no truly universal ribonuclease. While some organisms, like E.coli, have a large selection of ribonucleases, many with overlapping functions, others seem to have relatively few or have many that remain to be discovered.

Figure 1

(Opposite and above) The phylogenetic distribution of eubacterial RNases. The endonucleases are shown in the top row and the exonucleases in the bottom row of blocks for each species. The phylogenetic relationship between the different organisms was calculated by comparing 16S rRNA sequences using Clustal X (64). The phylogenetic tree was drawn using Phylodendron (http://iubio.bio.indiana.edu/soft/molbio/java/apps/trees/) and arranged according to Olsen et al. (65). The abbreviations for the different RNases are as follows: III, RNase III; P, RNase P; Z, RNase Z; M5, RNase M5; E, RNase E; G, RNase G; EG, RNase E/G; H1, RNase HI; H2, RNase HII; H3, RNase HIII; I, RNase I; Bsn, RNase Bsn; Bar, Barnase; R, RNase R; II, RNase II; Pnp, polynucleotide phosphorylase; PH, RNase PH; O, oligoribonuclease; T, RNase T; D, RNase D; BN, RNase BN; Y, RNase YhaM. ²Two potential orthologues present.

Figure 1

(Opposite and above) The phylogenetic distribution of eubacterial RNases. The endonucleases are shown in the top row and the exonucleases in the bottom row of blocks for each species. The phylogenetic relationship between the different organisms was calculated by comparing 16S rRNA sequences using Clustal X (64). The phylogenetic tree was drawn using Phylodendron (http://iubio.bio.indiana.edu/soft/molbio/java/apps/trees/) and arranged according to Olsen et al. (65). The abbreviations for the different RNases are as follows: III, RNase III; P, RNase P; Z, RNase Z; M5, RNase M5; E, RNase E; G, RNase G; EG, RNase E/G; H1, RNase HI; H2, RNase HII; H3, RNase HIII; I, RNase I; Bsn, RNase Bsn; Bar, Barnase; R, RNase R; II, RNase II; Pnp, polynucleotide phosphorylase; PH, RNase PH; O, oligoribonuclease; T, RNase T; D, RNase D; BN, RNase BN; Y, RNase YhaM. ²Two potential orthologues present.

Figure 2

RNase E/G protein families. The ∼500 amino acid core RNase E/G domain is shown in black. This domain is continuous in all RNase E/G proteins except those of the α-Proteobacteria, which have an insertion. N-terminal and C-terminal extensions (hatched or white bars) are depicted as the average size of those of the different family members examined. The different fillings reflect the lack of sequence homology.