Enabling comparative modeling of closely related genomes: Example genus Brucella
Abstract
For many scientific applications, it is highly desirable to be able to compare metabolic models of closely related genomes. In this study, we attempt to raise awareness to the fact that taking annotated genomes from public repositories and using them for metabolic model reconstructions is far from being trivial due to annotation inconsistencies. We are proposing a protocol for comparative analysis of metabolic models on closely related genomes, using fifteen strains of genus Brucella, which contains pathogens of both humans and livestock. This study lead to the identification and subsequent correction of inconsistent annotations in the SEED database, as well as the identification of 31 biochemical reactions that are common to Brucella, which are not originally identified by automated metabolic reconstructions. We are currently implementing this protocol for improving automated annotations within the SEED database and these improvements have been propagated into PATRIC, Model-SEED, KBase and RAST. This method is an enabling step for the future creation of consistent annotation systems and high-quality model reconstructions that will support in predicting accurate phenotypes such as pathogenicity, media requirements or type of respiration.
- Authors:
-
- Argonne National Lab. (ANL), Argonne, IL (United States); Univ. of Minho, Braga (Portugal)
- Argonne National Lab. (ANL), Argonne, IL (United States); Univ. of Chicago, Chicago, IL (United States)
- Argonne National Lab. (ANL), Argonne, IL (United States)
- Fellowship for Interpretation of Genomes, Burr Ridge, IL (United States)
- Argonne National Lab. (ANL), Argonne, IL (United States); Fellowship for Interpretation of Genomes, Burr Ridge, IL (United States)
- Virginia Polytechnic Inst. and State Univ. (Virginia Tech), Blacksburg, VA (United States)
- Publication Date:
- Research Org.:
- Argonne National Lab. (ANL), Argonne, IL (United States)
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1222724
- Grant/Contract Number:
- AC02-06CH11357
- Resource Type:
- Accepted Manuscript
- Journal Name:
- 3 Biotech
- Additional Journal Information:
- Journal Volume: 5; Journal Issue: 1; Journal ID: ISSN 2190-572X
- Publisher:
- Springer
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES
Citation Formats
Faria, José P., Edirisinghe, Janaka N., Davis, James J., Disz, Terrence, Hausmann, Anna, Henry, Christopher S., Olson, Robert, Overbeek, Ross A., Pusch, Gordon D., Shukla, Maulik, Vonstein, Veronika, and Wattam, Alice R. Enabling comparative modeling of closely related genomes: Example genus Brucella. United States: N. p., 2014.
Web. doi:10.1007/s13205-014-0202-4.
Faria, José P., Edirisinghe, Janaka N., Davis, James J., Disz, Terrence, Hausmann, Anna, Henry, Christopher S., Olson, Robert, Overbeek, Ross A., Pusch, Gordon D., Shukla, Maulik, Vonstein, Veronika, & Wattam, Alice R. Enabling comparative modeling of closely related genomes: Example genus Brucella. United States. https://doi.org/10.1007/s13205-014-0202-4
Faria, José P., Edirisinghe, Janaka N., Davis, James J., Disz, Terrence, Hausmann, Anna, Henry, Christopher S., Olson, Robert, Overbeek, Ross A., Pusch, Gordon D., Shukla, Maulik, Vonstein, Veronika, and Wattam, Alice R. Sat .
"Enabling comparative modeling of closely related genomes: Example genus Brucella". United States. https://doi.org/10.1007/s13205-014-0202-4. https://www.osti.gov/servlets/purl/1222724.
@article{osti_1222724,
title = {Enabling comparative modeling of closely related genomes: Example genus Brucella},
author = {Faria, José P. and Edirisinghe, Janaka N. and Davis, James J. and Disz, Terrence and Hausmann, Anna and Henry, Christopher S. and Olson, Robert and Overbeek, Ross A. and Pusch, Gordon D. and Shukla, Maulik and Vonstein, Veronika and Wattam, Alice R.},
abstractNote = {For many scientific applications, it is highly desirable to be able to compare metabolic models of closely related genomes. In this study, we attempt to raise awareness to the fact that taking annotated genomes from public repositories and using them for metabolic model reconstructions is far from being trivial due to annotation inconsistencies. We are proposing a protocol for comparative analysis of metabolic models on closely related genomes, using fifteen strains of genus Brucella, which contains pathogens of both humans and livestock. This study lead to the identification and subsequent correction of inconsistent annotations in the SEED database, as well as the identification of 31 biochemical reactions that are common to Brucella, which are not originally identified by automated metabolic reconstructions. We are currently implementing this protocol for improving automated annotations within the SEED database and these improvements have been propagated into PATRIC, Model-SEED, KBase and RAST. This method is an enabling step for the future creation of consistent annotation systems and high-quality model reconstructions that will support in predicting accurate phenotypes such as pathogenicity, media requirements or type of respiration.},
doi = {10.1007/s13205-014-0202-4},
journal = {3 Biotech},
number = 1,
volume = 5,
place = {United States},
year = {2014},
month = {3}
}
Web of Science
Works referenced in this record:
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
journal, September 1997
- Altschul, Stephen F.; Madden, Thomas L.; Schäffer, Alejandro A.
