RegulonDB

small RNA
Gene name:	gcvB
Synonym(s):	GcvB, IS145, PsrA11
Genome position:	2942696 --> 2942901
Strand:	forward
Sequence:	Get ribonucleotide sequence FastaFormat
GC content %:	42.72
Note(s):	GcvB is a small RNA of approximately 205 nt in length Argaman L,2001. Although its expression appears to be regulated by the glycine cleavage system regulators GcvA and GcvR, GcvB itself is not involved in regulating components of the glycine cleavage system. Instead, GcvB regulates expression of the periplasmic transporter components DppA and OppA Urbanowski ML,2000, the serine/threonine transporter SstT Pulvermacher SC,2009, CycA, a transporter for certain amino acids Pulvermacher SC,2009, the transcription factors CsgD Jorgensen MG,2012 and Lrp Modi SR,2011. Lee HJ,2016, and the PhoQ/PhoQ two-component system Coornaert A,2013. Both OppA Urbanowski ML,2000 and DppA Urban JH,2007 expression is repressed by GcvB at the level of translation. Repression of SstT Pulvermacher SC,2009, CycA Pulvermacher SC,2009 and DppA/OppA 19118352 expression by GcvB requires Hfq. GcvB is unstable in an hfq mutant Urban JH,2007. 19118352. Using a network biology approach, GcvB was predicted to be involved in the regulation of amino acid availability Modi SR,2011. GcvB-target interactions were investigated by RIL-seq Melamed S,2016. A screen using MS2-affinity purification coupled with RNA sequencing (MAPS) was used to identify additional targets of GcvB regulation Lalaouna D,2019. A candidate GcvB regulon was inferred by integrating information on experimentally supported targets and sRNA-mRNA interactions with transcription datasets; new targets with experimental support are aroG, aroP, asd, cysD, dcyD, hcxB, icd, ilvN, leuA, purU, ydiJ, and yecS 32487739. 21 new targets have been validated Miyakoshi M,2021. GcvB promotes mutagenic break repair 27698081. In exponential-phase cells, GcvB together with Hfq promotes the stability of the rbn mRNA by directly interacting with it and protecting it from RNase E cleavage Chen H,2019. Two transcripts, presumably due to two Rho-independent terminators, can be detected; transcriptional fusions indicate that the shorter, ~130 nt transcript predominates in vivo Urbanowski ML,2000, although the longer transcript predominated in a Northern blot experiment Ruiz-Larrabeiti O, Plágaro AH, Gracia C, Sevillano E, Gallego L, Hajnsdorf E, Kaberdin VR,2016. Mutagenesis of nucleotides predicted to be involved in binding to dppA and oppA mRNAs as well as compensatory mutations in the dppA and oppA UTRs showed mixed results, indicating that base pairing between GcvB and its targets is only part of its regulatory mechanism Pulvermacher SC,2008. A second predicted base pairing site within GcvB does not appear to be required for regulation of oppA expression 20603180. The GcvB homolog of Salmonella enterica was shown to inhibit translation initiation by binding to the dppA and oppA mRNAs 17974919. There are more than 20 validated targets of GcvB in Salmonella enterica 21696468. A gcvB mutant does not exhibit a defect in glycine cleavage system activity Urbanowski ML,2000. It overproduces OppA, DppA Urbanowski ML,2000 and Lrp Lee HJ,2016, is more sensitive to acid challenge 19379489 and to oxidative stress Ju X,2021 than wild type. A ΔgcvB mutant also shows an increased σ^E-dependent membrane stress response and reduced σ^S-dependent general stress response 27698081. Overexpression of GcvB increases biofilm formation and decreases swarming motility Bak G,2015. gcvB is expressed during early log phase, but its level decreases during cell growth Argaman L,2001; in LB, GcvB is produced from exponential through stationary phase, until ~OD_600nm 3 Lalaouna D,2019. Expression is much higher in rich (LB) medium than in glucose minimal medium Ruiz-Larrabeiti O, Plágaro AH, Gracia C, Sevillano E, Gallego L, Hajnsdorf E, Kaberdin VR,2016. Lalaouna D,2019. GcvB is expressed at higher levels when cells are grown in pyruvate compared to glucose \|C...
Evidence:	[EXP-IEP] Inferred from expression pattern [EXP-IGI] Inferred from genetic interaction [EXP-IMP] Inferred from mutant phenotype
Reference(s):	[1] Andreassen PR., et al., 2018 [2] Baisa G., et al., 2013 [3] Busi F., et al., 2009 [4] Chen S., et al., 2002 [5] Gorzelak P., et al., 2021 [6] Harwani D., et al., 2012 [7] Kuryllo K., et al., 2014 [8] Lalaouna D., et al., 2019 [9] Melamed S., et al., 2016 [10] Muto A., et al., 2021 [11] Pulvermacher SC., et al., 2008 [12] Pulvermacher SC., et al., 2009 [13] Tang Q., et al., 2019 [14] Urban JH., et al., 2007 [15] Urbanowski ML., et al., 2000 [16] Yang Q., et al., 2014
External database links:

