RegulonDB RegulonDB 10.8: smallRNA Form
   

RyhB small RNA in Escherichia coli K-12 genome


Gene local context to scale (view description)

yhhX yhhY ryhB Fur Fur Fur yhhYp yhhYp yhhXp5 yhhXp5 yhhXp4 yhhXp4 TSS_4054 TSS_4054
small RNA      
Gene name: ryhB    Texpresso search in the literature
Synonym(s): IS176, PsrA18, RyhB small regulatory RNA involved in iron homeostasis, SraI, psrA18, small regulatory RNA RyhB, sraI
Genome position: 3580927 <-- 3581016
Strand: reverse
Sequence: Get ribonucleotide sequence FastaFormat
GC content %:  
53.33
Note(s): RyhB is a small RNA which acts to reduce iron consumption under low-iron conditions by downregulating expression of iron-containing proteins, including enzymes of the TCA cycle and the aerobic respiratory chain Masse E,2002. Masse E,2005. 16982641. 22474262. In addition, RyhB promotes synthesis of the siderophore enterobactin 20696910. RyhB was first identified as a small RNA of approximately 90 nt in length Wassarman KM,2001. Argaman L,2001.
RIBOseq data suggests that in E. coli O157:H7 EDL933, a small open reading frame within RyhB that begins with an ATT start codon may be translated to the nonapeptide MAHIASSIT 28245801.
Structural and functional components of RyhB were identified using a library of single nucleotide mutants and evaluating their effects on known regulatory targets Peterman N,2014. Theoretical analysis and quantitative evaluation of regulation by RyhB has been performed 17713988. Prediction of regulatory targets of RyhB can be improved by considering accessible regions in both the sRNA and its target 22767260 and by simulation of the effect of the sRNA on translation initiation 23203192. Additional targets have been predicted by comparative genomics Wright PR,2013 and experimentally identified by an affinity purification method Lalaouna D,2015 and by Ribo-seq 26546513.
RyhB downregulates full-length sdhCDAB RNA abundance Masse E,2002. RyhB also mediates regulation of acnA, fumA, bfr, sodB Masse E,2002 and acnB Masse E,2005. Benjamin JA,2014 by Fur. Indirect regulation by Fur during anaerobic growth conditions revealed a new set of targets regulated by RyhB 26670385. RyhB was shown to inhibit translation of sodB in vitro Vecerek B,2003 and stimulate degradation of sodB mRNA by RNase E 12975324. In the absence of RNase E, gene silencing can occur by translational repression alone 16549791; conversely, RyhB-induced mRNA cleavage at a distal site by RNase E does not require translation 21289064. The characteristics of feed-forward regulation of SodA expression by Fur and RyhB has been modeled 24621982. The cysE gene has also been identified as a direct target of RyhB regulation. Downregulating the expression of the serine acetyltransferase CysE increases the availability of serine for the production of enterobactin 20696910. RyhB overexpression decreases expression of hemB and hemH in the engineered DALA strain Li F,2014.
RyhB was shown to promote cleavage of the polycistronic iscRSUA mRNA between the iscR and iscS open reading frames. The IscR-encoding 5' fragment remains stable, while the iscSUA 3' fragment appears to be degraded 19407815.
RyhB increases expression of the shikimate transporter ShiA by increasing shiA mRNA stability and activating translation Prevost K,2007. RyhB is required for synthesis of CirA during iron starvation: Hfq blocks translation initiation, and binding of RyhB leads to changes in the mRNA secondary structure, thereby displacing Hfq 24065131.
Affinity purification also identified direct interactions of RyhB with the 3' external transcribed spacer (ETS) sequence of a tRNA-encoding operon, |FRAME: TU00512|. In this context, the 3'ETSleuZ is thought to function as a sponge that absorbs transcriptional noise while RyhB expression is not induced Lalaouna D,2015.
Although ftnA expression was also thought to be regulated by RyhB Masse E,2002, microarray experiments indicated that expression of ftnA is not dependent on ryhB Masse E,2005. It was later shown that ftnA expression is directly regulated by Fur Nandal A,2010.
An efficient interaction between RyhB RNA and Hfq protein has been det...
Evidence: [IDA] Inferred from direct assay
[IMP] Inferred from mutant phenotype
Reference(s): [1] Arbel-Goren R., et al., 2016
[2] Baez A., et al., 2017
[3] Bos J., et al., 2013
[4] Chen S., et al., 2002
[5] Kang Z., et al., 2012
[6] Mandin P., et al., 2016
[7] Masse E., et al., 2002
[8] Mihailovic MK., et al., 2018
[9] Mitarai N., et al., 2009
[10] Orchard SS., et al., 2012
[11] Sheng H., et al., 2017
[12] Vecerek B., et al., 2003
[13] Zhang J., et al., 2016
External database links:  
ECOCYC:
SRAI-RNA
ECOLIWIKI:
b4451
M3D: RyhB


Regulation exerted by the small RNA    
  Target Regulation Type Mechanism Function Binding Site Evidence
Code
Reference(s)
LeftPos RightPos Distance
to the gene
Sequence
 
antisense
post-transcriptional regulation
repressor
 
 
 
 
 
 
 
antisense
post-transcriptional regulation
repressor
 
 
 
 
 
 
antisense
post-transcriptional regulation
repressor
 
 
 
 
 
 
antisense
post-transcriptional regulation
repressor
 
 
 
 
 
 
 
antisense
post-transcriptional regulation
repressor
 
 
 
 
 
 
antisense
post-transcriptional regulation
repressor
 
 
 
 
 
 
antisense
translational regulation
activator
 
 
 
