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	For this promoter, there is a cluster of 2 transcription start sites,in the interval 4050793 to 4050794, where the highest frequency is at position 4048817. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[8]
promoter	yihAp9	4050985	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 6.725. P-value: 1.304e-6 Read more >	[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