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K-shell Analysis Reveals Distinct Functional Parts in an Electron Transfer Network and Its Implications for Extracellular Electron Transfer.

Ding D, Li L, Shu C, Sun X - Front Microbiol (2016)

Bottom Line: We found that there was a negative correlation between the k s (k-shell values) and the average DR_100 (disordered regions per 100 amino acids) in every shell, which suggested that disordered regions of proteins played an important role during the formation and extension of the electron transfer network.Specifically, the fourth shell was responsible for EET and the c-type cytochromes in the remaining shells of the electron transfer network were involved in aiding EET.Taken together, these results show that there are distinct functional parts in the electron transfer network of S. oneidensis MR-1, and the EET processes could achieve high efficiency through cooperation through such an electron transfer network.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast UniversityNanjing, China; Department of Mathematics and Computer Science, Chizhou CollegeChizhou, China.

ABSTRACT
Shewanella oneidensis MR-1 is capable of extracellular electron transfer (EET) and hence has attracted considerable attention. The EET pathways mainly consist of c-type cytochromes, along with some other proteins involved in electron transfer processes. By whole genome study and protein interactions inquisition, we constructed a large-scale electron transfer network containing 2276 interactions among 454 electron transfer related proteins in S. oneidensis MR-1. Using the k-shell decomposition method, we identified and analyzed distinct parts of the electron transfer network. We found that there was a negative correlation between the k s (k-shell values) and the average DR_100 (disordered regions per 100 amino acids) in every shell, which suggested that disordered regions of proteins played an important role during the formation and extension of the electron transfer network. Furthermore, proteins in the top three shells of the network are mainly located in the cytoplasm and inner membrane; these proteins can be responsible for transfer of electrons into the quinone pool in a wide variety of environmental conditions. In most of the other shells, proteins are broadly located throughout the five cellular compartments (cytoplasm, inner membrane, periplasm, outer membrane, and extracellular), which ensures the important EET ability of S. oneidensis MR-1. Specifically, the fourth shell was responsible for EET and the c-type cytochromes in the remaining shells of the electron transfer network were involved in aiding EET. Taken together, these results show that there are distinct functional parts in the electron transfer network of S. oneidensis MR-1, and the EET processes could achieve high efficiency through cooperation through such an electron transfer network.

No MeSH data available.


Related in: MedlinePlus

(A) Visualization of the k-shell structure of the S. oneidensis MR-1 electron transfer network, using the program LaNet-vi (Beiro et al., 2008). The nodes are ordered by their ks values. Black panes indicate proteins that form representative EET pathways. (B) The negative correlation between the ks and the average DR_100.
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Figure 1: (A) Visualization of the k-shell structure of the S. oneidensis MR-1 electron transfer network, using the program LaNet-vi (Beiro et al., 2008). The nodes are ordered by their ks values. Black panes indicate proteins that form representative EET pathways. (B) The negative correlation between the ks and the average DR_100.

Mentions: We first performed k-shell decomposition for the S. oneidensis MR-1 electron transfer network (Figure 1A, Supplementary Methods, Supplementary Data Sheet S3). From the network formation and extension view, it is clear that the nodes with high k-shell values (ks) were those connected initially (Kitsak et al., 2010; Pei et al., 2014). These nodes form a core network that was reconstructed and expanded as new nodes were constantly connected. Since PPIs are strongly influenced by their local environment, the protein interaction system is constantly reconstructed (e.g., by rewiring interactions among existing proteins [Kim et al., 2012]) and expanded (e.g., by recruiting new proteins into the network for highly specific and/or more efficient functions [Nam et al., 2012]) according to changes in the environment. As a result, the structure of the PPI network evolves. Therefore, such a k-shell network structure reflects the formation and extension of the PPI network.


K-shell Analysis Reveals Distinct Functional Parts in an Electron Transfer Network and Its Implications for Extracellular Electron Transfer.

Ding D, Li L, Shu C, Sun X - Front Microbiol (2016)

(A) Visualization of the k-shell structure of the S. oneidensis MR-1 electron transfer network, using the program LaNet-vi (Beiro et al., 2008). The nodes are ordered by their ks values. Black panes indicate proteins that form representative EET pathways. (B) The negative correlation between the ks and the average DR_100.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4837345&req=5

Figure 1: (A) Visualization of the k-shell structure of the S. oneidensis MR-1 electron transfer network, using the program LaNet-vi (Beiro et al., 2008). The nodes are ordered by their ks values. Black panes indicate proteins that form representative EET pathways. (B) The negative correlation between the ks and the average DR_100.
Mentions: We first performed k-shell decomposition for the S. oneidensis MR-1 electron transfer network (Figure 1A, Supplementary Methods, Supplementary Data Sheet S3). From the network formation and extension view, it is clear that the nodes with high k-shell values (ks) were those connected initially (Kitsak et al., 2010; Pei et al., 2014). These nodes form a core network that was reconstructed and expanded as new nodes were constantly connected. Since PPIs are strongly influenced by their local environment, the protein interaction system is constantly reconstructed (e.g., by rewiring interactions among existing proteins [Kim et al., 2012]) and expanded (e.g., by recruiting new proteins into the network for highly specific and/or more efficient functions [Nam et al., 2012]) according to changes in the environment. As a result, the structure of the PPI network evolves. Therefore, such a k-shell network structure reflects the formation and extension of the PPI network.

Bottom Line: We found that there was a negative correlation between the k s (k-shell values) and the average DR_100 (disordered regions per 100 amino acids) in every shell, which suggested that disordered regions of proteins played an important role during the formation and extension of the electron transfer network.Specifically, the fourth shell was responsible for EET and the c-type cytochromes in the remaining shells of the electron transfer network were involved in aiding EET.Taken together, these results show that there are distinct functional parts in the electron transfer network of S. oneidensis MR-1, and the EET processes could achieve high efficiency through cooperation through such an electron transfer network.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast UniversityNanjing, China; Department of Mathematics and Computer Science, Chizhou CollegeChizhou, China.

ABSTRACT
Shewanella oneidensis MR-1 is capable of extracellular electron transfer (EET) and hence has attracted considerable attention. The EET pathways mainly consist of c-type cytochromes, along with some other proteins involved in electron transfer processes. By whole genome study and protein interactions inquisition, we constructed a large-scale electron transfer network containing 2276 interactions among 454 electron transfer related proteins in S. oneidensis MR-1. Using the k-shell decomposition method, we identified and analyzed distinct parts of the electron transfer network. We found that there was a negative correlation between the k s (k-shell values) and the average DR_100 (disordered regions per 100 amino acids) in every shell, which suggested that disordered regions of proteins played an important role during the formation and extension of the electron transfer network. Furthermore, proteins in the top three shells of the network are mainly located in the cytoplasm and inner membrane; these proteins can be responsible for transfer of electrons into the quinone pool in a wide variety of environmental conditions. In most of the other shells, proteins are broadly located throughout the five cellular compartments (cytoplasm, inner membrane, periplasm, outer membrane, and extracellular), which ensures the important EET ability of S. oneidensis MR-1. Specifically, the fourth shell was responsible for EET and the c-type cytochromes in the remaining shells of the electron transfer network were involved in aiding EET. Taken together, these results show that there are distinct functional parts in the electron transfer network of S. oneidensis MR-1, and the EET processes could achieve high efficiency through cooperation through such an electron transfer network.

No MeSH data available.


Related in: MedlinePlus