Transcriptional regulatory module analysis reveals that bridge proteins reconcile multiple signals in extracellular electron transfer pathways

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

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.

Relating Translation Efficiency to Protein Networks Provides Evolutionary Insights in Shewanella and Its Implications for Extracellular Electron Transfer

Shewanella species are well-known for their extracellular electron transfer (EET) capacity, by which these microorganisms can transfer the electrons from intracellular environment to extracellular space for the reduction of the extracellular insoluble electron acceptors. Using a time-stamped data for the paired protein-mRNA, we investigate the impact of differential translation on the EET process of Shewanella oneidensis MR-1. Firstly, differentially translated proteins when O₂ levels are switched from high-O₂ to low-O₂ are identified by using a soft clustering method, 629 up-regulated translated proteins and 767 down-regulated translated proteins are considered to reflect the changes from inactivated to activated EET process. Then, we showed that the degrees of connectivity of differentially translated proteins were significantly larger than those of non-differentially translated proteins, and thereby these differentially translated proteins will be more important in the protein networks. After that, we networked these differentially translated proteins to construct the differentially translated sub-networks, and discussed the most important proteins that are involved in the EET process with the help of centralization analysis of these differentially translated networks. Furthermore, we also studied the differentially translated operonic genes. Taking together, this work searches the key proteins that potentially activated the EET process from a translational efficiency viewpoint.