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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

Bar chart showing the GO biological process categories for the 77 proteins (or their encoding genes) in the top three shells of the S. oneidensis MR-1 electron transfer network (p < 0.0001). The most representative category is “metabolic processes”.
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Figure 3: Bar chart showing the GO biological process categories for the 77 proteins (or their encoding genes) in the top three shells of the S. oneidensis MR-1 electron transfer network (p < 0.0001). The most representative category is “metabolic processes”.

Mentions: As Figure 2 shows, the proteins in the top three shells (with ks 14, 13, and 10, respectively) are mainly located in the cytoplasm and inner membrane, with a small number in the periplasm, without outer membrane and extracellular space. Because there are dense interactions among network core proteins; by taking a larger fraction of their surface involved in many interactions, these proteins tend to be constrained, without further need of adaptive evolution that preferentially occurs in outer membrane and extracellular space (Kim et al., 2007). The Gene Ontology (GO) biological processes were exploited to obtain biological insights into these proteins; we found that the most representative category is metabolic processes (Figure 3). The results indicate that these proteins are mostly capable of cellular metabolism.


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)

Bar chart showing the GO biological process categories for the 77 proteins (or their encoding genes) in the top three shells of the S. oneidensis MR-1 electron transfer network (p < 0.0001). The most representative category is “metabolic processes”.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 3: Bar chart showing the GO biological process categories for the 77 proteins (or their encoding genes) in the top three shells of the S. oneidensis MR-1 electron transfer network (p < 0.0001). The most representative category is “metabolic processes”.
Mentions: As Figure 2 shows, the proteins in the top three shells (with ks 14, 13, and 10, respectively) are mainly located in the cytoplasm and inner membrane, with a small number in the periplasm, without outer membrane and extracellular space. Because there are dense interactions among network core proteins; by taking a larger fraction of their surface involved in many interactions, these proteins tend to be constrained, without further need of adaptive evolution that preferentially occurs in outer membrane and extracellular space (Kim et al., 2007). The Gene Ontology (GO) biological processes were exploited to obtain biological insights into these proteins; we found that the most representative category is metabolic processes (Figure 3). The results indicate that these proteins are mostly capable of cellular metabolism.

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