ECOCYC:	GCVB-RNA
ECOLIWIKI:	b4443
M3D:	small regulatory RNA GcvB

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)
asnA	MRNA-DEGRADATION	repressor	TU	3927136	3927148	GGACGCAGGAGUA	[EXP-IEP] [EXP-NUC-ACID-BINDING]	W	[8]
asnB	MRNA-DEGRADATION	repressor	TU	699202	699220	UGUUGCUUGUUGUGUUUGC	[EXP-IEP] [EXP-IPI] [EXP-NUC-ACID-BINDING]	W	[8]
csgDEFG	MRNA-DEGRADATION	repressor	TU	1103272	1103289	GAUGUUGCACUGCUGUGU	[EXP-IDA] [EXP-IEP]	W	[1] [17]
csgDEFG	MRNA-DEGRADATION	repressor	TU	1103272	1103289	GAUGUUGCACUGCUGUGU	[EXP-IDA] [EXP-IEP]	W	[1] [17]
inaA	MRNA-DEGRADATION	repressor	TU	2349421	2349444	CCUCUGUUGCCCACCAGUGAUUAA	[EXP-IEP] [EXP-NUC-ACID-BINDING]	W	[8]
nlpA	MRNA-DEGRADATION	repressor	TU	3839961	3839970	CCCUGUCCGU	[EXP-IEP] [EXP-NUC-ACID-BINDING]	W	[8]
panD	MRNA-DEGRADATION	repressor	Gene	146707	146717	UCUACCCUGUC	[EXP-IEP] [EXP-NUC-ACID-BINDING]	W	[8]
tcyJ	MRNA-DEGRADATION	repressor	TU	2000397	2000410	AUGUUGUUAUGUCU	[EXP-IEP] [EXP-NUC-ACID-BINDING]	W	[8]
ysgA	MRNA-DEGRADATION	repressor	TU	4016153	4016166	UGUUGUGUUGUUGC	[EXP-IEP] [EXP-IPI]	W	[8]
dppABCDF	TRANSLATION-BLOCKING	repressor	TU	3707714	3707747	UCCAAUUGUGAUGUUUGUUGUUUUAACCCUUUGC	[EXP-IGI]	W	[11] [14]
oppABCDF	TRANSLATION-BLOCKING	repressor	TU	1301163	1301202	UGAGGGAGUCCAAAAAACAAUGACCAACAUCACCAAGAGA	[EXP-IGI]	W	[11] [15]
phoPQ	TRANSLATION-BLOCKING, MRNA-DEGRADATION	repressor	TU	1190454	1190475	UUCUCCCUGUCUUAAUUAUUAA	[EXP-IEP] [EXP-IMP-SITE-MUTATION]	S	[18]
cycA	nd	repressor	TU	4429838	4429870	ACAGACAGGUACAGGAAGAAAAAAACAUGGUAG	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	W	[12]
lrp	nd	repressor	TU	932416	932420	GACAG	[EXP-IEP] [EXP-IMP-SITE-MUTATION] [EXP-IPI]	S	[19]
lrp	nd	repressor	TU	932556	932563	CAGACAGG	[EXP-IEP] [EXP-IMP-SITE-MUTATION] [EXP-IPI]	S	[19] [20]
sstT	nd	repressor	TU	3239920	3239930	ACAACACAAUG	[EXP-IEP] [EXP-IMP]	W	[21]

Evidence:

[EXP-IEP] Inferred from expression pattern
[EXP-NUC-ACID-BINDING] Nucleic acid binding evidence
[EXP-IPI] Inferred from physical interaction
[EXP-IDA] Inferred from direct assay
[EXP-IGI] Inferred from genetic interaction
[EXP-IMP-SITE-MUTATION] Site mutation
[EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis
[EXP-IMP] Inferred from mutant phenotype

