Abstract
BackgroundThe rnpB gene encodes for an essential catalytic RNA (RNase P). Like other essential RNAs, RNase P’s sequence is highly variable. However, unlike other essential RNAs (i.e. tRNA, 16 S, 6 S,...) its structure is also variable with at least 5 distinct structure types observed in prokaryotes. This structural variability makes it labor intensive and challenging to create and maintain covariance models for the detection of RNase P RNA in genomic and metagenomic sequences. The lack of a facile and rapid annotation algorithm has led to the rnpB gene being the most grossly under annotated essential gene in completed prokaryotic genomes with only a 24% annotation rate. Here we describe the coupling of the largest RNase P RNA database with the local alignment scoring algorithm to create the most sensitive and rapid prokaryote rnpB gene identification and annotation algorithm to date.ResultsOf the 2772 completed microbial genomes downloaded from GenBank only 665 genomes had an annotated rnpB gene. We applied P Finder to these genomes and were able to identify 2733 or nearly 99% of the 2772 microbial genomes examined. From these results four new rnpB genes that encode the minimal T-type P RNase P RNAs were identified computationally for the first time. In addition, only the second C-type RNase P RNA was identified in Sphaerobacter thermophilus. Of special note, no RNase P RNAs were detected in several obligate endosymbionts of sap sucking insects suggesting a novel evolutionary adaptation.ConclusionsThe coupling of the largest RNase P RNA database and associated structure class identification with the P Finder algorithm is both sensitive and rapid, yielding high quality results to aid researchers annotating either genomic or metagenomic data. It is the only algorithm to date that can identify challenging RNAse P classes such as C-type and the minimal T-type RNase P RNAs. P Finder is written in C# and has a user-friendly GUI that can run on multiple 64-bit windows platforms (Windows Vista/7/8/10). P Finder is free available for download at https://github.com/JChristopherEllis/P-Finder as well as a small sample RNase P RNA file for testing.
Highlights
ResultsOf the 2772 completed microbial genomes downloaded from GenBank only 665 genomes had an annotated rnpB gene
The rnpB gene encodes for an essential catalytic RNA (RNase P)
We have demonstrated that P Finder can rapidly and accurately identify all five structural types of Ribonuclease P (RNase P) RNA from large sequence data
Summary
To P or not to P: identifying RNase P RNA (rnpB) in genomic sequences RNAse P RNA (rnpB) is poorly annotated in completed genomic sequences available for download at GenBank. P Finder is composed of the largest prokaryote RNase P RNA database yet assembled with more than 8300 bacterial and archaeal sequences incorporated from the Using these results, we examined the distribution of the different structural types in the completed genomic sequences available for download at GenBank. To examine P Finder’s accuracy, we compared it to BCheck by having both algorithms identify the rnpB gene in the 2772 completed genomes downloaded from GenBank. The most variation of predicted rnpB genes occurs among the B-type RNase P RNAs. BCheck appears to identify the start location a few nucleotides before P Finder. Neither P finder nor BCheck were able to identify an rnpB gene in several bacterial obligate endosymbionts (Table 2) These organisms have extremely small genomes typically less than 400,000 base pairs. Is there a novel RNase P RNA in these obligate endosymbionts? Have they evolved a new process for the maturation of tRNA like N. equitans? Could they rely on the host mature tRNA for translation? Regardless of the answer, it will likely be a new evolutionary story in the bacterial kingdom
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