RegulonDB

Gene
Name:	rseP
Synonym(s):	ECK0175, EG12436, b0176, ecfE, yaeL
Genome position(nucleotides):	196546 --> 197898
Strand:	forward
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	50.92
External database links:

ASAP:	ABE-0000603
ECHOBASE:	EB2331
ECOLIHUB:	rseP
OU-MICROARRAY:	b0176
STRING:	511145.b0176
COLOMBOS:	rseP

Gene

Name:

rseP

Synonym(s):

ECK0175, EG12436, b0176, ecfE, yaeL

Genome position(nucleotides):

196546 --> 197898

Strand:

forward

Sequence:

Get nucleotide sequence FastaFormat

GC content %:

50.92

External database links:

ASAP:

ECHOBASE:

ECOLIHUB:

OU-MICROARRAY:

STRING:

COLOMBOS:

Type

Positions

Sequence

Comment

1 -> 21

MLSFLWDLASFIVALGVLITV

UniProt: Helical.

11 -> 215

FIVALGVLITVHEFGHFWVARRCGVRVERFSIGFGKALWRRTDKLGTEYVIALIPLGGYVKMLDERAEPVVPELRHHAFNNKSVGQRAAIIAAGPVANFIFAIFAYWLVFIIGVPGVRPVVGEIAANSIAAEAQIAPGTELKAVDGIETPDWDAVRLQLVDKIGDESTTITVAPFGSDQRRDVKLDLRHWAFEPDKEDPVSSLGI

19 -> 19

I → N/F: confers 8-fold resistance to Batimastat (in a ΔacrA background) and prevents inhibition of σ^E activity

22 -> 22

UniProt: Loss of protease activity..

23 -> 23

UniProt: Loss of protease activity..

Type

Positions

Sequence

Comment

1 -> 21

MLSFLWDLASFIVALGVLITV

UniProt: Helical.

11 -> 215

19 -> 19

I → N/F: confers 8-fold resistance to Batimastat (in a ΔacrA background) and prevents inhibition of σ^E activity

22 -> 22

UniProt: Loss of protease activity..

23 -> 23

UniProt: Loss of protease activity..

26 -> 26

UniProt: Does not complement deletion mutant..

34 -> 60

GVRVERFSIGFGKALWRRTDKLGTEYV

contains the conserved G⁴³FG motif that interacts directly with substrate; may be partly membrane-inserted; suggested functional interaction with the MRE β-loop;

61 -> 75

IALIPLGGYVKMLDE

membrane-reentrant β-loop; likely assumes a β-hairpin structure and is implicated in substrate recognition

104 -> 124

GPVANFIFAIFAYWLVFIIGV

UniProt: Helical.

115 -> 115

UniProt: No effect. Cleaves RseA without previous DegS cleavage; when associated with R-214..

127 -> 220

VRPVVGEIAANSIAAEAQIAPGTELKAVDGIETPDWDAVRLQLVDKIGDESTTITVAPFGSDQRRDVKLDLRHWAFEPDKEDPVSSLGIRPRGP

145 -> 145

UniProt: Cuts RseA without previous DegS cleavage..

151 -> 151

UniProt: Cuts RseA without previous DegS cleavage..

162 -> 162

UniProt: Cuts RseA without previous DegS cleavage..

169 -> 169

UniProt: Cuts RseA without previous DegS cleavage..

213 -> 213

UniProt: Cuts RseA without previous DegS cleavage..

214 -> 214

UniProt: Weakly cuts RseA without previous DegS cleavage. Stronger cleavage; when associated with V-115..

215 -> 215

UniProt: No cleavage of RseA in vitro (PubMed:19706448), cleavage of RseA (PubMed:23016873) in vivo..

220 -> 438

PQIEPVLENVQPNSAASKAGLQAGDRIVKVDGQPLTQWVTFVMLVRDNPGKSLALEIERQGSPLSLTLIPESKPGNGKAIGFVGIEPKVIPLPDEYKVVRQYGPFNAIVEATDKTWQLMKLTVSMLGKLITGDVKLNNLSGPISIAKGAGMTAELGVVYYLPFLALISVNLGIINLFPLPVLDGGHLLFLAIEKIKGGPVSERVQDFCYRIGSILLVLL

222 -> 309

IEPVLENVQPNSAASKAGLQAGDRIVKVDGQPLTQWVTFVMLVRDNPGKSLALEIERQGSPLSLTLIPESKPGNGKAIGFVGIEPKVI

227 -> 278

ENVQPNSAASKAGLQAGDRIVKVDGQPLTQWVTFVMLVRDNPGKSLALEIER

234 -> 235

UniProt: Cuts RseA without previous DegS cleavage..

