|Gene:||yidC||Accession Numbers: EG11197 (EcoCyc), b3705, ECK3698|
YidC mediates membrane insertion/assembly of inner membrane proteins [Scotti00, Houben00, Samuelson00, Urbanus01, Houben02, vanderLaan03, Yi03a]. YidC has been found to interact with the accessory SecDF and YajC proteins of the Sec translocon [Nouwen02] to form a heterotetrameric complex which then, through SecF and YajC interaction with SecY [Sagara94], is believed to facilitate Sec-dependent protein insertion. In addition to its Sec associated function YidC can also insert some membrane proteins such as phage proteins, MtlA, MscL and the F0c subunit of ATP synthase, independently [Samuelson00, Chen02a, vanderLaan04, Facey07, Welte12]. Purified, reconstituted YidC mediates the post-translational insertion of F0c. YidC is required for F0c to adopt its correct oligomerisation state [Robinson13].
YidC is essential [Samuelson00]. YidC depletion causes induction of the Psp stress response [vanderLaan03, Jones03a] resulting from defects in respiratory chain complex biogenesis [vanderLaan03]. YidC has also been implicated in membrane biogenesis of integral membrane subunits of the anaerobic respiratory chain [Price08].
YidC contains 5 transmembrane regions that are connected via a long periplasmic loop to an additional sixth N-terminal transmembrane region [Saaf98, Ravaud08]. A systematic mutational study indicates that the five most C-terminal transmembrane spanning regions are important for YidC activity [Jiang03]. A site-specific cross-linking approach has identified residues within the third transmembrane segement (TM3) which appear to be a generic docking site for hydrophobic domains in growing nascent inner-membrane proteins (IMPs) and provides a protected environment that facilitates their lipid partitioning and folding [Yu08].
Microscopy of 2D crystals suggests that full-length membrane bound YidC is dimeric [Lotz08]. A 3D structure of YidC in complex with translating ribosome shows dimers of YidC bound at the tunnel exit of the ribosome nascent chain complex [Kohler09]. Momomeric YidC represents the functional unit in vitro [Kedrov13]. Protein purification and cross-linking studies indicate that YidC is physically and functionally connected to FtsH and that this complex may be involved in quality control of inner membrane proteins (IMPs) during biogenesis [vanBloois08]. The C-terminus of YidC is in contact with the ribosome, the signal recognition particle (SRP) and FtsY [Welte12]. E. coli ribosomes do not associate with YidC unless they are synthesizing YidC substrates [Kedrov13].
Defects of an E. coli yidC mutant are functionally complemented by production of chloroplast Alb3 [Jiang02].
Citations: [vanderLaan01, Samuelson01, Beck01, vanDalen02, Watkins02, Froderberg03, Facey03, Chen03b , Hatzixanthis03, Raine03, Van04b, Martinez08a, Klenner08, Sachelaru13, Zhu12a, Kol09, Xie06 , Kol08a, vanBloois05, Yuan07, Klenner12, Winterfeld13, Imhof11, Wagner08 ]
Locations: inner membrane
|Map Position: [3,883,099 -> 3,884,745] (83.69 centisomes, 301°)||Length: 1647 bp / 548 aa|
Molecular Weight of Polypeptide: 61.526 kD (from nucleotide sequence)
Unification Links: ASAP:ABE-0012120, DIP:DIP-12442N, EchoBASE:EB1183, EcoGene:EG11197, EcoliWiki:b3705, Mint:MINT-6477960, OU-Microarray:b3705, PortEco:yidC, PR:PRO_000023473, Pride:P25714, Protein Model Portal:P25714, RefSeq:NP_418161, RegulonDB:EG11197, SMR:P25714, String:511145.b3705, UniProt:P25714
Relationship Links: InterPro:IN-FAMILY:IPR001708, InterPro:IN-FAMILY:IPR019998, InterPro:IN-FAMILY:IPR028053, InterPro:IN-FAMILY:IPR028055, Panther:IN-FAMILY:PTHR12428, PDB:Structure:3BLC, PDB:Structure:3BS6, PDB:Structure:4UTQ, Pfam:IN-FAMILY:PF02096, Pfam:IN-FAMILY:PF14849, Prints:IN-FAMILY:PR00701, Prints:IN-FAMILY:PR01900
|MultiFun Terms:||cell structure → membrane|
|information transfer → protein related → chaperoning, repair (refolding)|
|Growth Medium||Growth?||T (°C)||O2||pH||Osm/L||Growth Observations|
|LB Lennox||No||37||Aerobic||7||No [Baba06, Comment 1]|
Subunit of: SecD-SecF-YajC-YidC Secretion Complex
Subunit composition of
SecD-SecF-YajC-YidC Secretion Complex = [YidC][YajC][SecF][SecD]
inner-membrane protein insertion factor = YidC (extended summary available)
Component of: Sec Holo-Translocon (extended summary available)
SecD/SecF/YajC and YidC are all components of the Sec protein secretion pathway. They are believed to work in conjunction with SecYEG to stabilize the insertion of SecA and its bound preprotein into the inner membrane.
