Response regulator PorX coordinates oligonucleotide signalling and gene expression to control the secretion of virulence factors

Abstract

The PglZ family of proteins belongs to the alkaline phosphatase superfamily, which consists of metallohydrolases with limited sequence identity but similar metal-coordination architectures in otherwise divergent active sites. Proteins with a well-defined PglZ domain are ubiquitous among prokaryotes as essential components of BREX phage defence systems and two-component systems (TCSs). Whereas other members of the alkaline phosphatase superfamily are well characterized, the activity, structure and biological function of PglZ family proteins remain unclear. We therefore investigated the structure and function of PorX, an orphan response regulator of the Porphyromonas gingivalis TCS containing a putative PglZ effector domain. The crystal structure of PorX revealed a canonical receiver domain, a helical bundle, and an unprecedented PglZ domain, similar to the general organization of the phylogenetically related BREX-PglZ proteins. The PglZ domain of PorX features an active site cleft suitable for large substrates. An extensive search for substrates revealed that PorX is a phosphodiesterase that acts on cyclic and linear oligonucleotides, including signalling molecules such as cyclic oligoadenylates. These results, combined with mutagenesis, biophysical and enzymatic analysis, suggest that PorX coordinates oligonucleotide signalling pathways and indirectly regulates gene expression to control the secretion of virulence factors.

Structure–function analysis of PorXFj, the PorX homolog from Flavobacterium johnsioniae, suggests a role of the CheY-like domain in type IX secretion motor activity

“…Similarly to the recently released P. gingivalis PorX Pg structure 33 , PorX Fj displays three distinct domains: a N-terminal CheY-like RD (residues 2–121), followed by a three-helix bundle domain (HBD, residues 122–205), and a C-terminal PglZ domain (residues 206–517) (Fig. 1 A).…”

“…Very recently, a study provided further insights onto the structure–function relationship of PorX. It was notably shown that the PorX PglZ domain possesses a phosphodiesterase activity, and that dimerization of PorX, promoted by the presence of zinc, is required for its activity 33 . Substrates for the PglZ domain were determined, and an interdependence between the RD and PglZ domains through the dimerization surface was established.…”

“…Substrates for the PglZ domain were determined, and an interdependence between the RD and PglZ domains through the dimerization surface was established. Furthermore, the crystal structures of the dimeric, activated PorX, as well as its complex with pGpG, were solved 33 .…”

Molecular basis of foreign DNA recognition by BREX anti-phage immunity system

“…Supporting this hypothesis, Type II, III, V, and VI BREX systems that lack BrxL encode BrxH, a putative helicase. Another subunit of the BREX complex, BrxZ, is a distant homolog of PorX, a phosphodiesterase cleaving cyclic and linear oligonucleotides 35 and could be the tentative BREX effector.…”

“…BrxL is not required for DNA methylation but was shown to be required for BREX defense 38 . Another subunit of the BREX complex, BrxZ (PglZ), is homologous to the effector of the PorXY two-component system 35 . PglZ domain of PorX is a phosphodiesterase cleaving cyclic and linear oligonucleotides 35 and analogous function within BrxZ can be responsible for the effector response to phage infection.…”