RegulonDB

Gene
Name:	rcsF
Synonym(s):	ECK0196, EG11502, b0196
Genome position(nucleotides):	219591 <-- 219995 Genome Browser
Strand:	reverse
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	53.33
External database links:

ASAP:	ABE-0000663
CGSC:	29845
ECHOBASE:	EB1465
OU-MICROARRAY:	b0196
PortEco:	rcsF
STRING:	511145.b0196
COLOMBOS:	rcsF

Gene

Name:

rcsF

Synonym(s):

ECK0196, EG11502, b0196

Genome position(nucleotides):

219591 <-- 219995 Genome Browser

Strand:

reverse

Sequence:

Get nucleotide sequence FastaFormat

GC content %:

53.33

External database links:

ASAP:

CGSC:

ECHOBASE:

OU-MICROARRAY:

PortEco:

STRING:

COLOMBOS:

Type

Positions

Sequence

84 -> 99

SIPTARKRMQINASKM

103 -> 112

AVLLHSCEVT

7 -> 7

46 -> 46

48 -> 134

PVRIYTNAEELVGKPFRDLGEVSGDSCQASNQDSPPSIPTARKRMQINASKMKANAVLLHSCEVTSGTPGCYRQAVCIGSALNITAK

Type

Positions

Sequence

84 -> 99

SIPTARKRMQINASKM

103 -> 112

AVLLHSCEVT

7 -> 7

46 -> 46

48 -> 134

PVRIYTNAEELVGKPFRDLGEVSGDSCQASNQDSPPSIPTARKRMQINASKMKANAVLLHSCEVTSGTPGCYRQAVCIGSALNITAK

74 -> 74

37 -> 38

109 -> 109

29 -> 132

STAPQPKAEPAKPKAPRATPVRIYTNAEELVGKPFRDLGEVSGDSCQASNQDSPPSIPTARKRMQINASKMKANAVLLHSCEVTSGTPGCYRQAVCIGSALNIT

50 -> 52

RIY

1 -> 15

MRALPICLVALMLSG

13 -> 16

LSGC

16 -> 16

54 -> 59

NAEELV

90 -> 90

118 -> 118

89 -> 89

120 -> 131

RQAVCIGSALNI

17 -> 18

32 -> 50

PQPKAEPAKPKAPRATPVR

55 -> 55

63 -> 75

FRDLGEVSGDSCQ

124 -> 124

Multifun Terms (GenProtEC)

3 - regulation

6 - cell structure --> 6.1 - membrane

Gene Ontology Terms (GO)

cellular_component

GO:0106234 - outer membrane protein complex
GO:0009279 - cell outer membrane
GO:0016020 - membrane
GO:0030288 - outer membrane-bounded periplasmic space
GO:0036406 - anchored component of periplasmic side of cell outer membrane

molecular_function

GO:0005515 - protein binding

biological_process

GO:0070299 - positive regulation of phosphorelay signal transduction system
GO:0007165 - signal transduction
GO:0035556 - intracellular signal transduction
GO:0036460 - cellular response to cell envelope stress

RNA cis-regulatory element

Attenuation:	Transcriptional

RNA cis-regulatory element

Attenuation:

Transcriptional

Type	Name	Post Left	Strand	Notes	Evidence (Confirmed, Strong, Weak)	References
promoter	yaeFp1	217135	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: poor homology. Score: -3.04. P-value: 5.170e-5 Read more >	[ICWHO]	[15]
promoter	TSS_397	218831	reverse	nd	[RS-EPT-CBR]	[16]
promoter	TSS_398	220022	reverse	nd	[RS-EPT-CBR]	[16]
promoter	TSS_399	220386	reverse	nd	[RS-EPT-CBR]	[16]
promoter	TSS_400	220394	reverse	nd	[RS-EPT-CBR]	[16]
promoter	TSS_401	220539	reverse	nd	[RS-EPT-CBR]	[16]
promoter	TSS_402	220543	reverse	nd	[RS-EPT-CBR]	[16]
promoter	TSS_403	220638	forward	nd	[RS-EPT-CBR]	[16]

Type

Name

Post Left

Post Right

Strand

Notes

Evidence (Confirmed, Strong, Weak)