In studies of conditional lethal mutations of secD and secF genes, secA transcription was found to be stimulated due to severe general protein translocation defects. Deletions of secD result in cold-sensitive mutations which could be complemented by plasmids containing the gene [Gardel87]. Overexpression of SecD and SecF increases translocation in wild-type cells [Pogliano94]. Within the same operon as secD and secF is a third gene known as yajC which may also have a role in protein translocation [Pogliano94a]. Co-purification studies [Samuelson00] indicate that YidC is associated with the SecYEG translocase complex and plays a role in the assembly of inner membrane proteins. Subsequent studies [Nouwen02] show that, under conditions of SecD/SecF/YajC overproduction, YidC forms a heterotetrameric complex with SecD/SecF/YajC.
In vitro reconstitution studies demonstrated that the presence of SecD/SecF/YajC stabilizes the SecA insertion complex and inhibits movement of the SecA bound precursor in either direction [Duong97a]. If this model holds true, then the SecD/SecF/YajC/YidC stabilization complex must be released from the SecYEG complex or be otherwise inactivated in order for SecA to de-insert from the complex and to begin another round of stepwise translocation powered by ATP hydrolysis [Danese98].
Subunit of: Sec Holo-Translocon
Synonyms: Sec translocation complex
Subunit composition of
Sec Holo-Translocon = [(YidC)(YajC)(SecF)(SecD)][(SecE)(SecG)(SecY)]
SecD-SecF-YajC-YidC Secretion Complex = (YidC)(YajC)(SecF)(SecD) (extended summary available)
inner-membrane protein insertion factor = YidC (extended summary available)
SecYEG translocase = (SecE)(SecG)(SecY) (extended summary available)
The Sec 'holo-translocon' (HTL) is a large multisubunit complex that mediates the transport of nascent polypeptides across, or their integration into, the cytoplasmic membrane. The holo-translocon is a seven subunit complex containing an inner membrane heterotrimeric SecYEG complex that forms the protein conducting channel plus an ancillary complex, SecDFYajC and the Yid C membrane protein, both of which interact with SecYEG to enhance protein transport or integration. The energy for protein translocation is provided by the motor protein ATPase SecA and the proton motive force. The HTL complex is less effective in ATP-dependent SecA-driven protein secretion and more dependent on the PMF [Schulze14].
Simultaneous overexpression of all 7 subunits of the sec HTL facilitates purification and isolation of a complex that is competent for protein secretion and for membrane protein insertion in vitro. The complex contains one copy of SecYEG, one copy of SecDFYajC and one copy of YidC. The HTL associates preferentially with ribosomes displaying nascent peptide. Protein translocation in HTL containing proteoliposomes is stimulated by cardiolipin and by the PMF [Schulze14].
Two pathways of protein translocation converge at the Sec translocon. In the posttranslational pathway the newly synthesised polypeptide is bound by SecB, a cytosolic chaperone which aids targeting to the membrane and maintains a translocation competent conformation of the pre-protein, while in the co-translational pathway the SRP complex binds to the nascent protein as it emerges from the ribosome and the SRP/ribosome/protein complex is then targeted to the Sec translocase.
An experimental approach using alkaline phosphatase (PhoA) fusions to protein signal sequences has allowed discrimination between the major modes of transport, including the Sec protein translocase, across the inner membrane [Marrichi08].
Molecular Weight: 250.0 kD (experimental) [Schulze14]
|Transmembrane-Region||6 -> 23|
|Mutagenesis-Variant||24 -> 27|
|Protein-Segment||24 -> 264|
|Protein-Segment||215 -> 265|
|Protein-Segment||265 -> 346|
|Mutagenesis-Variant||334 -> 338|
|Transmembrane-Region||343 -> 370|
|Transmembrane-Region||417 -> 446|
|Transmembrane-Region||464 -> 481|
|Mutagenesis-Variant||483 -> 487|
|Transmembrane-Region||494 -> 509|
|Transmembrane-Region||513 -> 535|
|Protein-Segment||527 -> 548|
|Pfam PF14849||61 -> 343|
|Pfam PF02096||354 -> 533|
The database does not contain any information about transcription units for this gene.
