RNase Y targets

Regulator	RNase Y
Overview on the regulons (wiki page) Overview on the regulons (Excel file)

RNAs that are targeted by RNase Y

mRNAs directly cleaved by RNase Y

• processing of the gapA operon mRNA between cggR and gapA (cggR-gapA-pgk-tpi-pgm-eno), requires the YmcA-YlbF-YaaT complex PubMed
• processing of the ATPase operon mRNA between atpI and atpB (atpI-atpB-atpE-atpF-atpH-atpA-atpG-atpD-atpC), requires the YmcA-YlbF-YaaT complex PubMed
• processing of the dacA-pdxS-pdxT-serS mRNA upstream of dacA, requires the YmcA-YlbF-YaaT complex PubMed
• processing of the ddl-murF mRNA upstream of ddl, requires the YmcA-YlbF-YaaT complex PubMed
• processing of the yfjN leader mRNA, requires the YmcA-YlbF-YaaT complex PubMed
• processing of the glnR-glnA operon mRNA between glnR and glnA, requires the YmcA-YlbF-YaaT complex PubMed
• processing of the hbs leader mRNA PubMed
• processing of the menA leader mRNA, requires the YmcA-YlbF-YaaT complex PubMed
• processing of the metN-metP-metQ operon mRNA between metP and metQ, requires the YmcA-YlbF-YaaT complex PubMed
• processing of the ydiG-rex-tatAY-tatCY operon mRNA between rex and tatAY, requires the YmcA-YlbF-YaaT complex PubMed
• processing of the rplGB-rpsL-rpsG-fusA-tufA operon mRNA between rplGB and rpsL, requires the YmcA-YlbF-YaaT complex PubMed
• processing of the rpoB-rpoC leader mRNA, requires the YmcA-YlbF-YaaT complex PubMed
• processing of the rpoE-pyrG operon mRNA between rpoE and pyrG, requires the YmcA-YlbF-YaaT complex PubMed
• processing of the ruvA-ruvB-yrzS-queA-tgt-yrbF operon mRNA between tgt and yrbF, requires the YmcA-YlbF-YaaT complex PubMed
• processing of the tagA-tagB mRNA upstream of tagA, requires the YmcA-YlbF-YaaT complex PubMed
• processing of the ybfG-ybfF-ybfE operon mRNA between ybfG and ybfF, requires the YmcA-YlbF-YaaT complex PubMed
• processing of the ylxM-ffh-rpsP-ylqC-ylqD-rimM-trmD-rplS operon mRNA between ffh and rpsP, requires the YmcA-YlbF-YaaT complex PubMed
• processing of the yonR-yonS operon mRNA between yonR and yonS, requires the YmcA-YlbF-YaaT complex PubMed
• processing of the yqhL leader mRNA PubMed
• processing of the ywzH-dltA-dltB-dltC-dltD-dltE operon mRNA between ywzH and dltA, requires the YmcA-YlbF-YaaT complex PubMed
• initiates the degradation of rpsO, requires the YmcA-YlbF-YaaT complex mRNA PubMed
• infC-rpmI-rplT mRNA, requires the YmcA-YlbF-YaaT complex PubMed
• leader of the cwlO mRNA, requires the YmcA-YlbF-YaaT complex PubMed
• the RoxS sRNA PubMed
• the ppnKB mRNA PubMed

Riboswitch RNAs cleaved by RNase Y

• the S-box riboswitch RNAs in vivo and in vitro PubMed
• cysE PubMed
• cysH PubMed
• gcvT PubMed
• hisS, requires the YmcA-YlbF-YaaT complex PubMed
• ileS, requires the YmcA-YlbF-YaaT complex PubMed
• ilvB PubMed
• infC PubMed
• metE PubMed
• metH PubMed
• metN PubMed
• mtnK PubMed
• nupG, requires the YmcA-YlbF-YaaT complex PubMed
• pheS PubMed
• proB PubMed
• ribD PubMed
• rpsD PubMed
• prsO PubMed
• sacB PubMed
• tenA PubMed
• thiC PubMed
• thrS, requires the YmcA-YlbF-YaaT complex PubMed
• thrZ, requires the YmcA-YlbF-YaaT complex PubMed
• trpE PubMed
• trpS, requires the YmcA-YlbF-YaaT complex PubMed
• tyrS, requires the YmcA-YlbF-YaaT complex PubMed
• valS PubMed
• yitJ PubMed
• ykoY PubMed
• ylmB PubMed
• yoaD PubMed
• yvbW PubMed
• yxjG PubMed
• yxjH PubMed
• yybP PubMed

