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Comparative Study
. 2004 Oct;10(10):1533-40.
doi: 10.1261/rna.7970404. Epub 2004 Aug 30.

In search of RNase P RNA from microbial genomes

Yong Li  1 , Sidney Altman
Affiliations
Comparative Study

In search of RNase P RNA from microbial genomes

Yong Li et al. RNA. 2004 Oct.

Abstract

A simple procedure has been developed to quickly retrieve and validate the DNA sequence encoding the RNA subunit of ribonuclease P (RNase P RNA) from microbial genomes. RNase P RNA sequences were identified from 94% of bacterial and archaeal complete genomes where previously no RNase P RNA was annotated. A sequence was found in camelpox virus, highly conserved in all orthopoxviruses (including smallpox virus), which could fold into a putative RNase P RNA in terms of conserved primary features and secondary structure. New structure features of RNase P RNA that enable one to distinguish bacteria from archaea and eukarya were found. This RNA is yet another RNA that can be a molecular criterion to divide the living world into three domains (bacteria, archaea, and eukarya). The catalytic center of this RNA, and its detection from some environmental whole genome shotgun sequences, is also discussed.

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Figures

FIGURE 1.
FIGURE 1.
The conserved structures of RNase P RNA from bacteria (A) and archaea (B). Helices are numbered from 5′ to 3′ according to the structure of the E. coli RNA and are designated with P (“pairing”, e.g., P1, P2; Chen and Pace 1997; Massire et al. 1998). The loop regions are designated with L/J (L3 linking the same P3 helix, J2/3 linking P2 and P3). For reasons of simplicity, some helices and loops may be simplified into one loop (i.e., L10 of archaea may contain P11, P12, L12, J11/12, and J12/11; Chen and Pace 1997; Massire et al. 1998; Harris et al. 2001).
FIGURE 2.
FIGURE 2.
The core structure of RNase P RNA for both bacteria and archaea. (A) The conserved secondary structure of RNase P RNAs. There are some exceptions in the conserved regions in some microorganisms: (1) U→A in Sulfolobus tokadaii; (2) G→U, C→U in Phytoplasma asteris (onion yellows) and Phytoplasma sp. (periwinkle); (3) A→G in Shewanella putrefaciens and Shewanella oneidensis; (4) G→C in Mycoplasma pneumoniae; (5) A→G in Metallosphaera sedula; and (6) A→G in Herpetosiphon aurantiacus. (B) The schematic representation view of the catalytic domain of the core structure (based on previously established 3D modeling of bacterial RNase P RNA; Massire et al. 1998). This illustration attempts to render the respective spatial arrangement of helices and stacks in the 3D model. The arrows point to the 5′ to 3′ direction of the RNA. The structural elements have been implied to engage in catalysis: (1) polynuclear metal ion binding site in the catalytic domain by phosphorothioate modification and quantitative analysis of thiophilic metal ion rescue on catalysis (Christian et al. 2002); (2) metal ion specificity (C→U makes Ca2+ a better ion; Frank and Pace 1997); (3) nucleotides critical to catalysis identified by NAIM and site-specific modification (Kazantsev and Pace 1998; Kaye et al. 2002); the double arrows point to the locations of phosphate oxygen where sulfur substitution disrupts catalytic activity; and (4) the active site mapped by a photoaffinity agent coupled to the 5′-phosphate of a tRNA (Burgin and Pace 1990).
FIGURE 3.
FIGURE 3.
Comparison of the secondary structures of RNase P RNA from archaea (A), bacteria (B), and eukarya (E). The conserved structure of a bacterial RNA is depicted as a backbone. Different features are labeled by rectangles and descriptions with different colors.
FIGURE 4.
FIGURE 4.
A sequence from camelpox virus that forms a structure similar to the core structure of RNase P RNA from archaea and bacteria. The conserved residues, like those in Figure 2 ▶, are in uppercase letters. The L7 region could fold into a cruciform without the conserved P11 as in bacteria. The sequence (413 bp from 155,800 to 156,212 in camelpox genome) covers the intergenic region between a hypothetical ORF (155,444–155,689) and a gene coding for a DNA ligase (155,961–157,619), as well as part of the coding sequence for the ligase (Gubser and Smith 2002).
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