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

Ding, Dewu; Li, Ling; Shu, Chuanjun; Sun, Xiao

doi:10.3389/fmicb.2016.00530

Cited by 3 publications

(2 citation statements)

References 66 publications

(101 reference statements)

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“…In general, they can covalently bind heme through two cysteine (c) residues, and the sequence feature of the heme binding site is the CXXCH motif. Meyer et al identified 42 candidate c-type cytochrome genes in Shewanella oneidensis MR-1 through pattern matching (Meyer et al 2004), and the follow-up reports (Jin et al 2013;Ding et al 2016) confirmed 41 c-type cytochrome genes in this species (Supplementary Table 1).…”

Section: C-type Cytochromementioning

confidence: 89%

Co-fitness analysis identifies a diversity of signal proteins involved in the utilization of specific c-type cytochromes

et al. 2022

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Purpose c-Type cytochromes are essential for extracellular electron transfer (EET) in electroactive microorganisms. The expression of appropriate c-type cytochromes is an important feature of these microorganisms in response to different extracellular electron acceptors. However, how these diverse c-type cytochromes are tightly regulated is still poorly understood. Methods In this study, we identified the high co-fitness genes that potentially work with different c-type cytochromes by using genome-wide co-fitness analysis. We also constructed and studied the co-fitness networks that composed of c-type cytochromes and the top 20 high co-fitness genes of them. Results We found that high co-fitness genes of c-type cytochromes were enriched in signal transduction processes in Shewanella oneidensis MR-1 cells. We then checked the top 20 co-fitness proteins for each of the 41 c-type cytochromes and identified the corresponding signal proteins for different c-type cytochromes. In particular, through the analysis of the high co-fitness signal protein for CymA, we further confirmed the cooperation between signal proteins and c-type cytochromes and identified a novel signal protein that is putatively involved in the regulation of CymA. In addition, we showed that these signal proteins form two signal transduction modules. Conclusion Taken together, these findings provide novel insights into the coordinated utilization of different c-type cytochromes under diverse conditions.

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Section: C-type Cytochromementioning

confidence: 89%

Co-fitness analysis identifies a diversity of signal proteins involved in the utilization of specific c-type cytochromes

et al. 2022

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“…Later studies on Shewanella focused mainly on three characteristics of the bacterium: (1) the electrical conductivity (Lower et al, 2001; Heidelberg et al, 2002; Kim et al, 2002; Liu et al, 2004; Gorby et al, 2006), (2) iron reduction (Beliaev and Saffarini, 1998; Kim et al, 1999), and (3) anaerobic regulation in different Shewanella species (Ding et al, 2016; White et al, 2016). Some researchers also reported the ability of Shewanella to treat azo dye waste water and analyzed the mechanism byproducts (Pearce et al, 2006; Khalid et al, 2008; Liu et al, 2013; Yu et al, 2015).…”

Section: Discussionmentioning

confidence: 99%

A Comparison of Molecular Biology Mechanism of Shewanella putrefaciens between Fresh and Terrestrial Sewage Wastewater

Wang

et al. 2016

Front. Bioeng. Biotechnol.

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Municipal and industrial wastewater is often discharged into the environment without appropriate treatment, especially in developing countries. As a result, many rivers and oceans are contaminated. It is urgent to control and administer treatments to these contaminated rivers and oceans. However, most mechanisms of bacterial colonization in contaminated rivers and oceans were unknown, especially in sewage outlets. We found Shewanella putrefaciens to be the primary bacteria in the terrestrial sewage wastewater outlets around Ningbo City, China. Therefore, in this study, we applied a combination of differential proteomics, metabolomics, and real-time fluorescent quantitative PCR techniques to identify bacteria intracellular metabolites. We found S. putrefaciens had 12 different proteins differentially expressed in freshwater culture than when grown in wastewater, referring to the formation of biological membranes (Omp35, OmpW), energy metabolism (SOD, deoxyribose-phosphate pyrophosphokinase), fatty acid metabolism (beta-ketoacyl synthase), secondary metabolism, TCA cycle, lysine degradation (2-oxoglutarate reductase), and propionic acid metabolism (succinyl coenzyme A synthetase). The sequences of these 12 differentially expressed proteins were aligned with sequences downloaded from NCBI. There are also 27 differentially concentrated metabolites detected by NMR, including alcohols (ethanol, isopropanol), amines (dimethylamine, ethanolamine), amino acids (alanine, leucine), amine compounds (bilinerurine), nucleic acid compounds (nucleosides, inosines), and organic acids (formate, acetate). Formate and ethanolamine show significant difference between the two environments and are possibly involved in energy metabolism, glycerophospholipid and ether lipids metabolism to provide energy supply, and material basis for engraftment in sewage. Because understanding S. putrefaciens’s biological mechanism of colonization (protein, gene express, and metabolites) in terrestrial sewage outlets is so important to administering and improving contaminated river and to predicting and steering performance, we delved into the biological mechanism that sheds light on the effect of environmental conditions on metabolic pathways.

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A Comparative Study of Network Motifs in the Integrated Transcriptional Regulation and Protein Interaction Networks of <italic>Shewanella</italic>

Ding

Sun

2019

IEEE/ACM Trans. Comput. Biol. and Bioinf.

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The Shewanella species shows a remarkable respiratory versatility with a great variety of extracellular electron acceptors (termed Extracellular Electron Transfer, EET). To explore relevant mechanisms from the network motif view, we constructed the integrated networks that combined transcriptional regulation interactions (TRIs) and protein-protein interactions (PPIs) for 13 Shewanella species, identified and compared the network motifs in these integrated networks. We found that the network motifs were evolutionary conserved in these integrated networks. The functional significance of the highly conserved motifs was discussed, especially the important ones that were potentially involved in the Shewanella EET processes. More importantly, we found that: 1) the motif co-regulated PPI took a role in the standby mode of protein utilization, which will be helpful for cells to rapidly response to environmental changes; and 2) the type II cofactors, which involved in the motif TRI interacting with a third protein, mainly carried out a signalling role in Shewanella oneidensis MR-1.

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

Cited by 3 publications

References 66 publications

Co-fitness analysis identifies a diversity of signal proteins involved in the utilization of specific c-type cytochromes

Co-fitness analysis identifies a diversity of signal proteins involved in the utilization of specific c-type cytochromes

A Comparison of Molecular Biology Mechanism of Shewanella putrefaciens between Fresh and Terrestrial Sewage Wastewater

A Comparative Study of Network Motifs in the Integrated Transcriptional Regulation and Protein Interaction Networks of <italic>Shewanella</italic>

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