Difference between revisions of "RNase Y targets"

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(→‎Important publications on RNase Y targets)
 
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= RNAs that are targeted by [[rny|RNase Y]]=
 
= RNAs that are targeted by [[rny|RNase Y]]=
−
=== RNAs directly cleaved by [[rny|RNase Y]] ===
 
  
−
** the [[S-box]] [[riboswitch]] RNAs ''in vivo'' and ''in vitro'' {{PubMed|19779461}}
+
=== mRNAs directly cleaved by [[rny|RNase Y]] ===
−
** processing of the ''[[gapA]]'' operon mRNA {{PubMed|19193632}}  
+
 
−
** initiates the degradation of ''[[rpsO]]'' mRNA {{PubMed|20418391}}
+
* processing of the ''[[gapA]]'' operon mRNA between ''[[cggR]]'' and ''[[gapA]]'' (''[[cggR]]-[[gapA]]-[[pgk]]-[[tpi]]-[[pgm]]-[[eno]]''), requires the [[protein|YmcA]]-[[protein|YlbF]]-[[protein|YaaT]] complex {{PubMed|29794222,19193632}}
 +
* processing of the ATPase operon mRNA between ''[[atpI]]'' and ''[[atpB]]'' (''[[atpI]]-[[atpB]]-[[atpE]]-[[atpF]]-[[atpH]]-[[atpA]]-[[atpG]]-[[atpD]]-[[atpC]]''), requires the [[protein|YmcA]]-[[protein|YlbF]]-[[protein|YaaT]] complex {{PubMed|29794222}}
 +
* processing of the ''[[dacA]]-[[pdxS]]-[[pdxT]]-[[serS]]'' mRNA upstream of ''[[dacA]]'', requires the [[protein|YmcA]]-[[protein|YlbF]]-[[protein|YaaT]] complex {{PubMed|29794222}}
 +
* processing of the ''[[ddl]]-[[murF]]'' mRNA upstream of ''[[ddl]]'', requires the [[protein|YmcA]]-[[protein|YlbF]]-[[protein|YaaT]] complex {{PubMed|29794222}}
 +
* processing of the ''[[yfjN]]'' leader mRNA, requires the [[protein|YmcA]]-[[protein|YlbF]]-[[protein|YaaT]] complex {{PubMed|29794222}}
 +
* processing of the ''[[glnR]]-[[glnA]]'' operon mRNA between ''[[glnR]]'' and ''[[glnA]]'', requires the [[protein|YmcA]]-[[protein|YlbF]]-[[protein|YaaT]] complex {{PubMed|29794222}}
 +
* processing of the ''[[hbs]]'' leader mRNA {{PubMed|29794222}}
 +
* processing of the ''[[menA]]'' leader mRNA, requires the [[protein|YmcA]]-[[protein|YlbF]]-[[protein|YaaT]] complex {{PubMed|29794222}}
 +
* processing of the ''[[metN]]-[[metP]]-[[metQ]]'' operon mRNA between ''[[metP]]'' and ''[[metQ]]'', requires the [[protein|YmcA]]-[[protein|YlbF]]-[[protein|YaaT]] complex {{PubMed|29794222}}
 +
* processing of the ''[[ydiG]]-[[rex]]-[[tatAY]]-[[tatCY]]'' operon mRNA between ''[[rex]]'' and ''[[tatAY]]'', requires the [[protein|YmcA]]-[[protein|YlbF]]-[[protein|YaaT]] complex {{PubMed|29794222}}
