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 ks (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.
Highlights
The transmission of electrons to extracellular solid acceptors is an important reaction in some microorganisms, such as Geobacter sulfurreducens and Shewanella oneidensis (Shi et al, 2007)
Other proteins that are potentially involved in electron transfer processes were manually selected from the complete genome of S. oneidensis MR-1 (Heidelberg et al, 2002) via the KEGG genome database1
We found that the proteins in this shell can be categorized into several modules according to their roles in electron transfer (EET) (Figure 4): Module 1 – Reduction of Extracellular Insoluble Electron Acceptors With these outer membrane and extracellular proteins previously mentioned S. oneidensis MR-1 is capable of Metabolic pathways Oxidative phosphorylation Carbon metabolism Microbial metabolism in diverse environments Methane metabolism Glyoxylate and dicarboxylate metabolism Two-component system Pyruvate metabolism Citrate cycle (TCA cycle)
Summary
The transmission of electrons to extracellular solid acceptors (extracellular electron transfer, EET) is an important reaction in some microorganisms, such as Geobacter sulfurreducens and Shewanella oneidensis (Shi et al, 2007). C-type cytochromes play important roles in the EET processes (Shi et al, 2012; Tremblay and Zhang, 2015), for example, four c-type. Electron Transfer Network in MR-1 cytochromes, CymA, MtrA, MtrC, and OmcA, can form an electron transfer chain with a trans-outer membrane protein MtrB in S. oneidensis MR-1 (the classical MtrCAB pathway). Following initial work on a small-scale c-type cytochrome network (Zhang et al, 2008), a recent study constructed a network for all of 41 c-type cytochromes in S. oneidensis MR-1 and the classical EET pathways (e.g., MtrCAB, MtrDEF) can be identified from the c-type cytochrome network (Ding et al, 2014). From the view of steric properties of individual proteins, Volkov and van Nuland (2012) performed extensive conformational sampling, mapped out functional epitopes in c-type cytochrome complexes (involving cytochrome c and other redox-active proteins such as peroxidase and cytochrome b5) and assessed the electron transfer properties of such interactions
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