RegulonDB

Gene
Name:	csrB
Synonym(s):	ECK2787, G0-8785, b4408
Genome position(nucleotides):	2924156 <-- 2924524 Genome Browser
Strand:	reverse
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	51.49
External database links:

ASAP:	ABE-0047213
ECHOBASE:	EB4282
ECOLIHUB:	csrB
COLOMBOS:	csrB

Product

Name:

small regulatory RNA CsrB

Synonym(s):

CsrB

Type:

small RNA

Classification:

Multifun Terms (GenProtEC)
		2 - information transfer --> 2.2 - RNA related --> 2.2.4 - RNA degradation
		3 - regulation --> 3.1 - type of regulation --> 3.1.3 - posttranscriptional
Gene Ontology Terms (GO)
	molecular_function	GO:0005515 - protein binding
	biological_process	GO:1900192 - positive regulation of single-species biofilm formation GO:1902201 - negative regulation of bacterial-type flagellum-dependent cell motility GO:1904572 - negative regulation of mRNA binding

Note(s):

Note(s): ...[more].

Evidence:

[IDA] Inferred from direct assay

Reference(s):

[1] Chavez RG., et al., 2010
[2] Cui Y., et al., 2001
[3] Cui YY., et al., 2014
[4] Hayes ET., et al., 2006
[5] Jackson DW., et al., 2002
[6] Jiang GR., et al., 2001
[7] Jonas K., et al., 2006
[8] Krol JE. 2018
[9] Kulkarni PR., et al., 2006
[10] Leistra AN., et al., 2017
[11] Liu MY., et al., 1997
[12] Vakulskas CA., et al., 2014
[13] Yakandawala N., et al., 2008

External database links:

ECOCYC:

CSRB-RNA

ECOLIWIKI:

b4408

Operon

Name:

csrB

Operon arrangement:

Transcription unit	Promoter
csrB	csrBp

Transcriptional Regulation
	Display Regulation
Activated by:	UvrY, IHF

Elements in the selected gene context region unrelated to any object in RegulonDB

Type	Name	Post Left	Strand	Notes	Evidence (Confirmed, Strong, Weak)	References
promoter	TSS_3090	2924137	reverse	nd	[RS-EPT-CBR]	[14]
promoter	TSS_3091	2924349	reverse	nd	[RS-EPT-CBR]	[14]
promoter	TSS_3092	2924385	reverse	nd	[RS-EPT-CBR]	[14]
promoter	TSS_3093	2924391	reverse	nd	[RS-EPT-CBR]	[14]
promoter	TSS_3094	2924394	reverse	nd	[RS-EPT-CBR]	[14]
promoter	TSS_3095	2924415	reverse	nd	[RS-EPT-CBR]	[14]
promoter	TSS_3096 (cluster)	2924424	reverse	nd	[RS-EPT-CBR]	[14]
promoter	TSS_3097	2924436	reverse	nd	[RS-EPT-CBR]	[14]
promoter	TSS_3098 (cluster)	2924452	reverse	nd	[RS-EPT-CBR]	[14]
promoter	TSS_3099	2924464	reverse	nd	[RS-EPT-CBR]	[14]
promoter	TSS_3100	2924466	reverse	nd	[RS-EPT-CBR]	[14]
promoter	TSS_3101	2924468	reverse	nd	[RS-EPT-CBR]	[14]
promoter	TSS_3102 (cluster)	2924473	reverse	nd	[RS-EPT-CBR]	[14]
promoter	TSS_3103 (cluster)	2924477	reverse	nd	[RS-EPT-CBR]	[14]
promoter	TSS_3104	2924484	reverse	nd	[RS-EPT-CBR]	[14]
promoter	TSS_3105	2924496	reverse	nd	[RS-EPT-CBR]	[14]
promoter	TSS_3106	2924507	reverse	nd	[RS-EPT-CBR]	[14]
promoter	TSS_3107	2924509	reverse	nd	[RS-EPT-CBR]	[14]
promoter	TSS_3108 (cluster)	2924522	reverse	nd	[RS-EPT-CBR]	[14]
promoter	TSS_3110	2924528	reverse	nd	[RS-EPT-CBR]	[14]

Evidence
[RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

Reference(s)
[1] Chavez RG., Alvarez AF., Romeo T., Georgellis D., 2010, The physiological stimulus for the BarA sensor kinase., J Bacteriol 192(7):2009-12
[2] Cui Y., Chatterjee A., Chatterjee AK., 2001, Effects of the two-component system comprising GacA and GacS of Erwinia carotovora subsp. carotovora on the production of global regulatory rsmB RNA, extracellular enzymes, and harpinEcc., Mol Plant Microbe Interact 14(4):516-26
[3] Cui YY., Ling C., Zhang YY., Huang J., Liu JZ., 2014, Production of shikimic acid from Escherichia coli through chemically inducible chromosomal evolution and cofactor metabolic engineering., Microb Cell Fact 13:21
[4] Hayes ET., Wilks JC., Sanfilippo P., Yohannes E., Tate DP., Jones BD., Radmacher MD., BonDurant SS., Slonczewski JL., 2006, Oxygen limitation modulates pH regulation of catabolism and hydrogenases, multidrug transporters, and envelope composition in Escherichia coli K-12., BMC Microbiol 6:89
[5] Jackson DW., Suzuki K., Oakford L., Simecka JW., Hart ME., Romeo T., 2002, Biofilm formation and dispersal under the influence of the global regulator CsrA of Escherichia coli., J Bacteriol 184(1):290-301
[6] Jiang GR., Nikolova S., Clark DP., 2001, Regulation of the ldhA gene, encoding the fermentative lactate dehydrogenase of Escherichia coli., Microbiology 147(Pt 9):2437-46
[7] Jonas K., Tomenius H., Romling U., Georgellis D., Melefors O., 2006, Identification of YhdA as a regulator of the Escherichia coli carbon storage regulation system., FEMS Microbiol Lett 264(2):232-7
[8] Krol JE., 2018, Regulatory loop between the CsrA system and NhaR, a high salt/high pH regulator., PLoS One 13(12):e0209554
[9] Kulkarni PR., Cui X., Williams JW., Stevens AM., Kulkarni RV., 2006, Prediction of CsrA-regulating small RNAs in bacteria and their experimental verification in Vibrio fischeri., Nucleic Acids Res 34(11):3361-9
[10] Leistra AN., Amador P., Buvanendiran A., Moon-Walker A., Contreras LM., 2017, Rational Modular RNA Engineering Based on In Vivo Profiling of Structural Accessibility., ACS Synth Biol 6(12):2228-2240
[11] Liu MY., Gui G., Wei B., Preston JF., Oakford L., Yuksel U., Giedroc DP., Romeo T., 1997, The RNA molecule CsrB binds to the global regulatory protein CsrA and antagonizes its activity in Escherichia coli., J Biol Chem 272(28):17502-10
[12] Vakulskas CA., Pannuri A., Cortes-Selva D., Zere TR., Ahmer BM., Babitzke P., Romeo T., 2014, Global effects of the DEAD-box RNA helicase DeaD (CsdA) on gene expression over a broad range of temperatures., Mol Microbiol 92(5):945-58
[13] Yakandawala N., Romeo T., Friesen AD., Madhyastha S., 2008, Metabolic engineering of Escherichia coli to enhance phenylalanine production., Appl Microbiol Biotechnol 78(2):283-91
[14] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.