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Computational prediction of the osmoregulation network in Synechococcus sp. WH8102.

Mao X, Olman V, Stuart R, Paulsen IT, Palenik B, Xu Y - BMC Genomics (2010)

Bottom Line: In this study, we identified the key transporters, synthetases, signal sensor proteins and transcriptional regulator proteins, and found experimentally that of these proteins, 15 genes showed significantly changed expression levels under a mild hyperosmotic stress.From the predicted network model, we have made a number of interesting observations about WH8102.Specifically, we found that (i) the organism likely uses glycine betaine as the major osmolyte, and others such as glucosylglycerol, glucosylglycerate, trehalose, sucrose and arginine as the minor osmolytes, making it efficient and adaptable to its changing environment; and (ii) sigma38, one of the seven types of sigma factors, probably serves as a global regulator coordinating the osmoregulation network and the other relevant networks.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA.

ABSTRACT

Background: Osmotic stress is caused by sudden changes in the impermeable solute concentration around a cell, which induces instantaneous water flow in or out of the cell to balance the concentration. Very little is known about the detailed response mechanism to osmotic stress in marine Synechococcus, one of the major oxygenic phototrophic cyanobacterial genera that contribute greatly to the global CO2 fixation.

Results: We present here a computational study of the osmoregulation network in response to hyperosmotic stress of Synechococcus sp strain WH8102 using comparative genome analyses and computational prediction. In this study, we identified the key transporters, synthetases, signal sensor proteins and transcriptional regulator proteins, and found experimentally that of these proteins, 15 genes showed significantly changed expression levels under a mild hyperosmotic stress.

Conclusions: From the predicted network model, we have made a number of interesting observations about WH8102. Specifically, we found that (i) the organism likely uses glycine betaine as the major osmolyte, and others such as glucosylglycerol, glucosylglycerate, trehalose, sucrose and arginine as the minor osmolytes, making it efficient and adaptable to its changing environment; and (ii) sigma38, one of the seven types of sigma factors, probably serves as a global regulator coordinating the osmoregulation network and the other relevant networks.

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Genes recruited based on phylogenetic analyses. Circles represent genes in the initial network model, and the triangles are genes recruited based on phylogenetic analyses. All nodes are color-coded, representing different levels of fold-changes in gene expression in WH8102 under hyperosmotic stress versus normal conditions. (the Cytoscape program [46])
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Figure 2: Genes recruited based on phylogenetic analyses. Circles represent genes in the initial network model, and the triangles are genes recruited based on phylogenetic analyses. All nodes are color-coded, representing different levels of fold-changes in gene expression in WH8102 under hyperosmotic stress versus normal conditions. (the Cytoscape program [46])

Mentions: It has been well demonstrated that genes with highly similar phylogenetic profiles are functionally related [34]. We used the same 810 bacterial genomes mentioned earlier to construct a phylogenetic profile for each gene in WH8102 http://csbl.bmb.uga.edu/~xizeng/research/osmoregulation. Using the phylogenetic profile information, we identified 7 genes already in our initial network and added 13 additional genes to our network model, as shown in Figure 2. Specifically, EnvZ (SYNW0807) and OmpR (SYNW0808), ProVWX (SYNW1916-1918), and KtrBA (SYNW2168-2169) already in our initial network are identified again. SYNW0689, SYNW0746, SYNW0853, SYNW1282, SYNW1526-1527, and SYNW1530-1531 are added since they have very similar phylogenetic profiles with those of GgtCDA (SYNW1283-1285). We believe that they may be candidates for GgtB (b0529) of E. coli, and probably involved in glucosylglycerol synthesis. SYNW0754, SYNW0765, SYNW1250, SYNW2099 and SYNW2471 are added since they have very similar phylogenetic profiles with those of GpgSP (SYNW2436, 2434), and they are probably involved in glucosylglycerate synthesis.