 
 
 
antisense
post-transcriptional regulation
repressor
 
 
 
 
 
 
antisense
post-transcriptional regulation
repressor
 
 
 
 
 
 
antisense
post-transcriptional regulation
repressor
 
 
 
 
 
 
antisense
post-transcriptional regulation
repressor
 
 
 
 
 
 
antisense
post-transcriptional regulation
repressor
 
 
 
 
 
 
antisense
post-transcriptional regulation
repressor
 
 
 
 
 
 
antisense
post-transcriptional regulation
repressor
 
 
 
 
 
 
antisense
post-transcriptional regulation
repressor
 
 
 
 
 
 
antisense
post-transcriptional regulation
repressor
 
 
 
 
 
 
antisense
post-transcriptional regulation
repressor
 
 
 
 
 
 
antisense
post-transcriptional regulation
repressor
 
 
 
 
 
 
antisense
post-transcriptional regulation
repressor
 
 
 
 
 
 
antisense
post-transcriptional regulation
repressor
 
 
 
 
 
 
antisense
post-transcriptional regulation
repressor
 
 
 
 
 
 
antisense
post-transcriptional regulation
repressor
 
 
 
 
 
 
antisense
post-transcriptional regulation
repressor
 
 
 
 
 
 
antisense
post-transcriptional regulation
repressor
 
 
 
 
 
 
antisense
post-transcriptional regulation
repressor
 
 
 
 
 
 
remains elusive
 
activator
 
 
 
 
 
 
 
remains elusive
 
activator
 
 
 
 
 
 
 
remains elusive
 
activator
 
 
 
 
 
 
 
remains elusive
 
activator
 
 
 
 
 
 
 
remains elusive
 
activator
 
 
 
 
 
 
 
base-pairing
 
repressor
3782555
3782566
2
AGCAATGTCGT
 
 
 
stability of the transcript
 
repressor
 
 
 
 
 
 
 
stability of the transcript
 
repressor
 
 
 
 
 
 
 
stability of the transcript
 
repressor
 
 
 
 
 
 
 
stability of the transcript
 
activator
 
 
 
 
 
 
Evidence: [IMP] Inferred from mutant phenotype
[GEA] Gene expression analysis
[HIFS] Human inference of function from sequence


Reference(s)    

 [1] Arbel-Goren R., Tal A., Parasar B., Dym A., Costantino N., Munoz-Garcia J., Court DL., Stavans J., 2016, Transcript degradation and noise of small RNA-controlled genes in a switch activated network in Escherichia coli., Nucleic Acids Res 44(14):6707-20

 [2] Baez A., Shiloach J., 2017, Increasing dissolved-oxygen disrupts iron homeostasis in production cultures of Escherichia coli., Antonie Van Leeuwenhoek 110(1):115-124

 [3] Bos J., Duverger Y., Thouvenot B., Chiaruttini C., Branlant C., Springer M., Charpentier B., Barras F., 2013, The sRNA RyhB Regulates the Synthesis of the Escherichia coli Methionine Sulfoxide Reductase MsrB but Not MsrA., PLoS One 8(5):e63647

 [4] Chen S., Lesnik EA., Hall TA., Sampath R., Griffey RH., Ecker DJ., Blyn LB., 2002, A bioinformatics based approach to discover small RNA genes in the Escherichia coli genome., Biosystems 65(2-3):157-77

 [5] Kang Z., Wang X., Li Y., Wang Q., Qi Q., 2012, Small RNA RyhB as a potential tool used for metabolic engineering in Escherichia coli., Biotechnol Lett 34(3):527-31

 [6] Mandin P., Chareyre S., Barras F., 2016, A Regulatory Circuit Composed of a Transcription Factor, IscR, and a Regulatory RNA, RyhB, Controls Fe-S Cluster Delivery., MBio 7(5)

 [7] Masse E., Gottesman S., 2002, A small RNA regulates the expression of genes involved in iron metabolism in Escherichia coli., Proc Natl Acad Sci U S A 99(7):4620-5

 [8] Mihailovic MK., Vazquez-Anderson J., Li Y., Fry V., Vimalathas P., Herrera D., Lease RA., Powell WB., Contreras LM., 2018, High-throughput in vivo mapping of RNA accessible interfaces to identify functional sRNA binding sites., Nat Commun 9(1):4084

 [9] Mitarai N., Benjamin JA., Krishna S., Semsey S., Csiszovszki Z., Masse E., Sneppen K., 2009, Dynamic features of gene expression control by small regulatory RNAs., Proc Natl Acad Sci U S A 106(26):10655-9

 [10] Orchard SS., Rostron JE., Segall AM., 2012, Escherichia coli enterobactin synthesis and uptake mutants are hypersensitive to an antimicrobial peptide that limits the availability of iron in addition to blocking Holliday junction resolution., Microbiology 158(Pt 2):547-59

 [11] Sheng H., Stauffer WT., Hussein R., Lin C., Lim HN., 2017, Nucleoid and cytoplasmic localization of small RNAs in Escherichia coli., Nucleic Acids Res 45(5):2919-2934

 [12] Vecerek B., Moll I., Afonyushkin T., Kaberdin V., Blasi U., 2003, Interaction of the RNA chaperone Hfq with mRNAs: direct and indirect roles of Hfq in iron metabolism of Escherichia coli., Mol Microbiol 50(3):897-909

 [13] Zhang J., Kang Z., Ding W., Chen J., Du G., 2016, Integrated Optimization of the In Vivo Heme Biosynthesis Pathway and the In Vitro Iron Concentration for 5-Aminolevulinate Production., Appl Biochem Biotechnol 178(6):1252-62


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