HepK, a protein-histidine kinase from the cyanobacterium Anabaena sp. strain PCC 7120, binds sequence-specifically to DNA

By | January 18, 2015

Two-component phosphorelay systems are minimally consisted of a sensory protein-histidine kinase (HK) and a response regulator (RR). HK autophosphorylates its conserved histidine residue in response to stimulus from an environment, this phosphate group then is transferred to a conserved aspartic acid residue of an RR, which is generally a transcription factor. HepK is a member of the family of sensory protein-histidine kinases in two-component phosphorelay systems (TCPS). We previously showed that HepK is an autokinase, and that DevR is its cognate RR, together comprising a mini two-component phosphorelay system that mediates developmental regulation of biosynthesis of a heterocyst envelope polysaccharide in the cyanobacterium Anabaena sp. PCC 7120.  Unlike a typical TCPS, both HepK and DevR lack known DNA-binding domains. However, mutations in hepK, hepC and hepA all block the synthesis of heterocyst envelope polysaccharide. A hepK mutation of Anabaena blocks the induction of hepA expression. We hypothesized that HepK may regulate the transcription of hepA or hepC by binding to DNA. To test this hypothesis we have performed a gel-shift analysis and have shown that although lacking a known DNA-binding motif, a truncated, soluble version of HepK binds sequence-specifically to a fragment of DNA found upstream from hepC, a gene that is located immediately upstream from hepA and also required for the synthesis of heterocyst envelope polysaccharide. The conserved phosphorylation histidine residue of HepK kinase is not required for this DNA-binding activity. Therefore, regulation of the synthesis of heterocyst envelope polysaccharide by HepK may be, at least in part, independent of two-component phosphorylation. The membrane-anchored HepK kinase with specific DNA-binding activity may serve as a membrane-tethered transcription factor, which may require an activation of regulated intramembrane proteolysis. We have found no other example of a protein histidine kinase without a known DNA binding motif that binds DNA sequence-specifically. Our finding may enable development of small DNA molecule as highly specific anti-microbial drugs because protein histidine kinases are broadly conserved in microbial pathogens but absent in humans.

Genomic sequence data have identified no presumptive protein histidine kinase genes in animal genomes including human genome. Since some two-component phosphorelay proteins are essential for the viability, virulence, and drug resistance of microbial pathogens including human fungal and bacterial pathogens, novel anti-microbial drugs targeted to protein histidine kinase in two-component phosphorelay systems may prove high specificity and minimal toxicity.  Several series of inhibitors to bacterial histidine kinase have been reported in the literature, however, most appear to suffer from high hydrophobicity, poor selectivity, and excessive protein binding and/or limited bioavailability.  The strong hydrophobicity of these molecules makes formulation and drug delivery impossible.  Unlike these compounds, small DNA molecules bound specifically by a protein-histidine kinase HepK are able to bypass the drawbacks of conventional inhibitors. These sequence-specific small DNA molecules have several unique advantages in developing of novel anti-microbial drugs, such as high solubility, high specificity, minimal toxicity, efficient synthesis, easy of formulation and delivery.  Therefore, our finding provides an exciting opportunity for developing small DNA molecules as novel anti-microbial drugs.

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