Standalone RNA-seq from Direct regulation of a tRNA modification enzyme by ppGpp links stress signaling to translational control and biofilm development

Here, we identify a direct connection between stress signaling and codon-specific translational regulation. We show that the alarmone ppGpp directly inhibits MnmE (TrmE), a conserved GTPase required for wobble uridine modification.

High-resolution ribosome profiling in Bacillus subtilis revealed that loss of MnmE selectively increases ribosome pausing at AAG codons and reprograms translation of a subset of genes, including small open reading frames. Among these is a previously unrecognized AAG-containing leader peptide that controls expression of the biofilm repressor AbrB. Consistent with this mechanism, mnmE mutants exhibit constitutive extracellular matrix production and bypass the biofilm defect of a relA mutant.