Quasi-essentiality of RNase Y inBacillus subtilisis caused by its critical role in the control of mRNA homeostasis

Abstract

RNA turnover is essential in all domains of life. The endonuclease RNase Y (rny) is one of the key components involved in RNA metabolism of the model organism Bacillus subtilis. Essentiality of RNase Y has been a matter of discussion, since deletion of the rny gene is possible, but leads to severe phenotypic effects. In this work, we demonstrate that the rny mutant strain rapidly evolves suppressor mutations to at least partially alleviate these defects. All suppressor mutants had acquired a duplication of an about 60 kb long genomic region encompassing genes for all three core subunits of the RNA polymerase—α, β, β′. When the duplication of the RNA polymerase genes was prevented by relocation of the rpoA gene in the B. subtilis genome, all suppressor mutants carried distinct single point mutations in evolutionary conserved regions of genes coding either for the β or β’ subunits of the RNA polymerase that were not tolerated by wild type bacteria. In vitro transcription assays with the mutated polymerase variants showed a severe decrease in transcription efficiency. Altogether, our results suggest a tight cooperation between RNase Y and the RNA polymerase to establish an optimal RNA homeostasis in B. subtilis cells.

The Bacillus phage SPβ and its relatives: a temperate phage model system reveals new strains, species, prophage integration loci, conserved proteins and lysogeny management components

“…Of the SPβ conserved genes, five genes were transcriptionally active, yopR , yopQ , yopP , aimR and yokI (Table S5). The second data set from Popp and colleagues (Popp et al ., 2020) and the third data set from Benda and colleagues (Benda et al ., 2021) were up‐to‐date Illumina RNA‐seq data sets. They were generated as control experiments from cells cultured in LB‐medium at 37°C at vigorous shaking.…”

“…The microarray-based transcriptome data for SPβ were directly extracted from the Supporting Information Table S2 of the study by Nicolas et al (Nicolas et al, 2012). The RNA-seq-based SPβ transcriptome data were extracted from sequence data from Popp et al (Popp et al, 2020) and Benda et al (Benda et al, 2021). Raw transcriptome sequence reads were downloaded from the SRA archive using fastq-dump from sra-tools (https://github.com/ncbi/sra-tools).…”

Functional Redundancy and Specialization of the Conserved Cold Shock Proteins in Bacillus subtilis

“…Second, a B. subtilis strain lacking the quasi-essential endoribonuclease RNase Y readily acquires mutations that affect the RNA polymerase and different transcription factors, such as the transcription elongation factor GreA and the RNA polymerase recycling factor RpoE. In addition to these mutations, inactivation of CspD was found to compensate for the lack of RNase Y [ 44 ]. Since all other suppressor mutants affected transcription in B. subtilis , it is likely that this was also the case for CspD.…”

The current state of SubtiWiki, the database for the model organism Bacillus subtilis

“…Upon deletion of topA , the bacteria immediately acquire mutations resulting in an increased expression of DNA topoisomerase IV that can then take over the role of TopA ( 29 ). Similarly, deletion of the rny gene encoding RNase Y results in the acquisition of suppressor mutations that result in a globally reduced level of transcription activity ( 30 ) and deletion of the unknown gene yqhY triggers mutations that often affect conserved residues of acetyl-CoA synthetase indicating that YqhY prevents a potentially toxic accumulation of malonyl-CoA or fatty acids ( 31 ). Proteins involved in detoxification reactions have recently been recognized as very important for cellular metabolism as they remove harmful by-products or intermediates.…”