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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

Highly interconnected interactions of the 18 periplasmic c-type cytochromes in the periphery of the S. oneidensis MR-1 electron transfer network (ks < 9). These c-type cytochromes are indicated by green nodes, and their interacted partners are indicated by red nodes (other c-type cytochromes) or small nodes (non c-type cytochromes), respectively. Domain-domain interactions are shown with red lines, indicating that two clusters are formed.
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Figure 6: Highly interconnected interactions of the 18 periplasmic c-type cytochromes in the periphery of the S. oneidensis MR-1 electron transfer network (ks < 9). These c-type cytochromes are indicated by green nodes, and their interacted partners are indicated by red nodes (other c-type cytochromes) or small nodes (non c-type cytochromes), respectively. Domain-domain interactions are shown with red lines, indicating that two clusters are formed.

Mentions: We then analyzed the PPIs of these 18 periplasmic c-type cytochromes with all of their direct protein partners (interactions among these partners were not considered). As Figure 6 shows, these c-type cytochromes (green nodes) were highly interconnected. Indeed, the density of this sub-network was 2.12-times higher than that of the whole electron transfer network, even though many interactions were not considered here. Their interaction partners included both other c-type cytochromes (red nodes in Figure 6) and non c-type cytochromes (Figure 6, small nodes). To further investigate whether weaker interactions could be formed, we performed domain-domain interaction (DDI, which are correspond to strong interaction) analysis for this sub-network (see Supplementary Data Sheet S6 for protein domain). We found that there are only a few DDIs in the sub-network (Figure 6, red lines), and therefore, most of these periplasmic c-type cytochromes make weak, transient interactions with other proteins, rather than permanent interactions. Then, a dynamic electron transfer network forms in periplasm via the high frequency of transient protein interactions, as discussed elsewhere (Sturm et al., 2015). Since periplasmic electron transfer processes involve in assigning specific c-type cytochromes for particular electron acceptors and triggering of different pathways to achieve electron transfer (Sturm et al., 2015), thus the assignment of these periplasmic c-type cytochromes to different parts of the network (different shells here, see Table 3) is an effective strategy to achieve fast and efficient periplasmic electron transfer.


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)

Highly interconnected interactions of the 18 periplasmic c-type cytochromes in the periphery of the S. oneidensis MR-1 electron transfer network (ks < 9). These c-type cytochromes are indicated by green nodes, and their interacted partners are indicated by red nodes (other c-type cytochromes) or small nodes (non c-type cytochromes), respectively. Domain-domain interactions are shown with red lines, indicating that two clusters are formed.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 6: Highly interconnected interactions of the 18 periplasmic c-type cytochromes in the periphery of the S. oneidensis MR-1 electron transfer network (ks < 9). These c-type cytochromes are indicated by green nodes, and their interacted partners are indicated by red nodes (other c-type cytochromes) or small nodes (non c-type cytochromes), respectively. Domain-domain interactions are shown with red lines, indicating that two clusters are formed.
Mentions: We then analyzed the PPIs of these 18 periplasmic c-type cytochromes with all of their direct protein partners (interactions among these partners were not considered). As Figure 6 shows, these c-type cytochromes (green nodes) were highly interconnected. Indeed, the density of this sub-network was 2.12-times higher than that of the whole electron transfer network, even though many interactions were not considered here. Their interaction partners included both other c-type cytochromes (red nodes in Figure 6) and non c-type cytochromes (Figure 6, small nodes). To further investigate whether weaker interactions could be formed, we performed domain-domain interaction (DDI, which are correspond to strong interaction) analysis for this sub-network (see Supplementary Data Sheet S6 for protein domain). We found that there are only a few DDIs in the sub-network (Figure 6, red lines), and therefore, most of these periplasmic c-type cytochromes make weak, transient interactions with other proteins, rather than permanent interactions. Then, a dynamic electron transfer network forms in periplasm via the high frequency of transient protein interactions, as discussed elsewhere (Sturm et al., 2015). Since periplasmic electron transfer processes involve in assigning specific c-type cytochromes for particular electron acceptors and triggering of different pathways to achieve electron transfer (Sturm et al., 2015), thus the assignment of these periplasmic c-type cytochromes to different parts of the network (different shells here, see Table 3) is an effective strategy to achieve fast and efficient periplasmic electron transfer.

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