10/20/97 Gene b3705 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11197; confirmed by SwissProt match.
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
Beck01: Beck K, Eisner G, Trescher D, Dalbey RE, Brunner J, Muller M (2001). "YidC, an assembly site for polytopic Escherichia coli membrane proteins located in immediate proximity to the SecYE translocon and lipids." EMBO Rep 2(8);709-14. PMID: 11463745
Chen02a: Chen M, Samuelson JC, Jiang F, Muller M, Kuhn A, Dalbey RE (2002). "Direct interaction of YidC with the Sec-independent Pf3 coat protein during its membrane protein insertion." J Biol Chem 277(10);7670-5. PMID: 11751917
Chen02b: Chen M, Xie K, Jiang F, Yi L, Dalbey RE (2002). "YidC, a newly defined evolutionarily conserved protein, mediates membrane protein assembly in bacteria." Biol Chem 383(10);1565-72. PMID: 12452432
Chen03b: Chen M, Xie K, Nouwen N, Driessen AJ, Dalbey RE (2003). "Conditional lethal mutations separate the M13 procoat and Pf3 coat functions of YidC: different YIDC structural requirements for membrane protein insertion." J Biol Chem 278(26);23295-300. PMID: 12707259
Dalbey04: Dalbey RE, Kuhn A (2004). "YidC family members are involved in the membrane insertion, lateral integration, folding, and assembly of membrane proteins." J Cell Biol 166(6);769-74. PMID: 15364957
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
Facey07: Facey SJ, Neugebauer SA, Krauss S, Kuhn A (2007). "The mechanosensitive channel protein MscL is targeted by the SRP to the novel YidC membrane insertion pathway of Escherichia coli." J Mol Biol 365(4);995-1004. PMID: 17113597
Finn14: Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J, Sonnhammer EL, Tate J, Punta M (2014). "Pfam: the protein families database." Nucleic Acids Res 42(Database issue);D222-30. PMID: 24288371
Froderberg03: Froderberg L, Houben E, Samuelson JC, Chen M, Park SK, Phillips GJ, Dalbey R, Luirink J, De Gier JW (2003). "Versatility of inner membrane protein biogenesis in Escherichia coli." Mol Microbiol 47(4);1015-27. PMID: 12581356
Houben00: Houben EN, Scotti PA, Valent QA, Brunner J, de Gier JL, Oudega B, Luirink J (2000). "Nascent Lep inserts into the Escherichia coli inner membrane in the vicinity of YidC, SecY and SecA." FEBS Lett 476(3);229-33. PMID: 10913619
Houben02: Houben EN, Urbanus ML, Van Der Laan M, Ten Hagen-Jongman CM, Driessen AJ, Brunner J, Oudega B, Luirink J (2002). "YidC and SecY mediate membrane insertion of a Type I transmembrane domain." J Biol Chem 277(39);35880-6. PMID: 12107184
Jiang02: Jiang F, Yi L, Moore M, Chen M, Rohl T, Van Wijk KJ, De Gier JW, Henry R, Dalbey RE (2002). "Chloroplast YidC homolog Albino3 can functionally complement the bacterial YidC depletion strain and promote membrane insertion of both bacterial and chloroplast thylakoid proteins." J Biol Chem 277(22);19281-8. PMID: 11891220
Koch02: Koch HG, Moser M, Schimz KL, Muller M (2002). "The integration of YidC into the cytoplasmic membrane of Escherichia coli requires the signal recognition particle, SecA and SecYEG." J Biol Chem 277(8);5715-8. PMID: 11777926
Kohler09: Kohler R, Boehringer D, Greber B, Bingel-Erlenmeyer R, Collinson I, Schaffitzel C, Ban N (2009). "YidC and Oxa1 form dimeric insertion pores on the translating ribosome." Mol Cell 34(3);344-53. PMID: 19450532
Kol08a: Kol S, Nouwen N, Driessen AJ (2008). "The charge distribution in the cytoplasmic loop of subunit C of the F1F0 ATPase is a determinant for YidC targeting." J Biol Chem 283(15);9871-7. PMID: 18276587
Kol09: Kol S, Majczak W, Heerlien R, van der Berg JP, Nouwen N, Driessen AJ (2009). "Subunit a of the F(1)F(0) ATP synthase requires YidC and SecYEG for membrane insertion." J Mol Biol 390(5);893-901. PMID: 19497329