- Nucleic Acids Research, Vol. 25, Issue 17, p. 3389-3402
The RAST Server: Rapid Annotations using Subsystems Technology
journal, January 2008
- Aziz, Ramy K.; Bartels, Daniela; Best, Aaron A.
- BMC Genomics, Vol. 9, Issue 1, Article No. 75
The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003
journal, January 2003
- Boeckmann, B.
- Nucleic Acids Research, Vol. 31, Issue 1
Characterizing the Native Codon Usages of a Genome: An Axis Projection Approach
journal, August 2010
- Davis, J. J.; Olsen, G. J.
- Molecular Biology and Evolution, Vol. 28, Issue 1
Whole-genome random sequencing and assembly of Haemophilus influenzae Rd
journal, July 1995
- Fleischmann, R.; Adams, M.; White, O.
- Science, Vol. 269, Issue 5223
PATRIC: the Comprehensive Bacterial Bioinformatics Resource with a Focus on Human Pathogenic Species
journal, September 2011
- Gillespie, Joseph J.; Wattam, Alice R.; Cammer, Stephen A.
- Infection and Immunity, Vol. 79, Issue 11
High-throughput generation, optimization and analysis of genome-scale metabolic models
journal, August 2010
- Henry, Christopher S.; DeJongh, Matthew; Best, Aaron A.
- Nature Biotechnology, Vol. 28, Issue 9
Genome update: the 1000th genome - a cautionary tale
journal, January 2010
- Lagesen, K.; Ussery, D. W.; Wassenaar, T. M.
- Microbiology, Vol. 156, Issue 3
OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes
journal, September 2003
- Li, L.
- Genome Research, Vol. 13, Issue 9
IMG: the integrated microbial genomes database and comparative analysis system
journal, December 2011
- Markowitz, V. M.; Chen, I. -M. A.; Palaniappan, K.
- Nucleic Acids Research, Vol. 40, Issue D1
A comprehensive genome‐scale reconstruction of Escherichia coli metabolism—2011
journal, January 2011
- Orth, Jeffrey D.; Conrad, Tom M.; Na, Jessica
- Molecular Systems Biology, Vol. 7, Issue 1
The use of gene clusters to infer functional coupling
journal, March 1999
- Overbeek, R.; Fonstein, M.; D'Souza, M.
- Proceedings of the National Academy of Sciences, Vol. 96, Issue 6
The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes
journal, September 2005
- Overbeek, R.
- Nucleic Acids Research, Vol. 33, Issue 17
NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins
journal, January 2007
- Pruitt, K. D.; Tatusova, T.; Maglott, D. R.
- Nucleic Acids Research, Vol. 35, Issue Database
Building the repertoire of dispensable chromosome regions in Bacillus subtilis entails major refinement of cognate large-scale metabolic model
journal, October 2012
- Tanaka, Kosei; Henry, Christopher S.; Zinner, Jenifer F.
- Nucleic Acids Research, Vol. 41, Issue 1
A protocol for generating a high-quality genome-scale metabolic reconstruction
journal, January 2010
- Thiele, Ines; Palsson, Bernhard Ø
- Nature Protocols, Vol. 5, Issue 1
Comparative Genomics of Early-Diverging Brucella Strains Reveals a Novel Lipopolysaccharide Biosynthesis Pathway
journal, August 2012
- Wattam, Alice R.; Inzana, Thomas J.; Williams, Kelly P.
- mBio, Vol. 3, Issue 5
Works referencing / citing this record:
PATtyFams: Protein Families for the Microbial Genomes in the PATRIC Database
journal, February 2016
- Davis, James J.; Gerdes, Svetlana; Olsen, Gary J.
- Frontiers in Microbiology, Vol. 7