RegulonDB

small RNA
Gene name:	ryhB
Synonym(s):	IS176, PsrA18, RyhB, RyhB small regulatory RNA involved in iron homeostasis, SraI
Genome position:	3580922 <-- 3581016
Strand:	reverse
Sequence:	Get ribonucleotide sequence FastaFormat
GC content %:	50.53
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. Semsey S, Andersson AM, Krishna S, Jensen MH, Massé E, Sneppen K,2006. Desnoyers G,2012. In addition, RyhB promotes synthesis of the siderophore enterobactin Salvail H,2010. 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 Amman F, Flamm C, Hofacker I,2012. Additional targets have been predicted by microarray and computational analyses and comparative genomics Masse E,2005. 16717284. Wright PR,2013 and experimentally identified by an affinity purification method Lalaouna D,2015 and by Ribo-seq 26546513. A candidate RyhB regulon was inferred by integrating information on experimentally supported targets and sRNA-mRNA interactions with transcription datasets; new targets with experimental support are acpP, amn, cheY, fabZ, folX, gshB, mrp, rna, rsmE, tpx, ubiD, and ybaB 32487739. Regulatory Targets of RyhB 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 Beauchene NA, Myers KS, Chung D, Park DM, Weisnicht AM, Kele? S, Kiley PJ,2015. RyhB was shown to inhibit translation of sodB in vitro Vecerek B,2003 and stimulate degradation of sodB mRNA by RNase E Massé E, Escorcia FE, Gottesman S,2003. 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 Prevost K,2011. Quantitative analysis of the interaction between wild-type and mutant RyhB and sodB mRNA correlates with thermodynamic models of this interaction and show that a continuum of repression strengths is achievable. Surprisingly, a truncated form of RyhB is able to regulate certain targets independently of Hfq 21742981. Phenotypic noise caused by RyhB regulation of sodB and fumA has been measured; extrinsic noise was found to be dominant 23519613. RyhB indirectly down-regulates Fur expression by down-regulating expression of the translationally coupled upstream reading frame Uof Vecerek B,2007. The characteristics of feed-forward regulation of SodA expression by Fur and RyhB has been modeled Semsey S,2014. 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 Salvail H,2010. 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 Desnoyers G,2009. RyhB increases expression of the shi...
Evidence:	[EXP-IDA] Inferred from direct assay [EXP-IMP] Inferred from mutant phenotype
Reference(s):	[1] Arbel-Goren R., et al., 2016 [2] Baez A., et al., 2017 [3] Banerjee R., et al., 2020 [4] Bos J., et al., 2013 [5] Chen S., et al., 2002 [6] Kang Z., et al., 2012 [7] King AM., et al., 2019 [8] Kiselev S., et al., 2021 [9] Liu F., et al., 2018 [10] Lyu Y., et al., 2019 [11] Mandin P., et al., 2016 [12] Masse E., et al., 2002 [13] Mihailovic MK., et al., 2018 [14] Mitarai N., et al., 2009 [15] Orchard SS., et al., 2012 [16] Sheng H., et al., 2017 [17] Vecerek B., et al., 2003 [18] Zhang J., et al., 2016
External database links:

