Identification and analysis of polyserine linker domains in prokaryotic proteins with emphasis on the marine bacterium Microbulbifer degradans

Abstract

Polyserine linkers (PSLs) are interdomain, serine-rich sequences found in modular proteins. Though common among eukaryotes, their presence in prokaryotic enzymes is limited. We identified 46 extracellular proteins involved in complex carbohydrate degradation from Microbulbifer degradans that contain PSLs that separate carbohydrate-binding domains or catalytic domains from other binding domains. In nine M. degradans proteins, PSLs also separated amino-terminal lipoprotein acylation sites from the remainder of the polypeptide. Furthermore, among the 76 PSL proteins identified in sequence repositories, 65 are annotated as proteins involved in complex carbohydrate degradation. We discuss the notion that PSLs are flexible, disordered spacer regions that enhance substrate accessibility.

Figure 1.

An example of a polyserine linker (PSL) protein from Microbulbifer degradans. The protein sequence of ZP_00064986, a predicted cellulase, contains two binding domains (underlined) separated by a PSL. Further, the second binding domain is separated from the remainder of the protein (which contains the catalytic domain) by a second PSL. Note that glycine residues are found in the sequence flanking each PSL (bold G’s). Secretion signal has double underline.