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

Title: Comparative Genomics of Regulation of Fatty Acid and Branched-chain Amino Acid Utilization in Proteobacteria

Abstract

Bacteria can use branched-chain amino acids (ILV, i.e. isoleucine, leucine, valine) and fatty acids (FA) as sole carbon and energy sources convering ILV into acetyl-CoA, propanoyl-CoA and propionyl-CoA, respectively. In this work, we used the comparative genomic approach to identify candidate transcriptional factors and DNA motifs that control ILV and FA utilization pathways in proteobacteria. The metabolic regulons were characterized based on the identification and comparison of candidate transcription factor binding sites in groups of phylogenetically related genomes. The reconstructed ILV/FA regulatory network demonstrates considerable variability and involves six transcriptional factors from the MerR, TetR and GntR families binding to eleven distinct DNA motifs. The ILV degradation genes in gamma- and beta-proteobacteria are mainly regulated by anovel regulator from the MerR family (e.g., LiuR in Pseudomonas aeruginosa) (40 species), in addition, the TetR-type regulator LiuQ was identified in some beta-proteobacteria (8 species). Besides the core set of ILV utilization genes, the LiuR regulon in some lineages is expanded to include genes from other metabolic pathways, such as the glyoxylate shunt and glutamate synthase in the Shewanella species. The FA degradation genes are controlled by four regulators including FadR in gamma-proteobacteria (34 species), PsrA in gamma- and beta-proteobacteria (45 species), FadPmore » in beta-proteobacteria (14 species), and LiuR orthologs in alpha-proteobacteria (22 species). The remarkable variability of the regulatory systems associated with the FA degradation pathway is discussed from the functional and evolutionary points of view.« less

Authors:
; ; ; ; ;
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
Genomics Division
OSTI Identifier:
965370
Report Number(s):
LBNL-1870E
Journal ID: ISSN 0021-9193; JOBAAY; TRN: US200920%%578
DOE Contract Number:  
DE-AC02-05CH11231
Resource Type:
Journal Article
Journal Name:
Journal of Bacteriology
Additional Journal Information:
Journal Name: Journal of Bacteriology; Journal ID: ISSN 0021-9193
Country of Publication:
United States
Language:
English
Subject:
59; AMINO ACIDS; BACTERIA; BIOLOGICAL PATHWAYS; BYPASSES; CARBON; CARBOXYLIC ACIDS; DNA; ENERGY SOURCES; FUNCTIONALS; GENES; LEUCINE; PSEUDOMONAS; REGULATIONS; TRANSCRIPTION FACTORS; VALINE; Genomics, Fatty Acid, Branched-Chain Amino Acd, Proteobacteria

Citation Formats

Kazakov, Alexey E, Rodionov, Dmitry A, Arkin, Adam Paul, Dubchak, Inna, Gelfand, Mikhail S, and Alm, Eric. Comparative Genomics of Regulation of Fatty Acid and Branched-chain Amino Acid Utilization in Proteobacteria. United States: N. p., 2008. Web.
Kazakov, Alexey E, Rodionov, Dmitry A, Arkin, Adam Paul, Dubchak, Inna, Gelfand, Mikhail S, & Alm, Eric. Comparative Genomics of Regulation of Fatty Acid and Branched-chain Amino Acid Utilization in Proteobacteria. United States.
Kazakov, Alexey E, Rodionov, Dmitry A, Arkin, Adam Paul, Dubchak, Inna, Gelfand, Mikhail S, and Alm, Eric. 2008. "Comparative Genomics of Regulation of Fatty Acid and Branched-chain Amino Acid Utilization in Proteobacteria". United States. https://www.osti.gov/servlets/purl/965370.
@article{osti_965370,
title = {Comparative Genomics of Regulation of Fatty Acid and Branched-chain Amino Acid Utilization in Proteobacteria},
author = {Kazakov, Alexey E and Rodionov, Dmitry A and Arkin, Adam Paul and Dubchak, Inna and Gelfand, Mikhail S and Alm, Eric},
abstractNote = {Bacteria can use branched-chain amino acids (ILV, i.e. isoleucine, leucine, valine) and fatty acids (FA) as sole carbon and energy sources convering ILV into acetyl-CoA, propanoyl-CoA and propionyl-CoA, respectively. In this work, we used the comparative genomic approach to identify candidate transcriptional factors and DNA motifs that control ILV and FA utilization pathways in proteobacteria. The metabolic regulons were characterized based on the identification and comparison of candidate transcription factor binding sites in groups of phylogenetically related genomes. The reconstructed ILV/FA regulatory network demonstrates considerable variability and involves six transcriptional factors from the MerR, TetR and GntR families binding to eleven distinct DNA motifs. The ILV degradation genes in gamma- and beta-proteobacteria are mainly regulated by anovel regulator from the MerR family (e.g., LiuR in Pseudomonas aeruginosa) (40 species), in addition, the TetR-type regulator LiuQ was identified in some beta-proteobacteria (8 species). Besides the core set of ILV utilization genes, the LiuR regulon in some lineages is expanded to include genes from other metabolic pathways, such as the glyoxylate shunt and glutamate synthase in the Shewanella species. The FA degradation genes are controlled by four regulators including FadR in gamma-proteobacteria (34 species), PsrA in gamma- and beta-proteobacteria (45 species), FadP in beta-proteobacteria (14 species), and LiuR orthologs in alpha-proteobacteria (22 species). The remarkable variability of the regulatory systems associated with the FA degradation pathway is discussed from the functional and evolutionary points of view.},
doi = {},
url = {https://www.osti.gov/biblio/965370}, journal = {Journal of Bacteriology},
issn = {0021-9193},
number = ,
volume = ,
place = {United States},
year = {Fri Oct 31 00:00:00 EDT 2008},
month = {Fri Oct 31 00:00:00 EDT 2008}
}