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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 predicted protein-protein interactions. Circles represent genes in the initial network, and the triangles are the new genes recruited based on protein-protein interactions. The fold-change of gene expression levels in WH8102 under hyperosmotic stress against normal conditions is color-coded. (the Cytoscape program [46]).
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Figure 1: Genes recruited based on predicted protein-protein interactions. Circles represent genes in the initial network, and the triangles are the new genes recruited based on protein-protein interactions. The fold-change of gene expression levels in WH8102 under hyperosmotic stress against normal conditions is color-coded. (the Cytoscape program [46]).

Mentions: Protein-protein interactions, derived from large-scale two-hybrid experiments [31] or predicted based on protein fusion analyses [32], provide another source of information for expanding our initial network. We used the set of protein-protein interactions in WH8102 predicted previously by our group [5], which contains 950 interactions http://www.cs.uncc.edu/~zcsu/pathways/nitrogen/nitrogen. Specifically, SYNW0798 (a putative transcriptional regulator, ArsR family) and SYNW2141 (possibly a sterol-C-methyltransferase) are added into the network since they are predicted to form a protein complex with SdmT (SYNW1913) and gdmT (1914), respectively, which are already in the initial model. SYNW1232 (possibly a type-3 alternative RNA polymerase sigma factor), SYNW1416 (ABC transporter, nitrate-like) and SYNW2486 (putative cyanate ABC transporter) are added since they are predicted to form a protein complex with ProVWX (SYNW1915-1917). SYNW0412 (hypothetical protein), SYNW0641 (possible glycosyltransferase) and SYNW0645 (putative glycosyltransferase family 2 protein) are added since they are predicted to form a protein complex with Sps (SYNW2520). SYNW2236 (two-component response regulator) and SYNW2289 (two-component response regulator) are added since they are predicted to form a protein complex with SYNW0551. SYNW0125 (putative sugar-binding protein) is added since it is predicted to form a protein complex with SYNW2246. SYNW0034 (biotin carboxyl carrier protein subunit of acetyl-CoA carboxylase) and SYNW2324 (guanosine-3',5'-diphosphate) are added since they are predicted to form a protein complex with BetB (SYNW1956). SYNW0134 (SsrA-binding protein) is added since it is predicted to form a protein complex with SpeA (SYNW2359). SYNW0729 (hypothetical protein) is added since it is predicted to form a protein complex with KtrE (SYNW0663). Overall, 15 new proteins are added into the network based on their predicted interactions with proteins already in the network model (see Figure 1).


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 predicted protein-protein interactions. Circles represent genes in the initial network, and the triangles are the new genes recruited based on protein-protein interactions. The fold-change of gene expression levels in WH8102 under hyperosmotic stress against normal conditions is color-coded. (the Cytoscape program [46]).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: Genes recruited based on predicted protein-protein interactions. Circles represent genes in the initial network, and the triangles are the new genes recruited based on protein-protein interactions. The fold-change of gene expression levels in WH8102 under hyperosmotic stress against normal conditions is color-coded. (the Cytoscape program [46]).
Mentions: Protein-protein interactions, derived from large-scale two-hybrid experiments [31] or predicted based on protein fusion analyses [32], provide another source of information for expanding our initial network. We used the set of protein-protein interactions in WH8102 predicted previously by our group [5], which contains 950 interactions http://www.cs.uncc.edu/~zcsu/pathways/nitrogen/nitrogen. Specifically, SYNW0798 (a putative transcriptional regulator, ArsR family) and SYNW2141 (possibly a sterol-C-methyltransferase) are added into the network since they are predicted to form a protein complex with SdmT (SYNW1913) and gdmT (1914), respectively, which are already in the initial model. SYNW1232 (possibly a type-3 alternative RNA polymerase sigma factor), SYNW1416 (ABC transporter, nitrate-like) and SYNW2486 (putative cyanate ABC transporter) are added since they are predicted to form a protein complex with ProVWX (SYNW1915-1917). SYNW0412 (hypothetical protein), SYNW0641 (possible glycosyltransferase) and SYNW0645 (putative glycosyltransferase family 2 protein) are added since they are predicted to form a protein complex with Sps (SYNW2520). SYNW2236 (two-component response regulator) and SYNW2289 (two-component response regulator) are added since they are predicted to form a protein complex with SYNW0551. SYNW0125 (putative sugar-binding protein) is added since it is predicted to form a protein complex with SYNW2246. SYNW0034 (biotin carboxyl carrier protein subunit of acetyl-CoA carboxylase) and SYNW2324 (guanosine-3',5'-diphosphate) are added since they are predicted to form a protein complex with BetB (SYNW1956). SYNW0134 (SsrA-binding protein) is added since it is predicted to form a protein complex with SpeA (SYNW2359). SYNW0729 (hypothetical protein) is added since it is predicted to form a protein complex with KtrE (SYNW0663). Overall, 15 new proteins are added into the network based on their predicted interactions with proteins already in the network model (see Figure 1).

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