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A systems biology approach to investigate the response of Synechocystis sp. PCC6803 to a high salt environment.

Pandhal J, Noirel J, Wright PC, Biggs CA - Saline Syst. (2009)

Bottom Line: Differentially expressed proteins involved in metabolic responses were also analysed using the probabilitistic tool Mixed Model on Graphs (MMG), where the role of energy conversion through glycolysis and reducing power through pentose phosphate pathway were highlighted.This study demonstrates the effectiveness of using a systems biology approach in answering environmental, and in particular, salt adaptation questions in Synechocystis sp.PCC6803.

View Article: PubMed Central - HTML - PubMed

Affiliation: ChELSI Institute, Department of Chemical and Process Engineering, The University of Sheffield, Sheffield, UK. j.pandhal@sheffield.ac.uk

ABSTRACT

Background: Salt overloading during agricultural processes is causing a decrease in crop productivity due to saline sensitivity. Salt tolerant cyanobacteria share many cellular characteristics with higher plants and therefore make ideal model systems for studying salinity stress. Here, the response of fully adapted Synechocystis sp. PCC6803 cells to the addition of 6% w/v NaCl was investigated using proteomics combined with targeted analysis of transcripts.

Results: Isobaric mass tagging of peptides led to accurate relative quantitation and identification of 378 proteins, and approximately 40% of these were differentially expressed after incubation in BG-11 media supplemented with 6% salt for 9 days. Protein abundance changes were related to essential cellular functional alterations. Differentially expressed proteins involved in metabolic responses were also analysed using the probabilitistic tool Mixed Model on Graphs (MMG), where the role of energy conversion through glycolysis and reducing power through pentose phosphate pathway were highlighted. Temporal RT-qPCR experiments were also run to investigate protein expression changes at the transcript level, for 14 non-metabolic proteins. In 9 out of 14 cases the mRNA changes were in accordance with the proteins.

Conclusion: Synechocystis sp. PCC6803 has the ability to regulate essential metabolic processes to enable survival in high salt environments. This adaptation strategy is assisted by further regulation of proteins involved in non-metabolic cellular processes, supported by transcriptional and post-transcriptional control. This study demonstrates the effectiveness of using a systems biology approach in answering environmental, and in particular, salt adaptation questions in Synechocystis sp. PCC6803.

No MeSH data available.


Protein networks down regulated under high salt conditions identified using Mixed Model on Graphs (MMG). The nodes represent the single-unit and multiple-unit enzymes in Synechocystis's metabolic network, as per the KEGG database. Two enzymes are connected when a product of the reaction catalysed by one enzyme is a reactant of the reaction catalysed by the other enzyme.
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Figure 2: Protein networks down regulated under high salt conditions identified using Mixed Model on Graphs (MMG). The nodes represent the single-unit and multiple-unit enzymes in Synechocystis's metabolic network, as per the KEGG database. Two enzymes are connected when a product of the reaction catalysed by one enzyme is a reactant of the reaction catalysed by the other enzyme.

Mentions: The networks identified by MMG using the dataset resulting from Workflow 2 are presented in Figure 1 (up regulated in high salt conditions) and Figure 2 (down regulated in high salt conditions). They were obtained by selecting proteins with a probability of being up-regulated, p+, greater than 0.45 (for the up-regulated network) and a probability of being down-regulated, p-, greater than 0.45 (for the down-regulated network). The nodes in Figure 1 and 2, represent the single-unit and multiple-unit enzymes in Synechocystis' metabolic network, as per the KEGG database. Two enzymes are connected when a product of the reaction catalysed by one enzyme, is a reactant of the reaction catalysed by the other enzyme. Edges are weighted during the MMG analysis, and the weights are inversely proportional to the frequency of the compound within the metabolic network in order to give less prominence to currency metabolites such as ATP, ADP, NADPH, etc.


A systems biology approach to investigate the response of Synechocystis sp. PCC6803 to a high salt environment.

Pandhal J, Noirel J, Wright PC, Biggs CA - Saline Syst. (2009)

Protein networks down regulated under high salt conditions identified using Mixed Model on Graphs (MMG). The nodes represent the single-unit and multiple-unit enzymes in Synechocystis's metabolic network, as per the KEGG database. Two enzymes are connected when a product of the reaction catalysed by one enzyme is a reactant of the reaction catalysed by the other enzyme.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2743698&req=5

Figure 2: Protein networks down regulated under high salt conditions identified using Mixed Model on Graphs (MMG). The nodes represent the single-unit and multiple-unit enzymes in Synechocystis's metabolic network, as per the KEGG database. Two enzymes are connected when a product of the reaction catalysed by one enzyme is a reactant of the reaction catalysed by the other enzyme.
Mentions: The networks identified by MMG using the dataset resulting from Workflow 2 are presented in Figure 1 (up regulated in high salt conditions) and Figure 2 (down regulated in high salt conditions). They were obtained by selecting proteins with a probability of being up-regulated, p+, greater than 0.45 (for the up-regulated network) and a probability of being down-regulated, p-, greater than 0.45 (for the down-regulated network). The nodes in Figure 1 and 2, represent the single-unit and multiple-unit enzymes in Synechocystis' metabolic network, as per the KEGG database. Two enzymes are connected when a product of the reaction catalysed by one enzyme, is a reactant of the reaction catalysed by the other enzyme. Edges are weighted during the MMG analysis, and the weights are inversely proportional to the frequency of the compound within the metabolic network in order to give less prominence to currency metabolites such as ATP, ADP, NADPH, etc.

Bottom Line: Differentially expressed proteins involved in metabolic responses were also analysed using the probabilitistic tool Mixed Model on Graphs (MMG), where the role of energy conversion through glycolysis and reducing power through pentose phosphate pathway were highlighted.This study demonstrates the effectiveness of using a systems biology approach in answering environmental, and in particular, salt adaptation questions in Synechocystis sp.PCC6803.

View Article: PubMed Central - HTML - PubMed

Affiliation: ChELSI Institute, Department of Chemical and Process Engineering, The University of Sheffield, Sheffield, UK. j.pandhal@sheffield.ac.uk

ABSTRACT

Background: Salt overloading during agricultural processes is causing a decrease in crop productivity due to saline sensitivity. Salt tolerant cyanobacteria share many cellular characteristics with higher plants and therefore make ideal model systems for studying salinity stress. Here, the response of fully adapted Synechocystis sp. PCC6803 cells to the addition of 6% w/v NaCl was investigated using proteomics combined with targeted analysis of transcripts.

Results: Isobaric mass tagging of peptides led to accurate relative quantitation and identification of 378 proteins, and approximately 40% of these were differentially expressed after incubation in BG-11 media supplemented with 6% salt for 9 days. Protein abundance changes were related to essential cellular functional alterations. Differentially expressed proteins involved in metabolic responses were also analysed using the probabilitistic tool Mixed Model on Graphs (MMG), where the role of energy conversion through glycolysis and reducing power through pentose phosphate pathway were highlighted. Temporal RT-qPCR experiments were also run to investigate protein expression changes at the transcript level, for 14 non-metabolic proteins. In 9 out of 14 cases the mRNA changes were in accordance with the proteins.

Conclusion: Synechocystis sp. PCC6803 has the ability to regulate essential metabolic processes to enable survival in high salt environments. This adaptation strategy is assisted by further regulation of proteins involved in non-metabolic cellular processes, supported by transcriptional and post-transcriptional control. This study demonstrates the effectiveness of using a systems biology approach in answering environmental, and in particular, salt adaptation questions in Synechocystis sp. PCC6803.

No MeSH data available.