skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

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. https://doi.org/10.1186/s12864-020-6615-z.
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
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.
@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 = {2020},
month = {4}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.1186/s12864-020-6615-z

Save / Share:

Works referenced in this record:

Life without RNase P
journal, May 2008

  • Randau, Lennart; Schröder, Imke; Söll, Dieter
  • Nature, Vol. 453, Issue 7191
  • DOI: 10.1038/nature06833

Genome-wide search for yeast RNase P substrates reveals role in maturation of intron-encoded box C/D small nucleolar RNAs
journal, August 2008

  • Coughlin, D. J.; Pleiss, J. A.; Walker, S. C.
  • Proceedings of the National Academy of Sciences, Vol. 105, Issue 34
  • DOI: 10.1073/pnas.0801906105

Rfam: an RNA family database
journal, January 2003


Modulation of ribonuclease P expression in Escherichia coli by polyamines
journal, October 1992

  • Panagiotidis, Christos A.; Drainas, Denis; Shu-Ching, Huang
  • International Journal of Biochemistry, Vol. 24, Issue 10
  • DOI: 10.1016/0020-711X(92)90180-9

The enigma of ribonuclease P evolution
journal, October 2003


Physical mapping and nucleotide sequence of the rnpA gene that encodes the protein component of ribonuclease P in Escherichia coli
journal, January 1985


RNase P cleaves the adenine riboswitch and stabilizes pbuE mRNA in Bacillus subtilis
journal, April 2008


Minimal and RNA-free RNase P in Aquifex aeolicus
journal, October 2017

  • Nickel, Astrid I.; Wäber, Nadine B.; Gößringer, Markus
  • Proceedings of the National Academy of Sciences, Vol. 114, Issue 42
  • DOI: 10.1073/pnas.1707862114

Bcheck: a wrapper tool for detecting RNase P RNA genes
journal, January 2010


New insight into RNase P RNA structure from comparative analysis of the archaeal RNA
journal, February 2001


The Ribonuclease P Database
journal, January 1999


RNase P cleaves transient structures in some riboswitches
journal, August 2005

  • Altman, S.; Wesolowski, D.; Guerrier-Takada, C.
  • Proceedings of the National Academy of Sciences, Vol. 102, Issue 32
  • DOI: 10.1073/pnas.0505271102

In Vitro and in Vivo Processing of Cyanelle tmRNA by RNase P
journal, October 2001


In search of RNase P RNA from microbial genomes
journal, October 2004


Evolutionary variation in bacterial RNase P RNAs
journal, September 1998


Discovery of a minimal form of RNase P in Pyrobaculum
journal, December 2010

  • Lai, L. B.; Chan, P. P.; Cozen, A. E.
  • Proceedings of the National Academy of Sciences, Vol. 107, Issue 52
  • DOI: 10.1073/pnas.1013969107