References

promoter

yaeFp1

217135

reverse

Similarity to the consensus
Read more >

[ICWHO]

[15]

promoter

TSS_397

218831

reverse

[RS-EPT-CBR]

[16]

promoter

TSS_398

220022

reverse

[RS-EPT-CBR]

[16]

promoter

TSS_399

220386

reverse

[RS-EPT-CBR]

[16]

promoter

TSS_400

220394

reverse

[RS-EPT-CBR]

[16]

promoter

TSS_401

220539

reverse

[RS-EPT-CBR]

[16]

promoter

TSS_402

220543

reverse

[RS-EPT-CBR]

[16]

promoter

TSS_403

220638

forward

[RS-EPT-CBR]

[16]

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

Evidence

[ICWHO] Inferred computationally without human oversight

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

Reference(s)
[1] Asmar AT., Ferreira JL., Cohen EJ., Cho SH., Beeby M., Hughes KT., Collet JF., 2017, Communication across the bacterial cell envelope depends on the size of the periplasm., PLoS Biol 15(12):e2004303
[2] Callewaert L., Vanoirbeek KG., Lurquin I., Michiels CW., Aertsen A., 2009, The Rcs two-component system regulates expression of lysozyme inhibitors and is induced by exposure to lysozyme., J Bacteriol 191(6):1979-81
[3] Cho SH., Szewczyk J., Pesavento C., Zietek M., Banzhaf M., Roszczenko P., Asmar A., Laloux G., Hov AK., Leverrier P., Van der Henst C., Vertommen D., Typas A., Collet JF., 2014, Detecting envelope stress by monitoring β-barrel assembly., Cell 159(7):1652-64
[4] Evans KL., Kannan S., Li G., de Pedro MA., Young KD., 2013, Eliminating a set of four penicillin binding proteins triggers the Rcs phosphorelay and Cpx stress responses in Escherichia coli., J Bacteriol 195(19):4415-24
[5] Gervais FG., Drapeau GR., 1992, Identification, cloning, and characterization of rcsF, a new regulator gene for exopolysaccharide synthesis that suppresses the division mutation ftsZ84 in Escherichia coli K-12., J Bacteriol 174(24):8016-22
[6] Gupte G., Woodward C., Stout V., 1997, Isolation and characterization of rcsB mutations that affect colanic acid capsule synthesis in Escherichia coli K-12., J Bacteriol 179(13):4328-35
[7] Hagiwara D., Sugiura M., Oshima T., Mori H., Aiba H., Yamashino T., Mizuno T., 2003, Genome-wide analyses revealing a signaling network of the RcsC-YojN-RcsB phosphorelay system in Escherichia coli., J Bacteriol 185(19):5735-46
[8] Hart EM., Gupta M., Wuhr M., Silhavy TJ., 2019, The Synthetic Phenotype of Δ bamB Δ bamE Double Mutants Results from a Lethal Jamming of the Bam Complex by the Lipoprotein RcsF., MBio 10(3)
[9] Hersch SJ., Watanabe N., Stietz MS., Manera K., Kamal F., Burkinshaw B., Lam L., Pun A., Li M., Savchenko A., Dong TG., 2020, Envelope stress responses defend against type six secretion system attacks independently of immunity proteins., Nat Microbiol
[10] Majdalani N., Heck M., Stout V., Gottesman S., 2005, Role of RcsF in signaling to the Rcs phosphorelay pathway in Escherichia coli., J Bacteriol 187(19):6770-8
[11] Majdalani N., Hernandez D., Gottesman S., 2002, Regulation and mode of action of the second small RNA activator of RpoS translation, RprA., Mol Microbiol 46(3):813-26
[12] Nepper JF., Lin YC., Weibel DB., 2019, Rcs Phosphorelay Activation in Cardiolipin-Deficient Escherichia coli Reduces Biofilm Formation., J Bacteriol 201(9)
[13] Shiba Y., Yokoyama Y., Aono Y., Kiuchi T., Kusaka J., Matsumoto K., Hara H., 2004, Activation of the Rcs signal transduction system is responsible for the thermosensitive growth defect of an Escherichia coli mutant lacking phosphatidylglycerol and cardiolipin., J Bacteriol 186(19):6526-35
[14] Zhang Z., Luo F., 2019, [Role of mGluR5 in laterocapcular division of central nucleus of amygdala in fentanyl-induced hyperalgesia in rats]., Zhong Nan Da Xue Xue Bao Yi Xue Ban 44(4):364-369
[15] 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
[16] 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.

