RegulonDB

Gene
Name:	csrC
Synonym(s):	ECK3858, G0-8874, IS198, b4457, psrA21, ryiB, sraK, tpk2
Genome position(nucleotides):	4051036 --> 4051281 Genome Browser
Strand:	forward
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	48.37
External database links:

ASAP:	ABE-0047275
ECHOBASE:	EB4540
ECOLIHUB:	csrC
COLOMBOS:	csrC

Product

Name:

small regulatory RNA CsrC

Synonym(s):

CsrC, IS198, PsrA21, RNA inhibitor of CsrA, RyiB, SraK, Tpk2

Type:

small RNA

Classification:

Multifun Terms (GenProtEC)
Multifun Terms (GenProtEC)		2 - information transfer --> 2.2 - RNA related
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
[IMP] Inferred from mutant phenotype

Reference(s):

[1] Friedman RC., et al., 2017
[2] Jonas K., et al., 2006
[3] Krol JE. 2018
[4] Mercante J., et al., 2009
[5] Vakulskas CA., et al., 2014
[6] Wang X., et al., 2005
[7] Weilbacher T., et al., 2003

External database links:

ECOCYC:

CSRC-RNA

ECOLIWIKI:

b4457

Operon

Name:

csrC

Operon arrangement:

Transcription unit	Promoter
csrC	csrCp

Transcriptional Regulation
	Display Regulation
Activated by:	UvrY
Repressed by:	CRP

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_4540 (cluster)	4050794	reverse	nd	[RS-EPT-CBR]	[8]
promoter	yihAp9	4050985	reverse	nd	[ICWHO]	[9]
promoter	TSS_4543	4051320	forward	nd	[RS-EPT-CBR]	[8]

Evidence
[RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates
[ICWHO] Inferred computationally without human oversight

Reference(s)
[1] Friedman RC., Kalkhof S., Doppelt-Azeroual O., Mueller SA., Chovancova M., von Bergen M., Schwikowski B., 2017, Common and phylogenetically widespread coding for peptides by bacterial small RNAs., BMC Genomics 18(1):553
[2] 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
[3] Krol JE., 2018, Regulatory loop between the CsrA system and NhaR, a high salt/high pH regulator., PLoS One 13(12):e0209554
[4] Mercante J., Edwards AN., Dubey AK., Babitzke P., Romeo T., 2009, Molecular geometry of CsrA (RsmA) binding to RNA and its implications for regulated expression., J Mol Biol 392(2):511-28
[5] 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
[6] Wang X., Dubey AK., Suzuki K., Baker CS., Babitzke P., Romeo T., 2005, CsrA post-transcriptionally represses pgaABCD, responsible for synthesis of a biofilm polysaccharide adhesin of Escherichia coli., Mol Microbiol 56(6):1648-63
[7] Weilbacher T., Suzuki K., Dubey AK., Wang X., Gudapaty S., Morozov I., Baker CS., Georgellis D., Babitzke P., Romeo T., 2003, A novel sRNA component of the carbon storage regulatory system of Escherichia coli., Mol Microbiol 48(3):657-70
[8] 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.
[9] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78