Kuhn03: Kuhn A, Stuart R, Henry R, Dalbey RE (2003). "The Alb3/Oxa1/YidC protein family: membrane-localized chaperones facilitating membrane protein insertion?." Trends Cell Biol 13(10);510-6. PMID: 14507478
Marrichi08: Marrichi MJ, Camacho L, Russell DG, Delisa MP (2008). "Genetic toggling of alkaline phosphatase folding reveals signal peptides for all major modes of transport across the inner membrane of bacteria." J Biol Chem 283(50):35223-35. PMID: 18819916
Martinez08a: Martinez Molina D, Lundback AK, Niegowski D, Eshaghi S (2008). "Expression and purification of the recombinant membrane protein YidC: A case study for increased stability and solubility." Protein Expr Purif 62(1):49-52. PMID: 18586516
Ojemalm13: Ojemalm K, Botelho SC, Studle C, von Heijne G (2013). "Quantitative analysis of SecYEG-mediated insertion of transmembrane α-helices into the bacterial inner membrane." J Mol Biol 425(15);2813-22. PMID: 23659793
Ravaud08: Ravaud S, Stjepanovic G, Wild K, Sinning I (2008). "The crystal structure of the periplasmic domain of the Escherichia coli membrane protein insertase YidC contains a substrate binding cleft." J Biol Chem 283(14);9350-8. PMID: 18234665
Sachelaru13: Sachelaru I, Petriman NA, Kudva R, Kuhn P, Welte T, Knapp B, Drepper F, Warscheid B, Koch HG (2013). "YidC occupies the lateral gate of the SecYEG translocon and is sequentially displaced by a nascent membrane protein." J Biol Chem 288(23);16295-307. PMID: 23609445
Sagara94: Sagara K, Matsuyama S, Mizushima S (1994). "SecF stabilizes SecD and SecY, components of the protein translocation machinery of the Escherichia coli cytoplasmic membrane." J Bacteriol 176(13);4111-6. PMID: 8021192
Samuelson00: Samuelson JC, Chen M, Jiang F, Moller I, Wiedmann M, Kuhn A, Phillips GJ, Dalbey RE (2000). "YidC mediates membrane protein insertion in bacteria." Nature 406(6796);637-41. PMID: 10949305
Samuelson01: Samuelson JC, Jiang F, Yi L, Chen M, de Gier JW, Kuhn A, Dalbey RE (2001). "Function of YidC for the insertion of M13 procoat protein in Escherichia coli: translocation of mutants that show differences in their membrane potential dependence and Sec requirement." J Biol Chem 276(37);34847-52. PMID: 11457858
Schulze14: Schulze RJ, Komar J, Botte M, Allen WJ, Whitehouse S, Gold VA, Lycklama A Nijeholt JA, Huard K, Berger I, Schaffitzel C, Collinson I (2014). "Membrane protein insertion and proton-motive-force-dependent secretion through the bacterial holo-translocon SecYEG-SecDF-YajC-YidC." Proc Natl Acad Sci U S A 111(13);4844-9. PMID: 24550475
Scotti00: Scotti PA, Urbanus ML, Brunner J, de Gier JW, von Heijne G, van der Does C, Driessen AJ, Oudega B, Luirink J (2000). "YidC, the Escherichia coli homologue of mitochondrial Oxa1p, is a component of the Sec translocase." EMBO J 19(4);542-9. PMID: 10675323
Urbanus01: Urbanus ML, Scotti PA, Froderberg L, Saaf A, de Gier JW, Brunner J, Samuelson JC, Dalbey RE, Oudega B, Luirink J (2001). "Sec-dependent membrane protein insertion: sequential interaction of nascent FtsQ with SecY and YidC." EMBO Rep 2(6);524-9. PMID: 11415986
Urbanus02: Urbanus ML, Froderberg L, Drew D, Bjork P, de Gier JW, Brunner J, Oudega B, Luirink J (2002). "Targeting, insertion, and localization of Escherichia coli YidC." J Biol Chem 277(15);12718-23. PMID: 11821429
vanBloois05: van Bloois E, Nagamori S, Koningstein G, Ullers RS, Preuss M, Oudega B, Harms N, Kaback HR, Herrmann JM, Luirink J (2005). "The Sec-independent function of Escherichia coli YidC is evolutionary-conserved and essential." J Biol Chem 280(13);12996-3003. PMID: 15671040