Computational prediction of the osmoregulation network in Synechococcus sp. WH8102.

Mao X, Olman V, Stuart R, Paulsen IT, Palenik B, Xu Y - BMC Genomics (2010)

Genes recruited based on phylogenetic analyses. Circles represent genes in the initial network model, and the triangles are genes recruited based on phylogenetic analyses. All nodes are color-coded, representing different levels of fold-changes in gene expression in WH8102 under hyperosmotic stress versus normal conditions. (the Cytoscape program [46])
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2874817&req=5

Figure 2: Genes recruited based on phylogenetic analyses. Circles represent genes in the initial network model, and the triangles are genes recruited based on phylogenetic analyses. All nodes are color-coded, representing different levels of fold-changes in gene expression in WH8102 under hyperosmotic stress versus normal conditions. (the Cytoscape program [46])
Mentions: It has been well demonstrated that genes with highly similar phylogenetic profiles are functionally related [34]. We used the same 810 bacterial genomes mentioned earlier to construct a phylogenetic profile for each gene in WH8102 http://csbl.bmb.uga.edu/~xizeng/research/osmoregulation. Using the phylogenetic profile information, we identified 7 genes already in our initial network and added 13 additional genes to our network model, as shown in Figure 2. Specifically, EnvZ (SYNW0807) and OmpR (SYNW0808), ProVWX (SYNW1916-1918), and KtrBA (SYNW2168-2169) already in our initial network are identified again. SYNW0689, SYNW0746, SYNW0853, SYNW1282, SYNW1526-1527, and SYNW1530-1531 are added since they have very similar phylogenetic profiles with those of GgtCDA (SYNW1283-1285). We believe that they may be candidates for GgtB (b0529) of E. coli, and probably involved in glucosylglycerol synthesis. SYNW0754, SYNW0765, SYNW1250, SYNW2099 and SYNW2471 are added since they have very similar phylogenetic profiles with those of GpgSP (SYNW2436, 2434), and they are probably involved in glucosylglycerate synthesis.

Bottom Line: In this study, we identified the key transporters, synthetases, signal sensor proteins and transcriptional regulator proteins, and found experimentally that of these proteins, 15 genes showed significantly changed expression levels under a mild hyperosmotic stress.From the predicted network model, we have made a number of interesting observations about WH8102.Specifically, we found that (i) the organism likely uses glycine betaine as the major osmolyte, and others such as glucosylglycerol, glucosylglycerate, trehalose, sucrose and arginine as the minor osmolytes, making it efficient and adaptable to its changing environment; and (ii) sigma38, one of the seven types of sigma factors, probably serves as a global regulator coordinating the osmoregulation network and the other relevant networks.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA.

ABSTRACT

Background: Osmotic stress is caused by sudden changes in the impermeable solute concentration around a cell, which induces instantaneous water flow in or out of the cell to balance the concentration. Very little is known about the detailed response mechanism to osmotic stress in marine Synechococcus, one of the major oxygenic phototrophic cyanobacterial genera that contribute greatly to the global CO2 fixation.

Results: We present here a computational study of the osmoregulation network in response to hyperosmotic stress of Synechococcus sp strain WH8102 using comparative genome analyses and computational prediction. In this study, we identified the key transporters, synthetases, signal sensor proteins and transcriptional regulator proteins, and found experimentally that of these proteins, 15 genes showed significantly changed expression levels under a mild hyperosmotic stress.

Conclusions: From the predicted network model, we have made a number of interesting observations about WH8102. Specifically, we found that (i) the organism likely uses glycine betaine as the major osmolyte, and others such as glucosylglycerol, glucosylglycerate, trehalose, sucrose and arginine as the minor osmolytes, making it efficient and adaptable to its changing environment; and (ii) sigma38, one of the seven types of sigma factors, probably serves as a global regulator coordinating the osmoregulation network and the other relevant networks.

Show MeSH
Related in: MedlinePlus