 +
* processing of the ''[[rplGB]]-[[rpsL]]-[[rpsG]]-[[fusA]]-[[tufA]]'' operon mRNA between ''[[rplGB]]'' and ''[[rpsL]]'', requires the [[protein|YmcA]]-[[protein|YlbF]]-[[protein|YaaT]] complex {{PubMed|29794222}}
 +
* processing of the ''[[rpoB]]-[[rpoC]]'' leader mRNA, requires the [[protein|YmcA]]-[[protein|YlbF]]-[[protein|YaaT]] complex {{PubMed|29794222}}
 +
* processing of the ''[[rpoE]]-[[pyrG]]'' operon mRNA between ''[[rpoE]]'' and ''[[pyrG]]'', requires the [[protein|YmcA]]-[[protein|YlbF]]-[[protein|YaaT]] complex {{PubMed|29794222}}
 +
* processing of the ''[[ruvA]]-[[ruvB]]-[[yrzS]]-[[queA]]-[[tgt]]-[[yrbF]]'' operon mRNA between ''[[tgt]]'' and ''[[yrbF]]'', requires the [[protein|YmcA]]-[[protein|YlbF]]-[[protein|YaaT]] complex {{PubMed|29794222}}
 +
* processing of the ''[[tagA]]-[[tagB]]'' mRNA upstream of ''[[tagA]]'', requires the [[protein|YmcA]]-[[protein|YlbF]]-[[protein|YaaT]] complex {{PubMed|29794222}}
 +
* processing of the ''[[ybfG]]-[[ybfF]]-[[ybfE]]'' operon mRNA between ''[[ybfG]]'' and ''[[ybfF]]'', requires the [[protein|YmcA]]-[[protein|YlbF]]-[[protein|YaaT]] complex {{PubMed|29794222}}  
 +
* processing of the ''[[ylxM]]-[[ffh]]-[[rpsP]]-[[ylqC]]-[[ylqD]]-[[rimM]]-[[trmD]]-[[rplS]]'' operon mRNA between ''[[ffh]]'' and ''[[rpsP]]'', requires the [[protein|YmcA]]-[[protein|YlbF]]-[[protein|YaaT]] complex {{PubMed|29794222}}
 +
* processing of the ''[[yonR]]-[[yonS]]'' operon mRNA between ''[[yonR]]'' and ''[[yonS]]'', requires the [[protein|YmcA]]-[[protein|YlbF]]-[[protein|YaaT]] complex {{PubMed|29794222}}  
 +
* processing of the ''[[yqhL]]'' leader mRNA {{PubMed|29794222}}
 +
* processing of the ''[[ywzH]]-[[dltA]]-[[dltB]]-[[dltC]]-[[dltD]]-[[dltE]]'' operon mRNA between ''[[ywzH]]'' and ''[[dltA]]'', requires the [[protein|YmcA]]-[[protein|YlbF]]-[[protein|YaaT]] complex {{PubMed|29794222}}
 +
* initiates the degradation of ''[[rpsO]]'', requires the [[protein|YmcA]]-[[protein|YlbF]]-[[protein|YaaT]] complex mRNA {{PubMed|20418391}}
 +
* ''[[infC]]-[[rpmI]]-[[rplT]]'' mRNA, requires the [[protein|YmcA]]-[[protein|YlbF]]-[[protein|YaaT]] complex {{PubMed|21843271}}
 +
* leader of the ''[[cwlO]]'' mRNA, requires the [[protein|YmcA]]-[[protein|YlbF]]-[[protein|YaaT]] complex {{PubMed|29794222,24163346}}
 +
* the [[RoxS]] [[sRNA]] {{PubMed|25643072}}
 +
* the ''[[ppnKB]]'' mRNA {{PubMed|25643072}}
 +
 