vanBloois08: van Bloois E, Dekker HL, Froderberg L, Houben EN, Urbanus ML, de Koster CG, de Gier JW, Luirink J (2008). "Detection of cross-links between FtsH, YidC, HflK/C suggests a linked role for these proteins in quality control upon insertion of bacterial inner membrane proteins." FEBS Lett 582(10);1419-24. PMID: 18387365
vanDalen02: van Dalen A, van der Laan M, Driessen AJ, Killian JA, de Kruijff B (2002). "Components required for membrane assembly of newly synthesized K+ channel KcsA." FEBS Lett 511(1-3);51-8. PMID: 11821048
vanderLaan01: van der Laan M, Houben EN, Nouwen N, Luirink J, Driessen AJ (2001). "Reconstitution of Sec-dependent membrane protein insertion: nascent FtsQ interacts with YidC in a SecYEG-dependent manner." EMBO Rep 2(6);519-23. PMID: 11415985
vanderLaan03: van der Laan M, Urbanus ML, Ten Hagen-Jongman CM, Nouwen N, Oudega B, Harms N, Driessen AJ, Luirink J (2003). "A conserved function of YidC in the biogenesis of respiratory chain complexes." Proc Natl Acad Sci U S A 100(10);5801-6. PMID: 12724529
vanderLaan04: van der Laan M, Bechtluft P, Kol S, Nouwen N, Driessen AJ (2004). "F1F0 ATP synthase subunit c is a substrate of the novel YidC pathway for membrane protein biogenesis." J Cell Biol 165(2);213-22. PMID: 15096523
vanderLaan05: van der Laan M, Nouwen NP, Driessen AJ (2005). "YidC--an evolutionary conserved device for the assembly of energy-transducing membrane protein complexes." Curr Opin Microbiol 8(2);182-7. PMID: 15802250
Wagner08: Wagner S, Pop OI, Pop O, Haan GJ, Baars L, Koningstein G, Klepsch MM, Genevaux P, Luirink J, de Gier JW (2008). "Biogenesis of MalF and the MalFGK(2) maltose transport complex in Escherichia coli requires YidC." J Biol Chem 283(26);17881-90. PMID: 18456666
Watkins02: Watkins WE, Menon AK (2002). "Reconstitution of phospholipid flippase activity from E. coli inner membrane: a test of the protein translocon as a candidate flippase." Biol Chem 383(9);1435-40. PMID: 12437136
Welte12: Welte T, Kudva R, Kuhn P, Sturm L, Braig D, Muller M, Warscheid B, Drepper F, Koch HG (2012). "Promiscuous targeting of polytopic membrane proteins to SecYEG or YidC by the Escherichia coli signal recognition particle." Mol Biol Cell 23(3);464-79. PMID: 22160593
Winterfeld13: Winterfeld S, Ernst S, Borsch M, Gerken U, Kuhn A (2013). "Real time observation of single membrane protein insertion events by the Escherichia coli insertase YidC." PLoS One 8(3);e59023. PMID: 23527078
Xie06: Xie K, Kiefer D, Nagler G, Dalbey RE, Kuhn A (2006). "Different regions of the nonconserved large periplasmic domain of Escherichia coli YidC are involved in the SecF interaction and membrane insertase activity." Biochemistry 45(44);13401-8. PMID: 17073462
Yi03a: Yi L, Jiang F, Chen M, Cain B, Bolhuis A, Dalbey RE (2003). "YidC is strictly required for membrane insertion of subunits a and c of the F(1)F(0)ATP synthase and SecE of the SecYEG translocase." Biochemistry 42(35);10537-44. PMID: 12950181
Yu08: Yu Z, Koningstein G, Pop A, Luirink J (2008). "The conserved third transmembrane segment of YidC contacts nascent Escherichia coli inner membrane proteins." J Biol Chem 283(50):34635-42. PMID: 18840604
Yuan07: Yuan J, Phillips GJ, Dalbey RE (2007). "Isolation of cold-sensitive yidC mutants provides insights into the substrate profile of the YidC insertase and the importance of transmembrane 3 in YidC function." J Bacteriol 189(24);8961-72. PMID: 17933892
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
Zhu12a: Zhu L, Klenner C, Kuhn A, Dalbey RE (2012). "Both YidC and SecYEG are required for translocation of the periplasmic loops 1 and 2 of the multispanning membrane protein TatC." J Mol Biol 424(5);354-67. PMID: 23058713
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