Two Proteins Form a Heteromeric Bacterial Self-Recognition Complex in Which Variable Subdomains Determine Allele-Restricted Binding

Abstract

Self- versus nonself-recognition in bacteria has been described recently through genetic analyses in multiple systems; however, understanding of the biochemical properties and mechanisms of recognition-determinant proteins remains limited. Here we extend the molecular and biochemical understanding of two recognition-determinant proteins in bacteria. We have found that a heterotypic complex is formed between two bacterial self-recognition proteins, IdsD and IdsE, the genes of which have been shown to genetically encode the determinants for strain-specific identity in the opportunistic bacterial pathogen Proteus mirabilis. This IdsD-IdsE complex forms independently of other P. mirabilis-encoded self-recognition proteins. We have also shown that the binding between IdsD and IdsE is strain- and allele-specific. The specificity for interactions is encoded within a predicted membrane-spanning subdomain within each protein that contains stretches of unique amino acids in each P. mirabilis variant. Finally, we have demonstrated that this in vitro IdsD-IdsE binding interaction correlates to in vivo population identity, suggesting that the binding interactions between IdsD and IdsE are part of a cellular pathway that underpins self-recognition behavior in P. mirabilis and drives bacterial population sociality.

The Self-Identity Protein IdsD Is Communicated between Cells in Swarming Proteus mirabilis Colonies

“…D and E bind in vitro when the VRs of the two proteins originate from the same strain. Binding pairs of D and E are termed cognate (31). In contrast, when the VRs of D and E do not originate from the same strain, the proteins do not bind in vitro and the D-E pair is thus termed noncognate (31).…”

“…How the in vitro binding of D and E accounts for in vivo boundary behaviors remains unknown. Both D and E contain transmembrane domains (31). D has been found outside cells, and its export has been shown to be dependent on a functional T6SS (5).…”

“…D and E each contain a variable region (VR), a stretch of amino acids that is generally unique among strains (2,31). D and E bind in vitro when the VRs of the two proteins originate from the same strain.…”

“…In addition to a functional T6SS, the Ids system relies on the interactions between two proteins, D and IdsE (E), which together encode strain-specific identity information (2,31). D and E each contain a variable region (VR), a stretch of amino acids that is generally unique among strains (2,31).…”

“…Binding pairs of D and E are termed cognate (31). In contrast, when the VRs of D and E do not originate from the same strain, the proteins do not bind in vitro and the D-E pair is thus termed noncognate (31). Interestingly, swarming populations of strains producing cognate D-E pairs merge and thus recognize each other as self; however, swarms of strains producing noncognate D-E pairs form a visible boundary and are considered nonself (31).…”