 +
=== [[riboswitch|Riboswitch]] RNAs cleaved by [[rny|RNase Y]] ===
 +
 
 +
* the [[S-box]] [[riboswitch]] RNAs ''in vivo'' and ''in vitro'' {{PubMed|29794222,19779461}}
 +
* ''[[cysE]]'' {{PubMed|29794222}}
 +
* ''[[cysH]]'' {{PubMed|29794222}}
 +
* ''[[gcvT]]'' {{PubMed|29794222}}
 +
* ''[[hisS]]'', requires the [[protein|YmcA]]-[[protein|YlbF]]-[[protein|YaaT]] complex {{PubMed|29794222}}
 +
* ''[[ileS]]'', requires the [[protein|YmcA]]-[[protein|YlbF]]-[[protein|YaaT]] complex {{PubMed|29794222}}
 +
* ''[[ilvB]]'' {{PubMed|29794222}}
 +
* ''[[infC]]'' {{PubMed|29794222}}
 +
* ''[[metE]]'' {{PubMed|29794222}}
 +
* ''[[metH]]'' {{PubMed|29794222}}
 +
* ''[[metN]]'' {{PubMed|29794222}}
 +
* ''[[mtnK]]'' {{PubMed|29794222}}
 +
* ''[[nupG]]'', requires the [[protein|YmcA]]-[[protein|YlbF]]-[[protein|YaaT]] complex {{PubMed|29794222}}
 +
* ''[[pheS]]'' {{PubMed|29794222}}
 +
* ''[[proB]]'' {{PubMed|29794222}}
 +
* ''[[ribD]]'' {{PubMed|29794222}}
 +
* ''[[rpsD]]'' {{PubMed|29794222}}
 +
* ''[[prsO]]'' {{PubMed|29794222}}
 +
* ''[[sacB]]'' {{PubMed|29794222}}
 +
* ''[[tenA]]'' {{PubMed|29794222}}
 +
* ''[[thiC]]'' {{PubMed|29794222}}
 +
* ''[[thrS]]'', requires the [[protein|YmcA]]-[[protein|YlbF]]-[[protein|YaaT]] complex {{PubMed|29794222}}
 +
* ''[[thrZ]]'', requires the [[protein|YmcA]]-[[protein|YlbF]]-[[protein|YaaT]] complex {{PubMed|29794222}}
 +
* ''[[trpE]]'' {{PubMed|29794222}}
 +
* ''[[trpS]]'', requires the [[protein|YmcA]]-[[protein|YlbF]]-[[protein|YaaT]] complex {{PubMed|29794222}}
 +
* ''[[tyrS]]'', requires the [[protein|YmcA]]-[[protein|YlbF]]-[[protein|YaaT]] complex {{PubMed|29794222}}
 +
* ''[[valS]]'' {{PubMed|29794222}}
 +
* ''[[yitJ]]'' {{PubMed|29794222}}
 +
* ''[[ykoY]]'' {{PubMed|29794222}}
 +
* ''[[ylmB]]'' {{PubMed|29794222}}
 +
* ''[[yoaD]]'' {{PubMed|29794222}}
 +
* ''[[yvbW]]'' {{PubMed|29794222}}
 +
* ''[[yxjG]]'' {{PubMed|29794222}}
 +
* ''[[yxjH]]'' {{PubMed|29794222}}
 +
* ''[[yybP]]'' {{PubMed|29794222}}
  
 
=== Increased RNA amount upon [[rny|RNase Y]] depletion ===
 
=== Increased RNA amount upon [[rny|RNase Y]] depletion ===
  
−
=== Increased RNA amount upon [[rny|RNase Y]] depletion ===
+
* ''[[trpE]]-[[trpD]]-[[trpC]]-[[trpF]]-[[trpB]]-[[trpA]]-[[hisC]]-[[tyrA]]-[[aroE]]'' {{PubMed|21815947}}
 +
* ''[[yhbI]]-[[yhbJ]]-[[yhcA]]-[[yhcB]]-[[yhcC]]-[[yhcD]]-[[yhcE]]-[[yhcF]]-[[yhcG]]-[[yhcH]]-[[yhcI]]'' {{PubMed|21815947}}
 +
* ''[[ysbA]]-[[ysbB]]'' {{PubMed|21815947}}
 +
* ''[[yrhG]]'' {{PubMed|21815947}}
 +
* ''[[maeA]]-[[ywkB]]'' {{PubMed|21815947}}
 +
* ''[[nhaC]]'' {{PubMed|21815947}}
 +
* ''[[guaC]]'' {{PubMed|21815947}}
 +
* ''[[ydaB]]'' {{PubMed|21815947}}
 +
* ''[[maeN]]'' {{PubMed|21815947}}
 +
* ''[[cimH]]'' {{PubMed|21815947}}
 +
* ''[[ynfC]]'' {{PubMed|21815947}}
 +
* ''[[yrhE]]-[[yrhD]]'' {{PubMed|21815947}}
 +
* ''[[yjbC]]-[[spx]]'' {{PubMed|21815947}}
 +
* ''[[yrhF]]'' {{PubMed|21815947}}
 +
* ''[[speD]]'' {{PubMed|21815947}}
 +
* ''[[yhfH]]'' {{PubMed|21815947}}
 +
* ''[[pabA]]-[[pabC]]'' {{PubMed|21815947}}
 +
* ''[[yebC]]'' {{PubMed|21815947}}
 +
* ''[[yurR]]-[[yurQ]]-[[frlB]]-[[frlO]]-[[frlN]]-[[frlM]]-[[frlD]]'' {{PubMed|21815947}}
 +
* ''[[yuxJ]]'' {{PubMed|21815947}}
 +
* ''[[lmrA]]-[[lmrB]]'' {{PubMed|21815947}}
 +
* ''[[yrhH]]'' {{PubMed|21815947}}
 +
* ''[[acoA]]-[[acoB]]-[[acoC]]-[[acoL]]'' {{PubMed|21815947}}
 +
* ''[[ribU]]'' {{PubMed|21815947}}
 +
* ''[[pbpA]]'' {{PubMed|21815947}}
 +
* ''[[ytdI]]'' {{PubMed|21815947}}
 +
* ''[[cggR]]-[[gapA]]'' {{PubMed|21815947}}
 +
* ''[[yhdY]]'' {{PubMed|21815947}}
 +
* ''[[ywcI]]'' {{PubMed|21815947}}
 +
* ''[[yflS]]'' {{PubMed|21815947}}
 +
* several [[SP-beta prophage]] genes, exemplified by ''[[yorW]]'' {{PubMed|21815947}}
 +
* ''[[sinR]]'' {{PubMed|21815947}}
 +
* ''[[sinI]]-[[sinR]]'' {{PubMed|21815947}}
 +
 