ECOCYC:	SRAI-RNA
ECOLIWIKI:	b4451
M3D:	small regulatory RNA RyhB

Regulation exerted by the small RNA

Target	Mechanism	Function	Target Type	Binding Site			Evidence	Confidence level (C: Confirmed, S: Strong, W: Weak)	Reference(s)
Target	Mechanism	Function	Target Type	LeftPos	RightPos	Sequence	Evidence		Reference(s)
erpA	MRNA-DEGRADATION	repressor	Gene	176598	176623	UUGGAGCAAAAUAUGAGUGAUGACGU	[EXP-IEP] [EXP-IMP] [EXP-IMP-SITE-MUTATION]	S	[11] [19]
fumA	MRNA-DEGRADATION	repressor	TU	1688373	1688388	GACAUUGUUCUCUCAC	[EXP-IEP] [EXP-IPI]	W	[12] [20] [21]
sdhCDAB-sucABCD-sdhX	MRNA-DEGRADATION	repressor	TU	755162	755170	AUGUGGGCG	[EXP-IEP] [EXP-IMP-SITE-MUTATION] [EXP-IPI]	S	[22]
sdhCDAB-sucABCD-sdhX	MRNA-DEGRADATION	repressor	TU	755518	755557	UGUUAUUACUGUCGUGCUUUCACUUCUCGCAGGAGUCCUC	[EXP-IMP] [EXP-IPI]	W	[23] [12]
uof-fur	TRANSLATION-BLOCKING	repressor	TU	710693	710742	GACAGAAUUUGCUCUUGAGAUAAUGCGUAUCAUUAUAGAAUUGCCACGCC	[EXP-IEP] [EXP-IMP-SITE-MUTATION]	S	[24]
acnB	TRANSLATION-BLOCKING, MRNA-DEGRADATION	repressor	TU	131596	131624	GAGAGCGAGGAGAACCGUCGUGCUAGAAG	[EXP-IMP]	W	[25] [20]
cirA	TRANSLATION-BLOCKING, MRNA-DEGRADATION	activator	Gene	2246810	2246827	AUCGCUCACAUCUUCUUC	[EXP-IEP] [EXP-IMP-SITE-MUTATION] [EXP-IPI]	S	[26]
iscRSUA	TRANSLATION-BLOCKING, MRNA-DEGRADATION	repressor	TU	2661532	2661557	UGCUCUAUAAACUCCGUACAUCACUC	[EXP-IEP] [EXP-IMP-SITE-MUTATION] [EXP-IPI]	S	[27] [21]
msrB	TRANSLATION-BLOCKING, MRNA-DEGRADATION	repressor	TU	1862427	1862439	CAUUUGCUCACAU	[EXP-IDA] [EXP-IEP] [EXP-IMP-SITE-MUTATION]	S	[4]
msrB	TRANSLATION-BLOCKING, MRNA-DEGRADATION	repressor	TU	1862453	1862464	UGCUCACAUUAC	[EXP-IDA] [EXP-IEP] [EXP-IMP-SITE-MUTATION]	S	[4]
shiA	TRANSLATION-BLOCKING, MRNA-DEGRADATION	activator	TU	2053566	2053616	GUUCGUUUAUAGAUCGACGGCAAUGUGAGUUACCUUUUCCAUACUAAUUAU	[EXP-IEP] [EXP-IMP-SITE-MUTATION]	S	[28]
sodB	TRANSLATION-BLOCKING, MRNA-DEGRADATION	repressor	TU	1735365	1735382	AAGGAGAGUAGCAAUGUC	[EXP-IEP] [EXP-IMP-SITE-MUTATION] [EXP-IPI]	S	[29] [30] [21] [31] [17]
bfr	nd	repressor	Gene	nd	nd	nd	[EXP-IEP]	W	[12]
cysE	nd	repressor	TU	3782554	3782566	ACACGACAUUGCU	[EXP-IEP] [EXP-IMP-SITE-MUTATION] [EXP-IPI]	S	[32]
grxD	nd	repressor	TU	nd	nd	nd	[EXP-IMP]	W	[33]
hemB	nd	repressor	TU	388829	388854	GAACCUAAGCUUUCGAGCACGACUUU	[COMP] [EXP-IEP]	W	[34]
hemH	nd	repressor	TU	498841	498876	CAGGUGAUGUGCCCGGGCUUUGCUGCGGAUUGUCUG	[COMP] [EXP-IEP]	W	[34]
marA	nd	repressor	Gene	1619563	1619578	GAGGUAUGACGAUGUC	[COMP] [EXP-IEP]	W	[19]
nirB	nd	repressor	Gene	3494002	3494022	GAGGCAAAAAUGAGCAAAGUC	[COMP] [EXP-IEP] [EXP-IMP-SITE-MUTATION]	S	[19]
nuoABCEFGHIJKLMN	nd	repressor	TU	2405062	2405085	GACAUACUCAUUGCUUACUCAUCA	[EXP-IMP-SITE-MUTATION]	S	[35]
nuoABCEFGHIJKLMN	nd	repressor	TU	2405062	2405085	GACAUACUCAUUGCUUACUCAUCA	[EXP-IMP-SITE-MUTATION]	S	[35]
sodA	nd	repressor	TU	4100794	4100815	AAUACUGGAGAUGAAUAUGAGC	[EXP-IEP]	W	[36]

Evidence:

[EXP-IEP] Inferred from expression pattern
[EXP-IMP] Inferred from mutant phenotype
[EXP-IMP-SITE-MUTATION] Site mutation
[EXP-IPI] Inferred from physical interaction
[EXP-IDA] Inferred from direct assay
[COMP] Inferred by computational analysis

