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Escherichia coli K-12 substr. MG1655 Polypeptide: RseP zinc protease, signal peptide peptidase

Gene: rseP Accession Numbers: EG12436 (EcoCyc), b0176, ECK0175

Synonyms: ecfE, yaeL

Regulation Summary Diagram: ?

RseP (formerly YaeL) is a zinc metallo-protease that resides in the inner membrane [Dartigalongue01a]. Upon extracytoplasmic stress, DegS and RseP sequentially catalyze proteolytic cleavage of RseA, thereby relieving repression of σE and activating the σE-mediated stress response [Kanehara02, Alba02]. RseP is involved in the degradation of remnant signal peptides that are left in the inner membrane after their cleavage from preproteins by leader peptidase [Saito11].

RseP cleaves RseA in the cytoplasmic or intramembrane region [Kanehara02]. RseP has also been observed to exhibit proteolytic activity toward RpoE and RpoH [Dartigalongue01a], and a wide range of other membrane proteins [Akiyama04]. RseP can cleave remnant signal peptides from a variety of secretory proteins in vivo including OmpF, LivK, SecM, PhoA and others [Saito11]. RseE can cleave remnant signal peptides from proteins that are processed via the Sec and Tat pathways [Saito11]. RseP cleaves synthetic βlactamase signal peptides within the hydrophobic core region [Saito11].

RseP has an N-terminal domain containing the zinc metalloprotease motif HEXXH, and a C-terminal domain with an LDG sequence [Dartigalongue01a]. The HEXXH and LDG motifs are required [Kanehara01]. RseP also contains two circularly permutated PDZ domains (PDZ-N and PDZ-C) [Inaba08]. Mutational analyses of these two domains in an in vitro reconstitution of RseP catalysed proteolysis suggests that they are involved in ligand binding [Inaba08].

The sequential cleavage of RseA by DegS and RseP has been reconstituted in vitro [Li09f]. After cleavage by DegS, the single terminal residue (Val148) of the newly generated C-terminus of RseA binds to the PDZ-C domain of RseP and undergoes a second cleavage. Crystal structures of the PDZ-N and PDZ-C domains of RseP have been obtained suggesting that PDZ-N is in a 'closed' conformation whilst PDZ-C is 'open' to receive a ligand [Li09f] The structure of a DegS cleaved RseA peptide (residues 1-148) fused to the PDZ-C domain shows the C-terminal Val148 residue bound to the PDZ-C binding pocket [Li09f].

Mutants lacking or depleted of RseP are inviable [Dartigalongue01a, Kanehara01, Baba06]. Overproduction of RseP inhibits transcription directed by σE or σ32-containing polymerase holoenzyme [Dartigalongue01a]. The inviability of an rseP mutant is suppressed by overproduction of RpoE [Kanehara02]. Mutations in the PDZ domain do not appear to be lethal, but render the proteolytic activity of RseP independent of DegS activity, suggesting that the PDZ domain acts as an inhibitor [Bohn04, Kanehara03].

The membrane topology of RseP has been determined [Kanehara01, Drew02]; the protein has four membrane spanning sequences, and the termini are periplasmic [Kanehara01].

RseP is a member of the site-2 protease (S2P) family [Kinch06] of intra-membrane cleaving proteases (I-CLips) [Kanehara01]. E. coli and mammalian cells exhibit analogous responses to unfolded protein stress [Alba02].

rseP is subject to transcription by EσE polymerase [Dartigalongue01a, Dartigalongue01].

Ecf: "extracytoplasmic function" [Dartigalongue01].

Reviews: [Kanehara03a, Alba04].

