# Protein Kinases in Mediating Phage-Bacteria Interactions
## 2 Brief Sum of HKs and STKs in Bacterial Stress Response and Antibiotic Tolerance/Resistance  
Bacterial HKs and STKs are master regulators of stress adaptation and antibiotic tolerance/resistance. Their roles have been extensively reviewed across various organisms, including in several recent reviews [1; 2; 11; 12]. Therefore, only a brief summary is provided here to illustrate their distinct structural features and mechanistic strategies for counteracting environmental stress and therapeutic interventions. HKs, as core components of TCSs, are typically transmembrane proteins with a sensor domain that detects extracellular stressors such as osmotic shifts, nutrient deprivation, or antimicrobial presence. Upon signal perception, HKs autophosphorylate a conserved histidine residue within their cytoplasmic kinase domain, subsequently transferring the phosphate group to an aspartate residue on a cognate response regulator (RR) [13; 14]. This phosphorylation activates the specific RR, enabling it to modulate transcription of stress-response genes. For instance, _E. coli_ HK EnvZ phosphorylates RR OmpR to adjust porin expression in response to osmolarity, indirectly influencing antibiotic influx [15; 16]. In more complex signaling networks, additional phosphotransfer intermediates such as DHp and Hpt domains are involved, and signal crosstalk between different TCS pathways can occur, even though HK-RR specificity is generally maintained [13; 14]. For instance, _Pseudomonas aeruginosa_ LadS, an HK autophosphorplates and passes on the phosphate to a second HK GacS, then to RR GacA, leading to a switch from the acute to the chronic virulence program and drug tolerance [17]. In contrast, STKs operate through eukaryotic-like phosphorylation cascades, dynamically modifying substrate proteins by transferring phosphate groups from ATP to specific serine/threonine residues to orchestrate diverse cellular processes, including cell division, sporulation, biofilm formation, stress responses, and host interactions [1]. For instance, in _Bacillus subtilis_, PrkC directs cell wall remodeling and sporulation [18]; _Pseudomonas aeruginosa_ Stk1 modulates virulence and antibiotic resistance through transcription factor phosphorylation [19]; and _Mycobacterium tuberculosis_ STK PknG regulates metabolic adaptation by redirecting carbon flux via GarA phosphorylation [20]. Among STKs is another group of toxin-like kinase exemplified by the _E. coli_ HipA STK and its homologs/paralogs [21]. HipA is a component of the HipBA toxin-antitoxin (TA) system, orchestrating the formation of antibiotic-tolerant persister cells through a sophisticated phosphorylation cascade (reviewed in [22]). Under stress conditions, HipA phosphorylates glutamyl-tRNA synthetase (GlcX) at Ser239 [5], a critical enzyme responsible for charging tRNAGlu with glutamate during translation. This modification disrupts GltX's function, leading to the accumulation of uncharged tRNAGlu. The uncharged tRNA activates the stringent response via the alarmome (p)ppGpp, a global regulator of stress adaptation. Elevated (p)ppGpp levels halt ribosomal RNA synthesis [23], repress translation machinery assembly, and arrest growth-related processes [24; 25], effectively inducing a metabolically dormant state. This transient shutdown allows a subpopulation of cells (persisters) to evade bactericidal antibiotics (e.g., fluoroquinolones [26]) that target active cellular functions. While not genetically resistant, persisters survive treatment by entering this quiescent state, later resuscitating to repopulate the bacterial community post-stress. Alternatively, persisters could obtain mutations, becoming resistant to the applied antibiotics [27]. The HipA-GltX axis exemplifies how TA systems drive phenotypic heterogeneity [28], highlighting a key mechanism behind chronic infections and antibiotic recalcitrance [22; 27].