243 -> 243

UniProt: Cuts RseA without previous DegS cleavage..

244 -> 244

UniProt: Cuts RseA without previous DegS cleavage..

246 -> 246

UniProt: Cuts RseA without previous DegS cleavage..

261 -> 261

UniProt: Does not complement deletion mutant..

304 -> 304

UniProt: No cleavage of RseA in vitro (PubMed:19706448), cleavage of RseA (PubMed:23016873) in vivo..

376 -> 396

VVYYLPFLALISVNLGIINLF

UniProt: Helical.

389 -> 389

UniProt: Decreased substrate binding, retains some proteolytic activity..

394 -> 394

UniProt: Decreased substrate binding, retains some proteolytic activity..

397 -> 397

UniProt: Decreased substrate binding, retains some proteolytic activity..

399 -> 399

UniProt: Decreased substrate binding, retains some proteolytic activity..

402 -> 402

UniProt: Does not complement deletion mutant, loss of protease activity..

430 -> 450

IGSILLVLLMGLALFNDFSRL

UniProt: Helical.

Multifun Terms (GenProtEC)

1 - metabolism --> 1.2 - degradation of macromolecules --> 1.2.3 - proteins/peptides/glycopeptides

2 - information transfer --> 2.3 - protein related --> 2.3.6 - turnover, degradation

3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level --> 3.1.2.1 - sigma factors, anti-sigmafactors

3 - regulation --> 3.1 - type of regulation --> 3.1.3 - posttranscriptional --> 3.1.3.4 - proteases, cleavage of compounds

5 - cell processes --> 5.5 - adaptations --> 5.5.2 - temperature extremes

5 - cell processes --> 5.5 - adaptations --> 5.5.6 - other (mechanical, nutritional, oxidative stress)

Gene Ontology Terms (GO)

cellular_component

GO:0016020 - membrane
GO:0005886 - plasma membrane
GO:0005887 - integral component of plasma membrane
GO:0016021 - integral component of membrane

molecular_function

GO:0008233 - peptidase activity
GO:0016787 - hydrolase activity
GO:0046872 - metal ion binding
GO:0004222 - metalloendopeptidase activity
GO:0008237 - metallopeptidase activity
GO:0043856 - anti-sigma factor antagonist activity

biological_process

GO:0006508 - proteolysis
GO:0045893 - positive regulation of transcription, DNA-templated
GO:0036460 - cellular response to cell envelope stress

Type	Name	Post Left	Strand	Notes	Evidence (Confirmed, Strong, Weak)	References
promoter	TSS_339	196978	forward	nd	[RS-EPT-CBR]	[14]
promoter	TSS_341 (cluster)	197487	forward	nd	[RS-EPT-CBR]	[14]
promoter	TSS_342	197586	forward	nd	[RS-EPT-CBR]	[14]
promoter	TSS_343	197588	reverse	nd	[RS-EPT-CBR]	[14]
promoter	TSS_344	197883	forward	nd	[RS-EPT-CBR]	[14]
promoter	TSS_345	198507	forward	nd	[RS-EPT-CBR]	[14]
promoter	TSS_346	198777	forward	nd	[RS-EPT-CBR]	[14]
promoter	TSS_347	198782	forward	nd	[RS-EPT-CBR]	[14]
promoter	TSS_348 (cluster)	198858	forward	nd	[RS-EPT-CBR]	[14]
promoter	TSS_349	198875	forward	nd	[RS-EPT-CBR]	[14]
promoter	TSS_350 (cluster)	198877	forward	nd	[RS-EPT-CBR]	[14]
promoter	TSS_351 (cluster)	198881	forward	nd	[RS-EPT-CBR]	[14]
promoter	TSS_352	198887	forward	nd	[RS-EPT-CBR]	[14]
promoter	TSS_353	198889	forward	nd	[RS-EPT-CBR]	[14]
promoter	TSS_354	198893	forward	nd	[RS-EPT-CBR]	[14]
promoter	TSS_355 (cluster)	198908	forward	nd	[RS-EPT-CBR]	[14]
promoter	TSS_356	199004	forward	nd	[RS-EPT-CBR]	[14]
promoter	TSS_357	199007	forward	nd	[RS-EPT-CBR]	[14]
promoter	TSS_358	199009	forward	nd	[RS-EPT-CBR]	[14]
promoter	TSS_359	199012	forward	nd	[RS-EPT-CBR]	[14]
promoter	TSS_360	199980	forward	nd	[RS-EPT-CBR]	[14]
promoter	TSS_361	200131	forward	nd	[RS-EPT-CBR]	[14]
promoter	TSS_362 (cluster)	200135	forward	nd	[RS-EPT-CBR]	[14]
promoter	TSS_363 (cluster)	200138	forward	nd	[RS-EPT-CBR]	[14]
promoter	TSS_364	200212	forward	nd	[RS-EPT-CBR]	[14]
promoter	TSS_365	200317	forward	nd	[RS-EPT-CBR]	[14]

