Protein secretion systems in bacterial-host associations, and their description in the Gene Ontology

Abstract

Protein secretion plays a central role in modulating the interactions of bacteria with their environments. This is particularly the case when symbiotic bacteria (whether pathogenic, commensal or mutualistic) are interacting with larger host organisms. In the case of Gram-negative bacteria, secretion requires translocation across the outer as well as the inner membrane, and a diversity of molecular machines have been elaborated for this purpose. A number of secreted proteins are destined to enter the host cell (effectors and toxins), and thus several secretion systems include apparatus to translocate proteins across the plasma membrane of the host also. The Plant-Associated Microbe Gene Ontology (PAMGO) Consortium has been developing standardized terms for describing biological processes and cellular components that play important roles in the interactions of microbes with plant and animal hosts, including the processes of bacterial secretion. Here we survey bacterial secretion systems known to modulate interactions with host organisms and describe Gene Ontology terms useful for describing the components and functions of these systems, and for capturing the similarities among the diverse systems.

Figure 1

Summary of known bacterial secretion systems. In this simplified view only the basics of each secretion system are sketched. HM: Host membrane; OM: outer membrane; IM: inner membrane; MM: mycomembrane; OMP: outer membrane protein; MFP: membrane fusion protein. ATPases and chaperones are shown in yellow.

Figure 2

Gene Ontology terms for secretion systems under "cellular component" and "biological process.". GO terms for secretion systems described in this review article are encased in dashed boxes. (A) shows terms that are children of the process term "GO ID: 0009306 protein secretion". (B) shows terms that are children of the process term "GO:0044403: symbiosis, encompassing mutualism through parasitism". (C) shows terms that are children of "GO ID: 0005575 cellular component".