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

Abstract

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.

Network-Based Methods for Identifying Key Active Proteins in the Extracellular Electron Transfer Process in Shewanella oneidensis MR-1

“…Furthermore, to reveal the exclusive active network motifs involved in activating the EET process, we compared these seven active network motifs to the highly conserved ones in the Shewanella species, which were identified by comparative analysis of the integrated networks of 13 Shewanella species in our recent study [ 39 ]. We found that four of them were the highly conserved motifs in the Shewanella species.…”

“…We found that four of them were the highly conserved motifs in the Shewanella species. Their biological functions have been well discussed: (1) The motif Co-regulated PPI ( Table 4 , Motif ID 1) played an important role in the “standby mode” of protein utilization, which helps cells to rapidly respond to changing environmental conditions [ 39 , 40 , 41 , 42 ]. (2) The motif Protein Clique ( Table 4 , Motif ID 2) was expected to capture only some local, physically interacted components; such motifs could be used to build complex assemblies, which usually correspond to a multicomponent protein machine [ 43 ].…”

CBSSD: community-based semantic subgroup discovery

“…Complex networks are commonly used in modeling systems, where extensive background knowledge is not necessarily accessible. Motif finding, community detection and similar methods can provide valuable insights into the latent organization of the observed network (Ding and Sun 2017). Such networks are also known to include many communities, i.e.…”