Maturation of polycistronic mRNAs by the endoribonuclease RNase Y and its associated Y-complex in<i>Bacillus subtilis</i>

DeLoughery, Aaron; Lalanne, Jean-Benoît; Losick, Richard; Li, Gene-Wei

doi:10.1073/pnas.1803283115

Cited by 63 publications

(124 citation statements)

References 53 publications

(84 reference statements)

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“…Although previous studies showed that RNase Y is sensitive to secondary structures located downstream of the processing events [10,12], a recent transcriptomic analysis in B. subtilis did not identify any consensus motif (neither sequence nor RNA structure) in proximity of RNase Y cleavages [39]. Our mutational study indicates that the sequence requirement ( i.e .…”

Section: Discussioncontrasting

confidence: 58%

“…It has recently been shown that the processing by RNase Y of specific mRNA targets in B. subtilis depends on the so-called Y-complex, composed of RNase Y and interacting proteins [39,40]. Overall, the exact requirements for RNase Y activity in vivo still need to be determined, and current knowledge indicates that this enzyme may exhibit various characteristics in different bacteria.…”

Section: Discussionmentioning

confidence: 99%

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RNase Y-mediated regulation of the streptococcal pyrogenic exotoxin B

et al. 2018

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Endoribonuclease Y (RNase Y) is a crucial regulator of virulence in Gram-positive bacteria. In the human pathogen Streptococcus pyogenes, RNase Y is required for the expression of the major secreted virulence factor streptococcal pyrogenic exotoxin B (SpeB), but the mechanism involved in this regulation remains elusive. Here, we demonstrate that the 5′ untranslated region of speB mRNA is processed by several RNases including RNase Y. In particular, we identify two RNase Y cleavage sites located downstream of a guanosine (G) residue. To assess whether this nucleotide is required for RNase Y activity in vivo, we mutated it and demonstrate that the presence of this G residue is essential for the processing of the speB mRNA 5′ UTR by RNase Y. Although RNase Y directly targets and processes speB, we show that RNase Y-mediated regulation of speB expression occurs primarily at the transcriptional level and independently of the processing in the speB mRNA 5′ UTR. To conclude, we demonstrate for the first time that RNase Y processing of an mRNA target requires the presence of a G. We also provide new insights on the speB 5′ UTR and on the role of RNase Y in speB regulation.

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Section: Discussioncontrasting

confidence: 58%

Section: Discussionmentioning

confidence: 99%

RNase Y-mediated regulation of the streptococcal pyrogenic exotoxin B

et al. 2018

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“…More importantly, it indicates that in B. subtilis , serine biosynthesis is regulated in an unusual manner relative to biosynthesis of other amino acids. Decrease in serA expression upon entry into stationary phase in B. subtilis was also confirmed by RNA-seq in a recent study [(47) and DeLoughery A, personal communications].…”

Section: Resultssupporting

confidence: 57%

Decreasing Serine Levels During Growth Transition Triggers Biofilm Formation inBacillus subtilis

Greenwich

Reverdy

Gozzi

et al. 2019

Preprint

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25Biofilm development in Bacillus subtilis is regulated at multiple levels. While a number 26 of known signals that trigger biofilm formation do so through the activation of one or more 27 sensory histidine kinases, it was recently discovered that biofilm activation is also coordinated by 28 sensing intracellular metabolic signals, including serine starvation. Serine starvation causes 29 ribosomes to pause on specific serine codons, leading to a decrease in the translation rate of sinR, 30 which encodes a master repressor for biofilm matrix genes, and ultimately biofilm induction. 31 How serine levels change in different growth stages, how B. subtilis regulates intracellular serine 32 levels in response to metabolic status, and how serine starvation triggers ribosomes to pause on 33 selective serine codons remain unknown. Here we show that serine levels decrease as cells enter 34 stationary phase and that unlike most other amino acid biosynthesis genes, expression of serine 35 biosynthesis genes decreases upon the transition into stationary phase. Deletion of the gene for a 36 serine deaminase responsible for converting serine to pyruvate led to a delay in biofilm 37 formation, further supporting the idea that serine levels are a critical intracellular signal for 38 biofilm activation. Finally, we show that levels of all five serine tRNA isoacceptors are 39 decreased in stationary phase compared to exponential phase. Interestingly, the three 40 isoacceptors recognizing UCN serine codons are reduced to a much greater extent than the two 41 that recognize AGC and AGU serine codons. Our findings provide evidence for a link between 42 serine homeostasis and biofilm development in B. subtilis. 43 44 3 IMPORTANCE 45In Bacillus subtilis, biofilm formation is triggered in response to various environmental 46 and cellular signals. It was previously proposed that serine limitation acts as a proxy for nutrient 47 status and triggers biofilm formation at the onset of biofilm entry through a novel signaling 48 mechanism caused by global ribosome pausing on selective serine codons. In this study, we 49 revealed that serine levels decrease at the biofilm entry due to catabolite control and a shunt 50 mechanism. We also show that levels of five serine tRNA isoacceptors are differentially 51 decreased in stationary phase compared to exponential phase; three isoacceptors recognizing 52 UCN serine codons are reduced much greater than the two recognizing AGC and AGU codons. 53This indicates a possible mechanism for selective ribosome pausing. 54 55 4