Citations: [Koide07, Koide08]

Locations: inner membrane

Map Position: [196,546 -> 197,898] (4.24 centisomes)
Length: 1353 bp / 450 aa

Molecular Weight of Polypeptide: 49.071 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0000603 , DIP:DIP-48061N , EchoBASE:EB2331 , EcoGene:EG12436 , EcoliWiki:b0176 , ModBase:P0AEH1 , OU-Microarray:b0176 , PortEco:rseP , PR:PRO_000023880 , Pride:P0AEH1 , Protein Model Portal:P0AEH1 , RefSeq:NP_414718 , RegulonDB:EG12436 , SMR:P0AEH1 , String:511145.b0176 , UniProt:P0AEH1

Relationship Links: InterPro:IN-FAMILY:IPR001478 , InterPro:IN-FAMILY:IPR004387 , InterPro:IN-FAMILY:IPR008915 , PDB:Structure:2ZPL , PDB:Structure:2ZPM , PDB:Structure:3ID1 , PDB:Structure:3ID2 , PDB:Structure:3ID3 , PDB:Structure:3ID4 , Pfam:IN-FAMILY:PF00595 , Pfam:IN-FAMILY:PF02163 , Prosite:IN-FAMILY:PS00142 , Prosite:IN-FAMILY:PS50106 , Smart:IN-FAMILY:SM00228

GO Terms:

Biological Process: GO:0006950 - response to stress Inferred from experiment [Kanehara02, Alba02]
GO:0045893 - positive regulation of transcription, DNA-templated Inferred from experiment [Alba02, Kanehara02]
GO:0006508 - proteolysis Inferred by computational analysis [UniProtGOA11a, GOA01a]
Molecular Function: GO:0004222 - metalloendopeptidase activity Inferred from experiment Inferred by computational analysis [GOA01a, Li09f]
GO:0043856 - anti-sigma factor antagonist activity Inferred from experiment [Kanehara02, Alba02]
GO:0045152 - antisigma factor binding Inferred from experiment [Li09f]
GO:0008233 - peptidase activity Inferred by computational analysis [UniProtGOA11a]
GO:0008237 - metallopeptidase activity Inferred by computational analysis [UniProtGOA11a]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11a]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005886 - plasma membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, DiazMejia09, Zhang07, Daley05, Dartigalongue01a]
GO:0005887 - integral component of plasma membrane Inferred from experiment [Drew02]
GO:0016020 - membrane Inferred by computational analysis [UniProtGOA11a]
GO:0016021 - integral component of membrane Inferred by computational analysis [UniProtGOA11a, GOA01a]

MultiFun Terms: cell processes adaptations other (mechanical, nutritional, oxidative stress)
cell processes adaptations temperature extremes
information transfer protein related turnover, degradation
metabolism degradation of macromolecules proteins/peptides/glycopeptides
regulation type of regulation posttranscriptional proteases, cleavage of compounds
regulation type of regulation transcriptional level sigma factors, anti-sigmafactors

Essentiality data for rseP knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox No 37 Aerobic 7   No [Baba06, Comment 2]

Last-Curated ? 22-Aug-2011 by Mackie A , Macquarie University

Sequence Features

Feature Class Location Common Name Citations Comment
Mutagenesis-Variant 22  
[Dartigalongue01a, Akiyama04, UniProt11]
Alternate sequence: H → F; UniProt: Loss of activity.
Alternate sequence: H → A; UniProt: Loss of activity.
Metal-Binding-Site 22  
UniProt: Zinc; catalytic; Non-Experimental Qualifier: probable;
Active-Site 23  
UniProt: Non-Experimental Qualifier: potential;
Metal-Binding-Site 26  
UniProt: Zinc; catalytic; Non-Experimental Qualifier: potential;
Transmembrane-Region 107 -> 127  
UniProt: Helical;; Non-Experimental Qualifier: potential;
Conserved-Region 127 -> 220 PDZ-N
Conserved-Region 199 -> 291  
UniProt: PDZ;
Conserved-Region 222 -> 309 PDZ-C
Transmembrane-Region 376 -> 396  
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 430 -> 450  
UniProt: Helical;; Non-Experimental Qualifier: potential;

Gene Local Context (not to scale): ?

Transcription Unit:


10/20/97 Gene b0176 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG12436; confirmed by SwissProt match.