Reference(s)
[1] Andreassen PR., Pettersen JS., Szczerba M., Valentin-Hansen P., Moller-Jensen J., Jorgensen MG., 2018, sRNA-dependent control of curli biosynthesis in Escherichia coli: McaS directs endonucleolytic cleavage of csgD mRNA., Nucleic Acids Res 46(13):6746-6760
[2] Baisa G., Stabo NJ., Welch RA., 2013, Characterization of Escherichia coli D-Cycloserine Transport and Resistant Mutants., J Bacteriol 195(7):1389-99
[3] Busi F., Cayrol B., Lavelle C., LeDerout J., Pietrement O., Le Cam E., Geinguenaud F., Lacoste J., Regnier P., Arluison V., 2009, Auto-assembly as a new regulatory mechanism of noncoding RNA., Cell Cycle 8(6):952-4
[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] Gorzelak P., Klein G., Raina S., 2021, Molecular Basis of Essentiality of Early Critical Steps in the Lipopolysaccharide Biogenesis in Escherichia coli K-12: Requirement of MsbA, Cardiolipin, LpxL, LpxM and GcvB., Int J Mol Sci 22(10)
[6] Harwani D., Zangoui P., Mahadevan S., 2012, The β-Glucoside (bgl) Operon of Escherichia coli Is Involved in the Regulation of oppA, Encoding an Oligopeptide Transporter., J Bacteriol 194(1):90-9
[7] Kuryllo K., Jahanshahi S., Zhu W., Brown ED., Li Y., 2014, A dual reporter system for detecting RNA interactions in bacterial cells., Chembiochem 15(18):2703-9
[8] Lalaouna D., Eyraud A., Devinck A., Prevost K., Masse E., 2019, GcvB small RNA uses two distinct seed regions to regulate an extensive targetome., Mol Microbiol 111(2):473-486
[9] Melamed S., Peer A., Faigenbaum-Romm R., Gatt YE., Reiss N., Bar A., Altuvia Y., Argaman L., Margalit H., 2016, Global Mapping of Small RNA-Target Interactions in Bacteria., Mol Cell 63(5):884-97
[10] Muto A., Goto S., Kurita D., Ushida C., Himeno H., 2021, Involvement of GcvB small RNA in intrinsic resistance to multiple aminoglycoside antibiotics in Escherichia coli., J Biochem 169(4):485-489
[11] Pulvermacher SC., Stauffer LT., Stauffer GV., 2008, The role of the small regulatory RNA GcvB in GcvB/mRNA posttranscriptional regulation of oppA and dppA in Escherichia coli., FEMS Microbiol Lett 281(1):42-50
[12] Pulvermacher SC., Stauffer LT., Stauffer GV., 2009, Role of the sRNA GcvB in regulation of cycA in Escherichia coli., Microbiology 155(Pt 1):106-14
[13] Tang Q., Feng M., Xia H., Zhao Y., Hou B., Ye J., Wu H., Zhang H., 2019, Differential quantitative proteomics reveals the functional difference of two yigP locus products, UbiJ and EsrE., J Basic Microbiol 59(11):1125-1133
[14] Urban JH., Vogel J., 2007, Translational control and target recognition by Escherichia coli small RNAs in vivo., Nucleic Acids Res 35(3):1018-37
[15] Urbanowski ML., Stauffer LT., Stauffer GV., 2000, The gcvB gene encodes a small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli., Mol Microbiol 37(4):856-68
[16] Yang Q., Figueroa-Bossi N., Bossi L., 2014, Translation enhancing ACA motifs and their silencing by a bacterial small regulatory RNA., PLoS Genet 10(1):e1004026
[17] Jorgensen MG., Nielsen JS., Boysen A., Franch T., Moller-Jensen J., Valentin-Hansen P., 2012, Small regulatory RNAs control the multi-cellular adhesive lifestyle of Escherichia coli., Mol Microbiol 84(1):36-50
[18] Coornaert A., Chiaruttini C., Springer M., Guillier M., 2013, Post-transcriptional control of the Escherichia coli PhoQ-PhoP two-component system by multiple sRNAs involves a novel pairing region of GcvB., PLoS Genet 9(1):e1003156
[19] Lee HJ., Gottesman S., 2016, sRNA roles in regulating transcriptional regulators: Lrp and SoxS regulation by sRNAs., Nucleic Acids Res 44(14):6907-23
[20] Modi SR., Camacho DM., Kohanski MA., Walker GC., Collins JJ., 2011, Functional characterization of bacterial sRNAs using a network biology approach., Proc Natl Acad Sci U S A 108(37):15522-7
[21] Pulvermacher SC., Stauffer LT., Stauffer GV., 2009, The small RNA GcvB regulates sstT mRNA expression in Escherichia coli., J Bacteriol 191(1):238-48