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

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: PXD065462 | Pride | 2026-04-09

REPOSITORIES: Pride

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	L1_230511_MSB_DWB_0_001.raw	Raw
	L1_230511_MSB_DWB_0_002.raw	Raw
	L1_230511_MSB_DWB_0_003.raw	Raw
	L1_230511_MSB_DWB_15_001.raw	Raw
	L1_230511_MSB_DWB_15_002.raw	Raw

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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 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 | PXD065465 | 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.

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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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Maturation of polycistronic mRNA by RNase Y and its associated Y-complex in Gram-positive bacteria

Project description:Endonucleolytic cleavage within polycistronic mRNAs can lead to differential stability and discordant abundance among co-transcribed genes. RNase Y, the major endonuclease for mRNA decay in Bacillus subtilis, was originally identified for its cleavage activity towards the cggR-gapA operon, an event that differentiates the expression of a glycolytic enzyme from its transcriptional regulator. A three-protein Y-complex (YlbF, YmcA, and YaaT) was recently identified that is also required for this cleavage in vivo, raising the possibility that it is an accessory factor acting to regulate RNase Y. However, whether the Y-complex is broadly required for RNase Y activity is unknown. Here we used end-enrichment RNA sequencing (Rend-seq) to globally identify operon mRNAs that undergo maturation post-transcriptionally by RNase Y and the Y-complex. We found that the Y-complex is required for the majority of RNase Y-mediated mRNA maturation events and affects riboswitch abundance in B. subtilis. In contrast, noncoding RNA maturation by RNase Y often do not require the Y-complex. Furthermore, deletion of RNase Y has more pleiotropic effects on the transcriptome and cell growth than deletions of the Y-complex. We propose that the Y-complex is a specificity factor for RNase Y, with evidence that its role is broadly distributed across low-GC Firmicutes.

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RNA processing in Bacillus subtilis: Identification of targets of the essential RNase Y

Project description:RNA processing and degradation is initiated by endonucleolytic cleavage of the target RNAs. In many bacteria, this activity is performed by RNase E which is not present in Bacillus subtilis and other Gram-positive bacteria. Recently, the essential endoribonuclease RNase Y has been discovered in B. subtilis. This RNase is involved in the degradation of bulk mRNA suggesting a major role in mRNA metabolism. However, only a few targets of RNase Y have been identified so far. In order to assess the global impact of RNase Y, we compared the transcriptomes of strains expressing RNase Y or depleted for RNase Y. Our results indicate that processing by RNase Y results in accumulation of about 80 mRNAs. Some of these targets were substantially stabilized by RNase Y depletion, resulting in half-lives in the range of an hour. Moreover, about 40 mRNAs were less abundant when RNase Y was depleted among them the mRNAs of the operons required for biofilm formation. Interestingly, overexpression of RNase Y was sufficient to induce biofilm formation. The results emphasize the importance of RNase Y for B. subtilis and are in support of the idea that RNase Y is the functional equivalent of RNase E.

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Defining the impact of exoribonucleases in the shift between exponential and stationary phases

Project description:The transition between exponential and stationary phase is a natural phenomenon for all bacteria and requires a massive readjustment of the bacterial transcriptome. Exoribonucleases are key enzymes in the transition between the two growth phases. PNPase, RNase R and RNase II are the major degradative exoribonucleases in Escherichia coli. We analysed the whole transcriptome of exponential and stationary phases from the WT and mutants lacking these exoribonucleases (Δpnp, Δrnr, Δrnb, and ΔrnbΔrnr). When comparing the cells from exponential phase with the cells from stationary phase more than 1000 transcripts were differentially expressed, but only 491 core transcripts were common to all strains. There were some differences in the number and transcripts affected depending on the strain, suggesting that exoribonucleases influence the transition between these two growth phases differently. Interestingly, we found that the double mutant RNase II/RNase R is similar to the RNase R single mutant in exponential phase while in stationary phase it seems to be closer to the RNase II single mutant. This is the first global transcriptomic work comparing the roles of exoribonucleases in the transition between exponential and stationary phase.

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Bacillus subtilis SigA ChIP-chip (BsubT2 array)

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Transcriptome analysis of B. subtilis cells during recovery from injury after high hydrostatic pressure treatment

Project description:Vegetative cells of B. subtilis can recover from injury caused by high hydrostatic pressure (HHP) treatment at 250 MPa. DNA microarray analysis revealed that many ribosomal genes and translation relating factors (e.g. translation initiation factors) were induced during a growth-arrested phase after the HHP treatment. Expression of cold shock-responsive genes, whose products play key roles for efficient translation, and heat shock-responsive genes, whose product mediates the correct protein folding or degrades misfolded proteins, were also induced. In contrast, the expression of hpf, whose product (Hpf) is involved in ribosome inactivation through dimerization of 70S ribosomes, was repressed. Sucrose density gradient sedimentation analysis showed that ribosomes were dissociated in a pressure-dependent manner and then reconstructed during the growth-arrested phase. These results suggested that the translational machinery can be preferentially reconstructed in the HHP-injured cells. We also found that cell growth after HHP-induced injury was apparently inhibited by Mn2+ or Zn2+ supplemented to the recovery medium. Ribosome reconstruction in HHP-injured cells was significantly delayed in the presence of Mn2+ or Zn2+. Moreover, Zn2+ but not Mn2+ stimulated dimer formation of ribosomes in HHP-injured cells. This Zn2+-dependent accumulation of ribosome dimer was no longer observed in a Δhpf mutant lacking the functional Hpf. Furthermore, the growth recovery of the Δhpf mutant in the Zn2+-supplemented medium was faster than that of the parent strain. Thus, our results indicate that Zn2+ can prevent ribosome reconstruction by stimulating the Hpf-dependent ribosome dimerization, thereby inhibiting the growth recovery of the HHP-injured B. subtilis cells.

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