A Novel Regulation on the Developmental Checkpoint Protein Sda that Controls Sporulation and Biofilm Formation inBacillus subtilis

Abstract

AbstractBiofilm formation byBacillus subtilisis triggered by an unusually simple environmental sensing mechanism. Certain serine codons, the four TCN codons (N for A, T, C, or G), in the gene for the biofilm repressor SinR caused lowered SinR translation and subsequent biofilm induction during transition from exponential to stationary growth. Global ribosome profiling showed that ribosomes pause when translating the four UCN (U for T on the mRNA) serine codons on mRNA, but not the two AGC/AGU serine codons. We proposed a serine codon hierarchy (AGC/AGT vs TCN) in that genes enriched in the TCN serine codons may experience reduced translation efficiency when serine is limited. In this study, we designed an algorithm to score all protein-coding genes inB. subtilisNCIB3610 based on the serine codon hierarchy. We generated a short list of 50 genes that could be subject to regulation by this novel mechanism. We further investigated one such gene from the list,sda, which encodes a developmental checkpoint protein regulating both sporulation and biofilm formation. We showed that synonymously switching the TCN serine codons to AGC insdaled to delayed biofilm formation and sporulation. This engineered strain also outgrew strains with other synonymously substitutedsdaalleles (TCN) in competition assays for biofilm formation and sporulation. Lastly, we showed that the AGC serine codon substitutions insdaelevated the Sda protein levels. This serine codon hierarchy-based novel signaling mechanism could be exploited by bacteria in adapting to stationary phase and regulating important biological processes.ImportanceGenome-wide ribosome profiling inBacillus subtilisshows that under serine limitation, ribosomes pause on the four TCN (N for A, C, G, and T), but not AGC/AGT serine codons, during translation at a global scale. This serine codon hierarchy (AGC/T vs TCN) differentially influences translation efficiency of genes enriched in certain serine codons. In this study, we designed an algorism to score all 4000+ genes in theB. subtilisgenome and generated a list of 50 genes that could be subject to this novel serine codon hierarchy-mediated regulation. We further investigated one such gene,sda, encoding a developmental check point protein. We show thatsdaand cell developments controlled by Sda are also regulated by this novel mechanism.