Exploring the regulation of tRNA distribution on the genomic scale

Though up to 20% of the total RNA in bacterial cells is tRNA, the regulation of tRNA distribution on the genomic level remains unclear. tRNA distribution is governed by four processes: transcription, processing of precursor tRNA, degradation of precursor tRNA and degradation of mature tRNA. To elucidate the relationship between these processes in the regulation of tRNA production, the relative tRNA distribution was measured using a microarray specifically designed for tRNA. We developed a procedure that selectively labels 3'-CCA-containing RNAs with the fluorophores Cy3 or Cy5. The labeled tRNAs were then hybridized to microarrays printed with complementary DNA probes. The regulation of tRNA distribution in Bacillus subtilis was explored for a wild-type strain and a mutant strain with significantly decreased levels of RNase P, the enzyme required for the 5' maturation of all tRNA. The strains were either grown under a variety of conditions at doubling times ranging from 0.1 to 2.2 doublings per hour to investigate growth-related changes in the tRNA abundance or treated with the transcriptional inhibitor rifampicin to analyze mature tRNA degradation. Our results confirm that transcription and processing contribute significantly to the distribution of the 35 tRNA species in B. subtilis, and suggest a role for the degradation of precursor tRNA. Mature tRNA degradation occurs with little specificity for individual tRNA species and on the hour time-scale, indicating that degradation of mature tRNA plays only a minor role in the regulation of tRNA distribution. Aside from transcription, the final tRNA distribution appears to be derived from a balance between processing and precursor degradation activities. (C) 2004 Elsevier Ltd. All rights reserved.