Type

Name

Post Left

Post Right

Strand

Notes

Evidence (Confirmed, Strong, Weak)

References

promoter

TSS_339

196978

forward

[RS-EPT-CBR]

[14]

promoter

TSS_341 (cluster)

197487

forward

[RS-EPT-CBR]

[14]

promoter

TSS_342

197586

forward

[RS-EPT-CBR]

[14]

promoter

TSS_343

197588

reverse

[RS-EPT-CBR]

[14]

promoter

TSS_344

197883

forward

[RS-EPT-CBR]

[14]

promoter

TSS_345

198507

forward

[RS-EPT-CBR]

[14]

promoter

TSS_346

198777

forward

[RS-EPT-CBR]

[14]

promoter

TSS_347

198782

forward

[RS-EPT-CBR]

[14]

promoter

TSS_348 (cluster)

198858

forward

[RS-EPT-CBR]

[14]

promoter

TSS_349

198875

forward

[RS-EPT-CBR]

[14]

promoter

TSS_350 (cluster)

198877

forward

[RS-EPT-CBR]

[14]

promoter

TSS_351 (cluster)

198881

forward

[RS-EPT-CBR]

[14]

promoter

TSS_352

198887

forward

[RS-EPT-CBR]

[14]

promoter

TSS_353

198889

forward

[RS-EPT-CBR]

[14]

promoter

TSS_354

198893

forward

[RS-EPT-CBR]

[14]

promoter

TSS_355 (cluster)

198908

forward

[RS-EPT-CBR]

[14]

promoter

TSS_356

199004

forward

[RS-EPT-CBR]

[14]

promoter

TSS_357

199007

forward

[RS-EPT-CBR]

[14]

promoter

TSS_358

199009

forward

[RS-EPT-CBR]

[14]

promoter

TSS_359

199012

forward

[RS-EPT-CBR]

[14]

promoter

TSS_360

199980

forward

[RS-EPT-CBR]

[14]

promoter

TSS_361

200131

forward

[RS-EPT-CBR]

[14]

promoter

TSS_362 (cluster)

200135

forward

[RS-EPT-CBR]

[14]

promoter

TSS_363 (cluster)

200138

forward

[RS-EPT-CBR]

[14]

promoter

TSS_364

200212

forward

[RS-EPT-CBR]

[14]

promoter

TSS_365

200317

forward

[RS-EPT-CBR]

[14]

