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

• The targets listed below are affected >2.5 fold upon RNase Y depletion PubMed

RNAs directly cleaved by RNase Y

• the S-box riboswitch RNAs in vivo and in vitro PubMed
• processing of the gapA operon mRNA PubMed
• initiates the degradation of rpsO mRNA PubMed
• infC-rpmI-rplT mRNA 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

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)

Lehnik-Habrink M, Schaffer M, Mäder U, Diethmaier C, Herzberg C, Stülke J  
RNA processing in Bacillus subtilis: identification of targets of the essential RNase Y. 
Mol Microbiol. 2011 81(6): 1459-1473. 
PubMed:21815947