Reference(s)

[1] Asmar AT., Ferreira JL., Cohen EJ., Cho SH., Beeby M., Hughes KT., Collet JF., 2017, Communication across the bacterial cell envelope depends on the size of the periplasm., PLoS Biol 15(12):e2004303

[2] Callewaert L., Vanoirbeek KG., Lurquin I., Michiels CW., Aertsen A., 2009, The Rcs two-component system regulates expression of lysozyme inhibitors and is induced by exposure to lysozyme., J Bacteriol 191(6):1979-81

[3] Cho SH., Szewczyk J., Pesavento C., Zietek M., Banzhaf M., Roszczenko P., Asmar A., Laloux G., Hov AK., Leverrier P., Van der Henst C., Vertommen D., Typas A., Collet JF., 2014, Detecting envelope stress by monitoring β-barrel assembly., Cell 159(7):1652-64

[4] Evans KL., Kannan S., Li G., de Pedro MA., Young KD., 2013, Eliminating a set of four penicillin binding proteins triggers the Rcs phosphorelay and Cpx stress responses in Escherichia coli., J Bacteriol 195(19):4415-24

[5] Gervais FG., Drapeau GR., 1992, Identification, cloning, and characterization of rcsF, a new regulator gene for exopolysaccharide synthesis that suppresses the division mutation ftsZ84 in Escherichia coli K-12., J Bacteriol 174(24):8016-22

[6] Gupte G., Woodward C., Stout V., 1997, Isolation and characterization of rcsB mutations that affect colanic acid capsule synthesis in Escherichia coli K-12., J Bacteriol 179(13):4328-35

[7] Hagiwara D., Sugiura M., Oshima T., Mori H., Aiba H., Yamashino T., Mizuno T., 2003, Genome-wide analyses revealing a signaling network of the RcsC-YojN-RcsB phosphorelay system in Escherichia coli., J Bacteriol 185(19):5735-46

[8] Hart EM., Gupta M., Wuhr M., Silhavy TJ., 2019, The Synthetic Phenotype of Δ bamB Δ bamE Double Mutants Results from a Lethal Jamming of the Bam Complex by the Lipoprotein RcsF., MBio 10(3)

[9] Hersch SJ., Watanabe N., Stietz MS., Manera K., Kamal F., Burkinshaw B., Lam L., Pun A., Li M., Savchenko A., Dong TG., 2020, Envelope stress responses defend against type six secretion system attacks independently of immunity proteins., Nat Microbiol

[10] Majdalani N., Heck M., Stout V., Gottesman S., 2005, Role of RcsF in signaling to the Rcs phosphorelay pathway in Escherichia coli., J Bacteriol 187(19):6770-8

[11] Majdalani N., Hernandez D., Gottesman S., 2002, Regulation and mode of action of the second small RNA activator of RpoS translation, RprA., Mol Microbiol 46(3):813-26

[12] Nepper JF., Lin YC., Weibel DB., 2019, Rcs Phosphorelay Activation in Cardiolipin-Deficient Escherichia coli Reduces Biofilm Formation., J Bacteriol 201(9)

[13] Shiba Y., Yokoyama Y., Aono Y., Kiuchi T., Kusaka J., Matsumoto K., Hara H., 2004, Activation of the Rcs signal transduction system is responsible for the thermosensitive growth defect of an Escherichia coli mutant lacking phosphatidylglycerol and cardiolipin., J Bacteriol 186(19):6526-35

[14] Zhang Z., Luo F., 2019, [Role of mGluR5 in laterocapcular division of central nucleus of amygdala in fentanyl-induced hyperalgesia in rats]., Zhong Nan Da Xue Xue Bao Yi Xue Ban 44(4):364-369

[15] 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

[16] 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.