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

Evidence

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

Reference(s)
[1] Akiyama K., Mizuno S., Hizukuri Y., Mori H., Nogi T., Akiyama Y., 2015, Roles of the membrane-reentrant β-hairpin-like loop of RseP protease in selective substrate cleavage., Elife 4
[2] Alba BM., Leeds JA., Onufryk C., Lu CZ., Gross CA., 2002, DegS and YaeL participate sequentially in the cleavage of RseA to activate the sigma(E)-dependent extracytoplasmic stress response., Genes Dev 16(16):2156-68
[3] Bohn C., Collier J., Bouloc P., 2004, Dispensable PDZ domain of Escherichia coli YaeL essential protease., Mol Microbiol 52(2):427-35
[4] Douchin V., Bohn C., Bouloc P., 2006, Down-regulation of porins by a small RNA bypasses the essentiality of the regulated intramembrane proteolysis protease RseP in Escherichia coli., J Biol Chem 281(18):12253-9
[5] Dries DR., Yu G., 2009, Rip exposed: how ectodomain shedding regulates the proteolytic processing of transmembrane substrates., Proc Natl Acad Sci U S A 106(35):14737-8
[6] Hizukuri Y., Akiyama Y., 2012, PDZ domains of RseP are not essential for sequential cleavage of RseA or stress-induced σ(E) activation in vivo., Mol Microbiol 86(5):1232-45
[7] Kanehara K., Ito K., Akiyama Y., 2002, YaeL (EcfE) activates the sigma(E) pathway of stress response through a site-2 cleavage of anti-sigma(E), RseA., Genes Dev 16(16):2147-55
[8] Koide K., Ito K., Akiyama Y., 2008, Substrate recognition and binding by RseP, an Escherichia coli intramembrane protease., J Biol Chem 283(15):9562-70
[9] Koide K., Maegawa S., Ito K., Akiyama Y., 2007, Environment of the active site region of RseP, an Escherichia coli regulated intramembrane proteolysis protease, assessed by site-directed cysteine alkylation., J Biol Chem 282(7):4553-60
[10] Li X., Wang B., Feng L., Kang H., Qi Y., Wang J., Shi Y., 2009, Cleavage of RseA by RseP requires a carboxyl-terminal hydrophobic amino acid following DegS cleavage., Proc Natl Acad Sci U S A 106(35):14837-42
[11] Lindner E., White SH., 2019, Dropping Out and Other Fates of Transmembrane Segments Inserted by the SecA ATPase., J Mol Biol 431(10):2006-2019
[12] Miyake T., Hizukuri Y., Akiyama Y., 2020, Involvement of a Membrane-Bound Amphiphilic Helix in Substrate Discrimination and Binding by an Escherichia coli S2P Peptidase RseP., Front Microbiol 11:607381
[13] Strisovsky K., 2016, Why cells need intramembrane proteases - a mechanistic perspective., FEBS J 283(10):1837-45
[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.

Reference(s)

[1] Akiyama K., Mizuno S., Hizukuri Y., Mori H., Nogi T., Akiyama Y., 2015, Roles of the membrane-reentrant β-hairpin-like loop of RseP protease in selective substrate cleavage., Elife 4

[2] Alba BM., Leeds JA., Onufryk C., Lu CZ., Gross CA., 2002, DegS and YaeL participate sequentially in the cleavage of RseA to activate the sigma(E)-dependent extracytoplasmic stress response., Genes Dev 16(16):2156-68

[3] Bohn C., Collier J., Bouloc P., 2004, Dispensable PDZ domain of Escherichia coli YaeL essential protease., Mol Microbiol 52(2):427-35

[4] Douchin V., Bohn C., Bouloc P., 2006, Down-regulation of porins by a small RNA bypasses the essentiality of the regulated intramembrane proteolysis protease RseP in Escherichia coli., J Biol Chem 281(18):12253-9

[5] Dries DR., Yu G., 2009, Rip exposed: how ectodomain shedding regulates the proteolytic processing of transmembrane substrates., Proc Natl Acad Sci U S A 106(35):14737-8

[6] Hizukuri Y., Akiyama Y., 2012, PDZ domains of RseP are not essential for sequential cleavage of RseA or stress-induced σ(E) activation in vivo., Mol Microbiol 86(5):1232-45

[7] Kanehara K., Ito K., Akiyama Y., 2002, YaeL (EcfE) activates the sigma(E) pathway of stress response through a site-2 cleavage of anti-sigma(E), RseA., Genes Dev 16(16):2147-55

[8] Koide K., Ito K., Akiyama Y., 2008, Substrate recognition and binding by RseP, an Escherichia coli intramembrane protease., J Biol Chem 283(15):9562-70

[9] Koide K., Maegawa S., Ito K., Akiyama Y., 2007, Environment of the active site region of RseP, an Escherichia coli regulated intramembrane proteolysis protease, assessed by site-directed cysteine alkylation., J Biol Chem 282(7):4553-60

[10] Li X., Wang B., Feng L., Kang H., Qi Y., Wang J., Shi Y., 2009, Cleavage of RseA by RseP requires a carboxyl-terminal hydrophobic amino acid following DegS cleavage., Proc Natl Acad Sci U S A 106(35):14837-42

[11] Lindner E., White SH., 2019, Dropping Out and Other Fates of Transmembrane Segments Inserted by the SecA ATPase., J Mol Biol 431(10):2006-2019

[12] Miyake T., Hizukuri Y., Akiyama Y., 2020, Involvement of a Membrane-Bound Amphiphilic Helix in Substrate Discrimination and Binding by an Escherichia coli S2P Peptidase RseP., Front Microbiol 11:607381

[13] Strisovsky K., 2016, Why cells need intramembrane proteases - a mechanistic perspective., FEBS J 283(10):1837-45

[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.