Increased RNA amount upon RNase Y depletion

• trpE-trpD-trpC-trpF-trpB-trpA-hisC-tyrA-aroE PubMed
• yhbI-yhbJ-yhcA-yhcB-yhcC-yhcD-yhcE-yhcF-yhcG-yhcH-yhcI PubMed
• ysbA-ysbB PubMed
• yrhG PubMed
• maeA-ywkB PubMed
• nhaC PubMed
• guaC PubMed
• ydaB PubMed
• maeN PubMed
• cimH PubMed
• ynfC PubMed
• yrhE-yrhD PubMed
• yjbC-spx PubMed
• yrhF PubMed
• speD PubMed
• yhfH PubMed
• pabA-pabC PubMed
• yebC PubMed
• yurR-yurQ-frlB-frlO-frlN-frlM-frlD PubMed
• yuxJ PubMed
• lmrA-lmrB PubMed
• yrhH PubMed
• acoA-acoB-acoC-acoL PubMed
• ribU PubMed
• pbpA PubMed
• ytdI PubMed
• cggR-gapA PubMed
• yhdY PubMed
• ywcI PubMed
• yflS PubMed
• several SP-beta prophage genes, exemplified by yorW PubMed
• sinR PubMed
• sinI-sinR PubMed

Decreased RNA amount upon RNase Y depletion

• slrR PubMed (this is likely due to the increased stability of the sinR mRNA upon RNase Y depletion PubMed)
• epsA-epsB-epsC-epsD-epsE-epsF-epsG-epsH-epsI-epsJ-epsK-epsL-epsM-epsN-epsO PubMed (this is likely due to the increased stability of the sinR mRNA upon RNase Y depletion PubMed)
• ctaO PubMed
• lip PubMed
• sunT-bdbA-yolJ PubMed
• yydF-yydG-yydH-yydI-yydJ PubMed
• tapA-sipW-tasA PubMed (this is likely due to the increased stability of the sinR mRNA upon RNase Y depletion PubMed)
• dhbA-dhbC-dhbE-dhbB-dhbF PubMed
• thrZ PubMed
• yfmG PubMed
• sdpA-sdpB-sdpC PubMed
• wprA PubMed
• yxeK-yxeL-yxeM PubMed
• yxbB PubMed

Important publications on RNase Y targets

Aaron DeLoughery, Jean-Benoît Lalanne, Richard Losick, Gene-Wei Li
##Title##
Proc Natl Acad Sci U S A: 2018, 115(24);E5585-E5594
[PubMed:29794222] [WorldCat.org] [DOI] (I p)

Soumaya Laalami, Philippe Bessières, Anna Rocca, Léna Zig, Pierre Nicolas, Harald Putzer
Bacillus subtilis RNase Y activity in vivo analysed by tiling microarrays.
PLoS One: 2013, 8(1);e54062
[PubMed:23326572] [WorldCat.org] [DOI] (I p)

Sylvain Durand, Laetitia Gilet, Philippe Bessières, Pierre Nicolas, Ciarán Condon
Three essential ribonucleases-RNase Y, J1, and III-control the abundance of a majority of Bacillus subtilis mRNAs.
PLoS Genet: 2012, 8(3);e1002520
[PubMed:22412379] [WorldCat.org] [DOI] (I p)

Martin Lehnik-Habrink, Marc Schaffer, Ulrike Mäder, Christine Diethmaier, Christina Herzberg, Jörg Stülke
RNA processing in Bacillus subtilis: identification of targets of the essential RNase Y.
Mol Microbiol: 2011, 81(6);1459-73
[PubMed:21815947] [WorldCat.org] [DOI] (I p)