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] Banerjee R., Weisenhorn E., Schwartz KJ., Myers KS., Glasner JD., Perna NT., Coon JJ., Welch RA., Kiley PJ., 2020, Tailoring a Global Iron Regulon to a Uropathogen., mBio 11(2)
[4] 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
[5] 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
[6] 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
[7] King AM., Vanderpool CK., Degnan PH., 2019, sRNA Target Prediction Organizing Tool (SPOT) Integrates Computational and Experimental Data To Facilitate Functional Characterization of Bacterial Small RNAs., mSphere 4(1)
[8] Kiselev S., Markelova N., Masulis I., 2021, Divergently Transcribed ncRNAs in Escherichia coli: Refinement of the Transcription Starts Assumes Functional Diversification., Front Mol Biosci 8:610453
[9] Liu F., Zheng K., Chen HC., Liu ZF., 2018, Capping-RACE: a simple, accurate, and sensitive 5' RACE method for use in prokaryotes., Nucleic Acids Res 46(21):e129
[10] Lyu Y., Wu J., Shi Y., 2019, Metabolic and physiological perturbations of Escherichia coli W3100 by bacterial small RNA RyhB., Biochimie 162:144-155
[11] 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)
[12] 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
[13] 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
[14] 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
[15] 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
[16] 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
[17] 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
[18] 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
[19] Wright PR., Richter AS., Papenfort K., Mann M., Vogel J., Hess WR., Backofen R., Georg J., 2013, Comparative genomics boosts target prediction for bacterial small RNAs., Proc Natl Acad Sci U S A 110(37):E3487-96
[20] Masse E., Vanderpool CK., Gottesman S., 2005, Effect of RyhB small RNA on global iron use in Escherichia coli., J Bacteriol 187(20):6962-71
[21] Prevost K., Desnoyers G., Jacques JF., Lavoie F., Masse E., 2011, Small RNA-induced mRNA degradation achieved through both translation block and activated cleavage., Genes Dev 25(4):385-96
[22] Desnoyers G., Masse E., 2012, Noncanonical repression of translation initiation through small RNA recruitment of the RNA chaperone Hfq., Genes Dev 26(7):726-39
[23] Geissmann TA., Touati D., 2004, Hfq, a new chaperoning role: binding to messenger RNA determines access for small RNA regulator., EMBO J 23(2):396-405
[24] Vecerek B., Moll I., Blasi U., 2007, Control of Fur synthesis by the non-coding RNA RyhB and iron-responsive decoding., EMBO J 26(4):965-75
[25] Benjamin JA., Masse E., 2014, The iron-sensing aconitase B binds its own mRNA to prevent sRNA-induced mRNA cleavage., Nucleic Acids Res 42(15):10023-36
[26] Salvail H., Caron MP., Belanger J., Masse E., 2013, Antagonistic functions between the RNA chaperone Hfq and an sRNA regulate sensitivity to the antibiotic colicin., EMBO J 32(20):2764-78
[27] Desnoyers G., Morissette A., Prevost K., Masse E., 2009, Small RNA-induced differential degradation of the polycistronic mRNA iscRSUA., EMBO J 28(11):1551-61
[28] Prevost K., Salvail H., Desnoyers G., Jacques JF., Phaneuf E., Masse E., 2007, The small RNA RyhB activates the translation of shiA mRNA encoding a permease of shikimate, a compound involved in siderophore synthesis., Mol Microbiol 64(5):1260-73
[29] Afonyushkin T., Vecerek B., Moll I., Blasi U., Kaberdin VR., 2005, Both RNase E and RNase III control the stability of sodB mRNA upon translational inhibition by the small regulatory RNA RyhB., Nucleic Acids Res 33(5):1678-89
[30] Chen J., To L., de Mets F., Luo X., Majdalani N., Tai CH., Gottesman S., 2021, A fluorescence-based genetic screen reveals diverse mechanisms silencing small RNA signaling in E. coli., Proc Natl Acad Sci U S A 118(27)
[31] Urban JH., Vogel J., 2007, Translational control and target recognition by Escherichia coli small RNAs in vivo., Nucleic Acids Res 35(3):1018-37
[32] Salvail H., Lanthier-Bourbonnais P., Sobota JM., Caza M., Benjamin JA., Mendieta ME., Lepine F., Dozois CM., Imlay J., Masse E., 2010, A small RNA promotes siderophore production through transcriptional and metabolic remodeling., Proc Natl Acad Sci U S A 107(34):15223-8
[33] Lalaouna D., Carrier MC., Semsey S., Brouard JS., Wang J., Wade JT., Masse E., 2015, A 3' external transcribed spacer in a tRNA transcript acts as a sponge for small RNAs to prevent transcriptional noise., Mol Cell 58(3):393-405
[34] Li F., Wang Y., Gong K., Wang Q., Liang Q., Qi Q., 2014, Constitutive expression of RyhB regulates the heme biosynthesis pathway and increases the 5-aminolevulinic acid accumulation in Escherichia coli., FEMS Microbiol Lett 350(2):209-15
[35] Chareyre S., Barras F., Mandin P., 2019, A small RNA controls bacterial sensitivity to gentamicin during iron starvation., PLoS Genet 15(4):e1008078
[36] Argaman L., Elgrably-Weiss M., Hershko T., Vogel J., Altuvia S., 2012, RelA protein stimulates the activity of RyhB small RNA by acting on RNA-binding protein Hfq., Proc Natl Acad Sci U S A 109(12):4621-6