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Stress-induced ribosome degradation in Bacillus subtilis is mediated by the RNase Y-specificity complex

ABSTRACT: Limiting the synthesis and activity of ribosomes is crucial for responding to various stresses, including nutrient starvation or proteotoxic stress. In Bacillus subtilis, this is achieved through the coordinated action of the alarmones (p)ppGpp and the transcription factor Spx. In this study, we performed a genetic screening for new factors involved in the heat shock response of B. subtilis. We discovered that the RNase Y specificity factor Y-complex is important for the heat shock response and the transition to the stationary growth phase. The Y-complex is required for processing different RNAs, including mRNA maturation. We further demonstrate that the Y-complex and RNase Y initiate rRNA degradation in mature ribosomes, lowering their abundance. We propose the Y-complex as a system by which B. subtilis regulates protein synthesis and resource allocation at the entry to stationary phase.

INSTRUMENT(S):

ORGANISM(S): Bacillus Subtilis

SUBMITTER: Kathirvel Alagesan

LAB HEAD: Kathirvel Alagesan

PROVIDER: PXD065465 | Pride | 2026-04-09

REPOSITORIES: Pride

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			Action	DRS
	22C012Groups.txt	Txt
	E1_220707_22C012_sample_01.raw	Raw
	E1_220707_22C012_sample_02.raw	Raw
	E1_220707_22C012_sample_03.raw	Raw
	E1_220707_22C012_sample_04.raw	Raw

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Targeting the translation machinery: The RNase Y specificity factor Y-complex coordinates ribosome degradation

Project description:Limiting the synthesis and activity of ribosomes is crucial for responding to various stresses, including nutrient starvation or proteotoxic stress. In Bacillus subtilis, this is achieved through the coordinated action of the alarmones (p)ppGpp and the transcription factor Spx. In this study, we performed a genetic screening for new factors involved in the heat shock response of B. subtilis. We discovered that the RNase Y specificity factor Y-complex is important for the heat shock response and the transition to the stationary growth phase. The Y-complex is required for processing different RNAs, including mRNA maturation. We further demonstrate that the Y-complex and RNase Y initiate rRNA degradation in mature ribosomes, lowering their abundance. We propose the Y-complex as a system by which B. subtilis regulates protein synthesis and resource allocation at the entry to stationary phase.

2026-04-09 | PXD065462 | Pride

Stress-induced ribosome degradation in Bacillus subtilis is mediated by the RNase Y-specificity complex

Project description:Limiting the synthesis and activity of ribosomes is crucial for adaptation to stresses, such as heat or nutrient starvation. In Bacillus subtilis, this can be achieved through the coordinated action of the alarmones (p)ppGpp and the transcription factor Spx. Here, we performed a genetic screen to uncover novel factors contributing to the heat shock response of B. subtilis. We identified the Y-complex, which confers specificity to the endonuclease RNase Y, as a critical player during stress conditions, such as heat or transition into stationary phase. This protein complex is required for processing diverse RNAs, notably the maturation of mRNAs encoding proteins involved in translation and metabolism. We further demonstrate that the Y- complex and RNase Y initiate the degradation of rRNAs of mature ribosomes, lowering their abundance. We propose that the Y-complex is a regulatory hub that modulates gene expression, adjusts protein synthesis and resource allocation.

2026-04-09 | PXD074523 | Pride

Structure of Escherichia coli heat shock protein Hsp15 in complex with ribosomal 50S sununits bearing peptidyl-tRNA

Project description:In Escherichia coli, the heat shock protein 15 (Hsp15) is part of the cellular response to elevated temperature. Hsp15 interacts with peptidyl-tRNA-50S complexes that arise upon dissociation of translating 70S ribosomes, and is proposed to facilitate their rescue and recycling. A previous structure of E. coli Hsp15 in complex with peptidyl-tRNA-50S complex reported a binding site located at the central protuberance of the 50S subunit. By contrast, recent structures of RqcP, the Hsp15 homolog in Bacillus subtilis, in complex with peptidyl-tRNA-50S complexes have revealed a distinct site positioned between the anticodon-stem-loop (ASL) of the P-site tRNA and H69 of the 23S rRNA. Here we demonstrate that exposure of E. coli cells to heat shock leads to dissociation of 70S ribosomes and accumulation of 50S subunits, thus identifying a natural substrate for Hsp15 binding. Additionally, we have determined a cryo-EM reconstruction of the Hsp15-50S-peptidyl-tRNA complex isolated from heat shocked E. coli cells, revealing that Hsp15 binds to the 50S-peptidyl-tRNA complex analogously to its B. subtilis homolog RqcP. Collectively, our findings support a model where Hsp15 promotes access to the A-site for putative rescue factors to release the aberrant nascent polypeptide chain.

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The alarmone (p)ppGpp is part of the heat shock response of Bacillus subtilis

Project description:Here, B. subtilis was used as a model organism to investigate how cells respond and adapt to proteotoxic stress conditions. Our experiments suggested that the stringent response, caused by raised levels of the (p)ppGpp alarmone, plays a role during thermotolerance development and the heat shock response. Accordingly, our experiments revealed a rapid increase of cellular (p)ppGpp levels upon heat shock as well as salt- and oxidative stress. Strains lacking (p)ppGpp exhibited increased stress sensitivity, while raised (p)ppGpp levels conferred increased stress tolerance to heat- and oxidative stress. During thermotolerance development, stress response genes were highly up-regulated together with a concurrent transcriptional down-regulation of the rRNA, which was influenced by the second messenger (p)ppGpp and the transcription factor Spx. Remarkably, we observed that (p)ppGpp appeared to control the cellular translational capacity and that during heat stress the raised cellular levels of the alarmone were able to curb the rate of protein synthesis. Furthermore, (p)ppGpp controls the heat-induced expression of Hpf and thus the formation of translationally inactive 100S disomes. These results indicate that B. subtilis cells respond to heat-mediated protein unfolding and aggregation, not only by raising the cellular repair capacity, but also by decreasing translation involving (p)ppGpp mediated stringent response to concurrently reduce the protein load for the cellular protein quality control system.

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Developmentally regulated alternate 3’ end cleavage of nascent transcripts controls dynamic changes in protein expression in an adult stem cell lineage

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2024-05-14 | GSE267303 | GEO

Bifidobacterium longum mutants and resistance to Heat-Shock

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Light activation of the sigmaB-mediated general stress-response of Bacillus subtilis

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Heat shock induces silent ribosomes and reorganizes mRNA turnover

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| PRJNA1223295 | ENA

Heat shock induces silent ribosomes and reorganizes mRNA turnover

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