Akiyama04: Akiyama Y, Kanehara K, Ito K (2004). "RseP (YaeL), an Escherichia coli RIP protease, cleaves transmembrane sequences." EMBO J 23(22);4434-42. PMID: 15496982

Alba02: 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. PMID: 12183369

Alba04: Alba BM, Gross CA (2004). "Regulation of the Escherichia coli sigma-dependent envelope stress response." Mol Microbiol 52(3);613-9. PMID: 15101969

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Bohn04: Bohn C, Collier J, Bouloc P (2004). "Dispensable PDZ domain of Escherichia coli YaeL essential protease." Mol Microbiol 52(2);427-35. PMID: 15066031

Daley05: Daley DO, Rapp M, Granseth E, Melen K, Drew D, von Heijne G (2005). "Global topology analysis of the Escherichia coli inner membrane proteome." Science 308(5726);1321-3. PMID: 15919996

Dartigalongue01: Dartigalongue C, Missiakas D, Raina S (2001). "Characterization of the Escherichia coli sigma E regulon." J Biol Chem 276(24);20866-75. PMID: 11274153

Dartigalongue01a: Dartigalongue C, Loferer H, Raina S (2001). "EcfE, a new essential inner membrane protease: its role in the regulation of heat shock response in Escherichia coli." EMBO J 20(21);5908-18. PMID: 11689431

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Drew02: Drew D, Sjostrand D, Nilsson J, Urbig T, Chin CN, de Gier JW, von Heijne G (2002). "Rapid topology mapping of Escherichia coli inner-membrane proteins by prediction and PhoA/GFP fusion analysis." Proc Natl Acad Sci U S A 99(5);2690-5. PMID: 11867724

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

Inaba08: Inaba K, Suzuki M, Maegawa KI, Akiyama S, Ito K, Akiyama Y (2008). "A pair of circularly permutated PDZ domains control RseP, the S2P family intramembrane protease of E. coli." J Biol Chem 283(50):35042-52. PMID: 18945679

Kanehara01: Kanehara K, Akiyama Y, Ito K (2001). "Characterization of the yaeL gene product and its S2P-protease motifs in Escherichia coli." Gene 281(1-2);71-9. PMID: 11750129

Kanehara02: 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. PMID: 12183368

Kanehara03: Kanehara K, Ito K, Akiyama Y (2003). "YaeL proteolysis of RseA is controlled by the PDZ domain of YaeL and a Gln-rich region of RseA." EMBO J 22(23);6389-98. PMID: 14633997

Kanehara03a: Kanehara K, Akiyama Y (2003). "[RIP(regulated intramembrane proteolysis): from bacteria to higher organism]." Tanpakushitsu Kakusan Koso 48(7);836-41. PMID: 12795200

Kinch06: Kinch LN, Ginalski K, Grishin NV (2006). "Site-2 protease regulated intramembrane proteolysis: sequence homologs suggest an ancient signaling cascade." Protein Sci 15(1);84-93. PMID: 16322567

Koide07: 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. PMID: 17179147

Koide08: 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. PMID: 18268014

Li09f: 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. PMID: 19706448

Saito11: Saito A, Hizukuri Y, Matsuo E, Chiba S, Mori H, Nishimura O, Ito K, Akiyama Y (2011). "Post-liberation cleavage of signal peptides is catalyzed by the site-2 protease (S2P) in bacteria." Proc Natl Acad Sci U S A 108(33);13740-5. PMID: 21810987

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt11: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Zhang07: Zhang N, Chen R, Young N, Wishart D, Winter P, Weiner JH, Li L (2007). "Comparison of SDS- and methanol-assisted protein solubilization and digestion methods for Escherichia coli membrane proteome analysis by 2-D LC-MS/MS." Proteomics 7(4);484-93. PMID: 17309111

Other References Related to Gene Regulation

Viveiros07: Viveiros M, Dupont M, Rodrigues L, Couto I, Davin-Regli A, Martins M, Pages JM, Amaral L (2007). "Antibiotic stress, genetic response and altered permeability of E. coli." PLoS ONE 2;e365. PMID: 17426813

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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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