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Probing regulon of ArcA in Shewanella oneidensis MR-1 by integrated genomic analyses.

Gao H, Wang X, Yang ZK, Palzkill T, Zhou J - BMC Genomics (2008)

Bottom Line: To further determine genes regulated by the Arc system, an ArcA recognition weight matrix from DNA-binding data and bioinformatics analysis was generated and used to produce an ArcA sequence affinity map.By combining both techniques, we identified an ArcA regulon of at least 50 operons, of which only 6 were found to be directly controlled by ArcA in E. coli.These results indicate that the Arc system in S. oneidensis differs from that in E. coli substantially in terms of its physiological function and regulon while their binding motif are strikingly similar.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute for Environmental Genomics and Department of Botany and Microbiology, University of Oklahoma, Norman, Oklahoma 73019, USA. haichun@ou.edu

ABSTRACT

Background: The Arc two-component system is a global regulator controlling many genes involved in aerobic/anaerobic respiration and fermentative metabolism in Escherichia coli. Shewanella oneidensis MR-1 contains a gene encoding a putative ArcA homolog with ~81% amino acid sequence identity to the E. coli ArcA protein but not a full-length arcB gene.

Results: To understand the role of ArcA in S. oneidensis, an arcA deletion strain was constructed and subjected to both physiological characterization and microarray analysis. Compared to the wild-type MR-1, the mutant exhibited impaired aerobic growth and a defect in utilizing DMSO in the absence of O2. Microarray analyses on cells grown aerobically and anaerobically on fumarate revealed that expression of 1009 genes was significantly affected (p < 0.05) by the mutation. In contrast to E. coli ArcA, the protein appears to be dispensable in regulation of the TCA cycle in S. oneidensis. To further determine genes regulated by the Arc system, an ArcA recognition weight matrix from DNA-binding data and bioinformatics analysis was generated and used to produce an ArcA sequence affinity map. By combining both techniques, we identified an ArcA regulon of at least 50 operons, of which only 6 were found to be directly controlled by ArcA in E. coli.

Conclusion: These results indicate that the Arc system in S. oneidensis differs from that in E. coli substantially in terms of its physiological function and regulon while their binding motif are strikingly similar.

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Hierarchical clustering of selected genes. All these genes are listed in Table S2 (in additional file 3). Expression differences (ΔarcA/MR-1) were represented by colors: red, induced, yellow, insignificant, and green, repressed. Each pattern is identified by different colors on the dendrogram and by numbers that correspond to the gene expression patterns. +O2, aerobic conditions; -O2, anaerobic conditions.
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Figure 3: Hierarchical clustering of selected genes. All these genes are listed in Table S2 (in additional file 3). Expression differences (ΔarcA/MR-1) were represented by colors: red, induced, yellow, insignificant, and green, repressed. Each pattern is identified by different colors on the dendrogram and by numbers that correspond to the gene expression patterns. +O2, aerobic conditions; -O2, anaerobic conditions.

Mentions: While 1009 genes significantly affected in terms of their level of expression by the arcA mutation provide a large amount of information, it is less practical to discuss all of them in detail. Thus we generated a high-confidence list of 317 genes with at least a 2-fold change in expression and an ANOVA P value of < 0.01 (Table S2 in additional file 3). To identify co-regulated patterns of gene expression, we classified these 317 differentially expressed genes into 7 hierarchical clusters based on their log ratio of expression (Fig. 3).


Probing regulon of ArcA in Shewanella oneidensis MR-1 by integrated genomic analyses.

Gao H, Wang X, Yang ZK, Palzkill T, Zhou J - BMC Genomics (2008)

Hierarchical clustering of selected genes. All these genes are listed in Table S2 (in additional file 3). Expression differences (ΔarcA/MR-1) were represented by colors: red, induced, yellow, insignificant, and green, repressed. Each pattern is identified by different colors on the dendrogram and by numbers that correspond to the gene expression patterns. +O2, aerobic conditions; -O2, anaerobic conditions.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2262068&req=5

Figure 3: Hierarchical clustering of selected genes. All these genes are listed in Table S2 (in additional file 3). Expression differences (ΔarcA/MR-1) were represented by colors: red, induced, yellow, insignificant, and green, repressed. Each pattern is identified by different colors on the dendrogram and by numbers that correspond to the gene expression patterns. +O2, aerobic conditions; -O2, anaerobic conditions.
Mentions: While 1009 genes significantly affected in terms of their level of expression by the arcA mutation provide a large amount of information, it is less practical to discuss all of them in detail. Thus we generated a high-confidence list of 317 genes with at least a 2-fold change in expression and an ANOVA P value of < 0.01 (Table S2 in additional file 3). To identify co-regulated patterns of gene expression, we classified these 317 differentially expressed genes into 7 hierarchical clusters based on their log ratio of expression (Fig. 3).

Bottom Line: To further determine genes regulated by the Arc system, an ArcA recognition weight matrix from DNA-binding data and bioinformatics analysis was generated and used to produce an ArcA sequence affinity map.By combining both techniques, we identified an ArcA regulon of at least 50 operons, of which only 6 were found to be directly controlled by ArcA in E. coli.These results indicate that the Arc system in S. oneidensis differs from that in E. coli substantially in terms of its physiological function and regulon while their binding motif are strikingly similar.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute for Environmental Genomics and Department of Botany and Microbiology, University of Oklahoma, Norman, Oklahoma 73019, USA. haichun@ou.edu

ABSTRACT

Background: The Arc two-component system is a global regulator controlling many genes involved in aerobic/anaerobic respiration and fermentative metabolism in Escherichia coli. Shewanella oneidensis MR-1 contains a gene encoding a putative ArcA homolog with ~81% amino acid sequence identity to the E. coli ArcA protein but not a full-length arcB gene.

Results: To understand the role of ArcA in S. oneidensis, an arcA deletion strain was constructed and subjected to both physiological characterization and microarray analysis. Compared to the wild-type MR-1, the mutant exhibited impaired aerobic growth and a defect in utilizing DMSO in the absence of O2. Microarray analyses on cells grown aerobically and anaerobically on fumarate revealed that expression of 1009 genes was significantly affected (p < 0.05) by the mutation. In contrast to E. coli ArcA, the protein appears to be dispensable in regulation of the TCA cycle in S. oneidensis. To further determine genes regulated by the Arc system, an ArcA recognition weight matrix from DNA-binding data and bioinformatics analysis was generated and used to produce an ArcA sequence affinity map. By combining both techniques, we identified an ArcA regulon of at least 50 operons, of which only 6 were found to be directly controlled by ArcA in E. coli.

Conclusion: These results indicate that the Arc system in S. oneidensis differs from that in E. coli substantially in terms of its physiological function and regulon while their binding motif are strikingly similar.

Show MeSH
Related in: MedlinePlus