Dedicated system

The term dedicated system refers to a degenerate example of a system that more commonly features a many-to-one relationship between members of two different families of proteins. In a dedicated system, the role of the "many" is filled by a single examplar. Identifying examples of dedicated systems can provide opportunities to study a biological phenomenon in greater detail.

Most examples of protein sorting system, including LPXTG/sortase, PEP-CTERM/exosortase, and GlyGly-CTERM/rhombosortase systems, occur in species that encode multiple target proteins processed by a single-copy membrane-associated sorting enzyme. There is no a priori reason to expect expression of any one member of the family of targets to closely follow the expression of its sorting enzyme. As might be expected, the genes for most target proteins are encoded far from the gene for the sorting enzyme in the majority of prokaryotic genomes.

When only a single target occurs in a genome, coordinated expression of processing protein and its target is more expected. A tandem arrangement of genes for the processing protein and its target thus becomes more likely. In the case of rhombosortases and their GlyGly-CTERM domain target proteins, the majority of dedicated (single target) systems feature tandem genes. In fact, it is far more likely that a rhombosortase gene will have an adjacent gene encoding a GlyGly-CTERM protein if the entire genome encodes only one target protein.

Similar results can be observed for LPXTG systems, twin-arginine translocation (TAT) systems, etc. Many-to-one relationships likewise occur between cofactor-dependent enzymes and the cassette that makes the cofactor, in HPr-activated sugar transport, maturases for anaerobic sulfatases (see, for example, Bacteroides thetaiotaomicron), transcriptional regulation using sigma factors, and in various other types of system. The increased likelihood of co-clustering in dedicated systems is a testable hypothesis that may be used a bioinformatics journey aimed at characterizing new examples of systems that feature many-to-one biological relationships.