 +
=== Decreased RNA amount upon [[rny|RNase Y]] depletion ===
  
 +
* ''[[slrR]]'' {{PubMed|21815947}} (this is likely due to the increased stability of the ''[[sinR]]'' mRNA upon [[rny|RNase Y]] depletion {{PubMed|21815947}})
 +
* ''[[epsA]]-[[epsB]]-[[epsC]]-[[epsD]]-[[epsE]]-[[epsF]]-[[epsG]]-[[epsH]]-[[epsI]]-[[epsJ]]-[[epsK]]-[[epsL]]-[[epsM]]-[[epsN]]-[[epsO]]'' {{PubMed|21815947}} (this is likely due to the increased stability of the ''[[sinR]]'' mRNA upon [[rny|RNase Y]] depletion {{PubMed|21815947}})
 +
* ''[[ctaO]]'' {{PubMed|21815947}}
 +
* ''[[lip]]'' {{PubMed|21815947}}
 +
* ''[[sunT]]-[[bdbA]]-[[yolJ]]'' {{PubMed|21815947}}
 +
* ''[[yydF]]-[[yydG]]-[[yydH]]-[[yydI]]-[[yydJ]]'' {{PubMed|21815947}}
 +
* ''[[tapA]]-[[sipW]]-[[tasA]]'' {{PubMed|21815947}} (this is likely due to the increased stability of the ''[[sinR]]'' mRNA upon [[rny|RNase Y]] depletion {{PubMed|21815947}})
 +
* ''[[dhbA]]-[[dhbC]]-[[dhbE]]-[[dhbB]]-[[dhbF]]'' {{PubMed|21815947}}
 +
* ''[[thrZ]]'' {{PubMed|21815947}}
 +
* ''[[yfmG]]'' {{PubMed|21815947}}
 +
* ''[[sdpA]]-[[sdpB]]-[[sdpC]]'' {{PubMed|21815947}}
 +
* ''[[wprA]]'' {{PubMed|21815947}}
 +
* ''[[yxeK]]-[[yxeL]]-[[yxeM]]'' {{PubMed|21815947}}
 +
* ''[[yxbB]]'' {{PubMed|21815947}}
  
 
= Important publications on [[rny|RNase Y]] targets =
 
= Important publications on [[rny|RNase Y]] targets =
−
<big>''Lehnik-Habrink M, Schaffer M, Mäder U, Diethmaier C, Herzberg C, Stülke J.''  </big>
+
<pubmed>22412379 23326572 21815947 29794222</pubmed>
−
<big>'''RNA processing in ''Bacillus subtilis'': identification of targets of the essential RNase Y.''' </big>
 
−
<big>Mol Microbiol. 2011 Aug 4. doi: 10.1111/j.1365-2958.2011.07777.x. [Epub ahead of print] </big>
 
−
[http://www.ncbi.nlm.nih.gov/pubmed/21815947 PubMed:21815947]
 
  
 
=Back to [[regulons]]=
 
=Back to [[regulons]]=

Latest revision as of 17:19, 30 May 2018

Regulator

RNase Y

RNAs that are targeted by RNase Y

mRNAs directly cleaved by RNase Y

Riboswitch RNAs cleaved by RNase Y

Increased RNA amount upon RNase Y depletion

Decreased RNA amount upon RNase Y depletion

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)


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