Towards an elucidation of the roles of the ribosome during different growth phases in Bacillus subtilis

Abstract

Sporulation is one of the adaptive responses used by Bacillus subtilis, a well-characterized gram-positive soil bacterium, when cells encounter adverse growth conditions, such as nutrient limitation. The activity and/or intracellular levels of ribosomes must be tightly controlled during sporulation, because protein translation and ribosome synthesis consume vast amounts of energy, but very little is known about the mechanisms that regulate these processes during sporulation in B. subtilis. Therefore, to understand the role of the ribosome in sporulation, as well as the function of the B. subtilis ribosome in translation, we developed genetic and biochemical systems to analyze the constituents of the ribosome. In developing a proteomic map of ribosomal proteins, we found that two types of L31 protein (RpmE and YtiA) were associated alternatively with the ribosome. Expression of ytiA is induced under zinc-limiting conditions due to de-repression of transcription by Zur, a transcriptional repressor that represses the transcription of genes encoding the zinc-uptake machinery. Under zinc-limiting conditions, RpmE, which contains one zinc atom per molecule, is replaced by YtiA, which does not contain zinc, in the 50S subunit of the ribosome. Given that RpmE released from the ribosome is unstable in cells, this replacement might contribute to the mobilization of zinc by supplying the zinc from the released RpmE into the cells under zinc-limiting conditions. In addition, genes that encode two types of S14 (RpsN and YhzA) were also found in the genome of B. subtilis. RpsN contains zinc-binding motifs whereas YhzA does not. As in the case of ytiA, the transcription of yhzA is negatively regulated by Zur. However, unlike the L31 proteins, switching between the two types of S14 protein was not observed even under zinc-limiting conditions. Further studies strongly suggested that YhzA forms a "fail-safe" mechanism to maintain the function of the 30S subunit of the ribosome under zinc-limiting conditions. These results can provide novel insight into the role of ribosomal protein paralogs in the ribosome under zinc-limiting conditions.