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Title: P finder: genomic and metagenomic annotation of RNase P RNA gene (rnpB)

Abstract

Abstract Background The 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. Results Of 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 computationallymore » 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. Conclusions The 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.« less

Authors:
ORCiD logo
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
OSTI Identifier:
1779954
Alternate Identifier(s):
OSTI ID: 1631254
Grant/Contract Number:  
AC05-00OR2272; AC05-00OR22725
Resource Type:
Published Article
Journal Name:
BMC Genomics
Additional Journal Information:
Journal Name: BMC Genomics Journal Volume: 21 Journal Issue: 1; Journal ID: ISSN 1471-2164
Publisher:
Springer Science + Business Media
Country of Publication:
United Kingdom
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Ellis, J. Christopher. P finder: genomic and metagenomic annotation of RNase P RNA gene (rnpB). United Kingdom: N. p., 2020. Web. doi:10.1186/s12864-020-6615-z.
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Ellis, J. Christopher. P finder: genomic and metagenomic annotation of RNase P RNA gene (rnpB). United Kingdom. https://doi.org/10.1186/s12864-020-6615-z
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Ellis, J. Christopher. Wed . "P finder: genomic and metagenomic annotation of RNase P RNA gene (rnpB)". United Kingdom. https://doi.org/10.1186/s12864-020-6615-z.
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@article{osti_1779954,
title = {P finder: genomic and metagenomic annotation of RNase P RNA gene (rnpB)},
author = {Ellis, J. Christopher},
abstractNote = {Abstract Background The 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. Results Of 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. Conclusions The 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.},
doi = {10.1186/s12864-020-6615-z},
journal = {BMC Genomics},
number = 1,
volume = 21,
place = {United Kingdom},
year = {Wed Apr 29 00:00:00 EDT 2020},
month = {Wed Apr 29 00:00:00 EDT 2020}
}
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Journal Article:
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Publisher's Version of Record
https://doi.org/10.1186/s12864-020-6615-z
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Figures / Tables:

Fig. 1 Fig. 1: Structural variability of RNase P RNA (RNase P RNA structures were adapted with permission from the RNAse P Database). RNase P RNA varies in both structure and length. a) Escherichia coli A-type b) Methanococcus jannaschii M-type c) Pyrobaculum aerophilum T-type d) Bacillus subtilis B-type e) Thermomicrobium roseum C-typemore » RNase P RNA« less
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Works referenced in this record:

Life without RNase P
journal, May 2008

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Genome-wide search for yeast RNase P substrates reveals role in maturation of intron-encoded box C/D small nucleolar RNAs
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  • Proceedings of the National Academy of Sciences, Vol. 107, Issue 52
  • DOI: 10.1073/pnas.1013969107
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