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“…This result contradicted the upshift of the msmE transcription reported by Nicolas et al (19). Perhaps, another mechanism, such as mRNA endonucleolytic cleavage, as observed in the regulation of the cggR-gapA operon, is involved (22,23). In contrast to P msmE , melibiose and raffinose strongly induced P msmR activity in the wild-type strain, while stachyose had no effect on P msmR activity compared to the uninduced control ( Fig.…”

mentioning

confidence: 58%

The melREDCA Operon Encodes a Utilization System for the Raffinose Family of Oligosaccharides in Bacillus subtilis

2019

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Bacillus subtilis is a heterotrophic soil bacterium that hydrolyzes different polysaccharides mainly found in the decomposed plants. These carbohydrates are mainly cellulose, hemicellulose, and the raffinose family of oligosaccharides (RFOs). RFOs are soluble ␣-galactosides, such as raffinose, stachyose, and verbascose, that rank second only after sucrose in abundance. Genome sequencing and transcriptome analysis of B. subtilis indicated the presence of a putative ␣-galactosidaseencoding gene (melA) located in the msmRE-amyDC-melA operon. Characterization of the MelA protein showed that it is a strictly Mn 2ϩ -and NAD ϩ -dependent ␣galactosidase able to hydrolyze melibiose, raffinose, and stachyose. Transcription of the msmER-amyDC-melA operon is under control of a A -type promoter located upstream of msmR (P msmR ), which is negatively regulated by MsmR. The activity of P msmR was induced in the presence of melibiose and raffinose. MsmR is a transcriptional repressor that binds to two binding sites at P msmR located upstream of the Ϫ35 box and downstream of the transcriptional start site. MsmEX-AmyCD forms an ATP-binding cassette (ABC) transporter that probably transports melibiose into the cell. Since msmRE-amyDC-melA is a melibiose utilization system, we renamed the operon melREDCA. IMPORTANCE Bacillus subtilis utilizes different polysaccharides produced by plants. These carbohydrates are primarily degraded by extracellular hydrolases, and the resulting oligo-, di-, and monosaccharides are transported into the cytosol via phosphoenolpyruvate-dependent phosphotransferase systems (PTS), major facilitator superfamily, and ATP-binding cassette (ABC) transporters. In this study, a new carbohydrate utilization system of B. subtilis responsible for the utilization of ␣galactosides of the raffinose family of oligosaccharides (RFOs) was investigated. RFOs are synthesized from sucrose in plants and are mainly found in the storage organs of plant leaves. Our results revealed the modus operandi of a new carbohydrate utilization system in B. subtilis. B acillus subtilis is a soil bacterium found in the rhizosphere of many plants. Because of such a habitat, B. subtilis can utilize a variety of poly-and oligosaccharides present in the rhizosphere as a major carbon source and therefore has different systems for the utilization of poly-, oligo-, and monosaccharides synthesized by plants. The polysaccharides are primarily degraded to oligosaccharides with shorter chain lengths and to monosaccharides by extracellular enzymes such as ␣-amylase, pullulanase, or xylanase. The generated oligosaccharides and monosaccharides can be then taken up via the carbohydrate-specific transporters of the phosphoenolpyruvate-dependent phosphotransferase system (PTS), ATP-binding cassette (ABC) transporters, and the major facilitator superfamily (uniporters, symporters, and antiporters) (1, 2). Depending on the transport system, the carbohydrates are phosphorylated during (for PTS) andCitation Morabbi Heravi K, Watzlawick H, Altenbuchner J. 2019....

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Maturation of polycistronic mRNAs by the endoribonuclease RNase Y and its associated Y-complex inBacillus subtilis

Cited by 63 publications

References 53 publications

RNase Y-mediated regulation of the streptococcal pyrogenic exotoxin B

RNase Y-mediated regulation of the streptococcal pyrogenic exotoxin B

Decreasing Serine Levels During Growth Transition Triggers Biofilm Formation inBacillus subtilis

The melREDCA Operon Encodes a Utilization System for the Raffinose Family of Oligosaccharides in Bacillus subtilis

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