Homologous HipA-like kinases are controlled by internal translational initiation and genetic organisation

HipA-like kinases are widespread bacterial serine-threonine kinases, yet their regulatory mechanisms remain poorly understood. Here, we characterise two novel HipA-like systems, the monocistronic hipL and bicistronic hipIN, also encoding HipS-like and HIRAN domains. We show that the hipL gene contains an internal translation initiation site producing a smaller variant, HipL_S, which counteracts HipL-mediated toxicity via its HipS-like domain. Contrary to this, HipN requires both the HipS-like and the HIRAN domains to neutralise HipI-mediated toxicity. Neither system forms stable toxin-antitoxin (TA) complexes in vitro, distinguishing them from classical type II systems. Finally, we show that autophosphorylation affects HipL but not HipI-mediated toxicity. These findings reveal diverse regulatory architectures in HipA-like TA systems, shaped by domain composition and operon structure. Impact statement Kinases are increasingly recognised as key regulators in bacteria. Here, we show how complex operon and domain structures can contribute to kinase function and regulation, revealing increasingly complex regulatory networks in microbes.