Regulation of the LAMMER Kinase Kns1, a TORC1 Effector and RNA Pol III Modulator in Saccharomyces cerevisiae

The major regulator of cell growth, TORC1, mediates the stress response through conserved LAMMER kinases. In humans, these proteins play significant roles in the treatment of cancer and metabolic disorders. Human LAMMER kinases are well understood, but Kns1, a member of the LAMMER kinases in the yeast S. cerevisiae, is not yet well characterised in terms of its functions and regulation. Kns1 has the potential for various functions under unfavourable conditions, and its structure has not been resolved. An in vivo study confirmed that Kns1, a negative effector kinase of TORC1, directly phosphorylates Rpc53, a regulatory subunit of RNA polymerase III, under TORC1-inhibited conditions. Hyperphosphorylation of Rpc53 inhibits RNA polymerase III reinitiation, thereby reducing its activity. This study investigated the regulation of Kns1 and its role in stress response. To gain a deeper understanding of its role, we examined the properties of the Kns1 protein. We employed various non-preferential carbon sources and mutants that replicated diminished global translation initiation, inhibited glycolytic flux, or blocked TORC1 activity to investigate the consequences on Kns1. The research unveils that Kns1 protein levels increase under stress, and elevated Rpc53 phosphorylation suggests a direct effect on RNA polymerase III activity. This study proposes that Kns1 protein levels rise due to the integrated stress response and altered carbon source availability, suggesting a novel regulation for Kns1-facilitated RNA polymerase III inhibition under unfavourable conditions. The regulation of Kns1 is intricate and occurs rapidly under changing conditions. RNA sequencing data from prior studies have indicated increased mRNA levels in the presence of reduced global translation initiation, and preliminary findings from the current study suggest a similar trend for non-optimal carbon sources. The precise mechanism underlying the differential transcription remains unclear, but KNS1 transcription is likely regulated by stress-dependent transcription factors and could include a carbon source-responsive element (CSRE). An increase in translation under non-optimal conditions, similar to Gcn4, is also possible. This study suggests that Kns1 is an unstable protein under favourable conditions but becomes slightly stabilised under stress response, supposedly due to an increase in autophosphorylation. Overall, this study uncovered a new physiological role for Kns1 in the nutrient stress response, which is likely activated through increased transcription, changes in protein localisation, and stabilisation by autophosphorylation.