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.

Automated summary

This study identified high co-fitness genes that potentially work with different c-type cytochromes and found that these genes are enriched in signal transduction processes in Shewanella oneidensis MR-1 cells. The study also identified a novel signal protein involved in the regulation of CymA and showed the existence of two signal transduction modules. These findings provide new insights into the coordinated utilization of different c-type cytochromes.