title: In situ structural analysis of the Yersinia enterocolitica injectisome.
abstract: Injectisomes are multi-protein transmembrane machines allowing pathogenic bacteria to inject effector proteins into eukaryotic host cells, a process called type III secretion. Here we present the first three-dimensional structure of Yersinia enterocolitica and Shigella flexneri injectisomes in situ and the first structural analysis of the Yersinia injectisome. Unexpectedly, basal bodies of injectisomes inside the bacterial cells showed length variations of 20%. The in situ structures of the Y. enterocolitica and S. flexneri injectisomes had similar dimensions and were significantly longer than the isolated structures of related injectisomes. The crystal structure of the inner membrane injectisome component YscD appeared elongated compared to a homologous protein, and molecular dynamics simulations documented its elongation elasticity. The ring-shaped secretin YscC at the outer membrane was stretched by 30-40% in situ, compared to its isolated liposome-embedded conformation. We suggest that elasticity is critical for some two-membrane spanning protein complexes to cope with variations in the intermembrane distance. DOI:http://dx.doi.org/10.7554/eLife.00792.001.
authors.affiliation: Center for Cellular Imaging and NanoAnalytics (C-CINA) , Biozentrum, University of Basel , Basel , Switzerland.
authors.forename: Mikhail
authors.initials: M
authors.lastname: Kudryashev
authors.forename: Marco
authors.initials: M
authors.lastname: Stenta
authors.forename: Stefan
authors.initials: S
authors.lastname: Schmelz
authors.forename: Marlise
authors.initials: M
authors.lastname: Amstutz
authors.forename: Ulrich
authors.initials: U
authors.lastname: Wiesand
authors.forename: Daniel
authors.initials: D
authors.lastname: Castaño-Díez
authors.forename: Matteo T
authors.initials: MT
authors.lastname: Degiacomi
authors.forename: Stefan
authors.initials: S
authors.lastname: Münnich
authors.forename: Christopher Ke
authors.initials: CK
authors.lastname: Bleck
authors.forename: Julia
authors.initials: J
authors.lastname: Kowal
authors.forename: Andreas
authors.initials: A
authors.lastname: Diepold
authors.forename: Dirk W
authors.initials: DW
authors.lastname: Heinz
authors.forename: Matteo
authors.initials: M
authors.lastname: Dal Peraro
authors.forename: Guy R
authors.initials: GR
authors.lastname: Cornelis
authors.forename: Henning
authors.initials: H
authors.lastname: Stahlberg
mesh_terms: D020285:Cryoelectron Microscopy; D008565:Membrane Proteins / Q000737:chemistry / Q000378:metabolism*; D009997:Osmotic Pressure; D011487:Protein Conformation; D015008:Yersinia enterocolitica / Q000378:metabolism*
chemical_list: D008565:Membrane Proteins
keywords: Yersinia enterocolitica; cryo-electron tomography; injectisome; molecular dynamics; other; type III secretion system; x-ray crystallography
references.citation: EMBO J. 2010 Jun 2;29(11):1928-40
references.pmid: 20453832
references.citation: Science. 2004 Nov 5;306(5698):1040-2
references.pmid: 15528446
references.citation: Mol Microbiol. 2005 Mar;55(6):1658-70
references.pmid: 15752191
references.citation: Nature. 2006 Nov 30;444(7119):567-73
references.pmid: 17136086
references.citation: Bioinformatics. 2006 Nov 1;22(21):2619-27
references.pmid: 16928735
references.citation: Nature. 2012 Feb 26;483(7388):182-6
references.pmid: 22367545
references.citation: Proc Natl Acad Sci U S A. 2000 Sep 26;97(20):11008-13
references.pmid: 10984518
references.citation: Annu Rev Biophys. 2011;40:289-313
references.pmid: 21351880
references.citation: PLoS One. 2011;6(5):e19716
references.pmid: 21611119
references.citation: Nature. 2007 Oct 4;449(7162):611-5
references.pmid: 17851530
references.citation: Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 1):2256-68
references.pmid: 15572779
references.citation: Acta Crystallogr D Biol Crystallogr. 1994 Sep 1;50(Pt 5):760-3
references.pmid: 15299374
references.citation: Nat Methods. 2012 Sep;9(9):853-4
references.pmid: 22842542
references.citation: J Bacteriol. 2009 Aug;191(16):5026-36
references.pmid: 19429612
references.citation: Proc Natl Acad Sci U S A. 2012 Jan 31;109(5):1380-7
references.pmid: 22307589
references.citation: Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W368-71
references.pmid: 15980491
references.citation: Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 1):2288-94
references.pmid: 15572783
references.citation: J Bacteriol. 2004 Jul;186(14):4645-54
references.pmid: 15231798
references.citation: Proc Natl Acad Sci U S A. 1995 Dec 19;92(26):11998-2002
references.pmid: 8618831
references.citation: Methods Enzymol. 2003;374:229-44
references.pmid: 14696376
references.citation: mBio. 2010 Aug 03;1(3):
references.pmid: 20824104
references.citation: J Bacteriol. 1995 Aug;177(15):4230-7
references.pmid: 7635810
references.citation: Curr Opin Microbiol. 2011 Feb;14(1):3-8
references.pmid: 21112241
references.citation: J Mol Graph. 1996 Feb;14(1):33-8, 27-8
references.pmid: 8744570
references.citation: J Comput Chem. 2004 Aug;25(11):1400-15
references.pmid: 15185334
references.citation: Nature. 2012 May 20;486(7402):276-9
references.pmid: 22699623
references.citation: Science. 2011 Mar 4;331(6021):1192-5
references.pmid: 21385715
references.citation: Nat Rev Microbiol. 2006 Nov;4(11):811-25
references.pmid: 17041629
references.citation: Annu Rev Biophys. 2010;39:23-42
references.pmid: 20192781
references.citation: Nature. 2007 Nov 29;450(7170):695-701
references.pmid: 18046406
references.citation: Acta Crystallogr D Biol Crystallogr. 1997 May 1;53(Pt 3):240-55
references.pmid: 15299926
references.citation: Rev Infect Dis. 1991 Mar-Apr;13 Suppl 4:S285-92
references.pmid: 2047651
references.citation: J Biol Chem. 2006 Jan 6;281(1):599-607
references.pmid: 16246841
references.citation: Mol Biosyst. 2008 Nov;4(11):1105-15
references.pmid: 18931786
references.citation: Proc Natl Acad Sci U S A. 2012 Mar 20;109(12):4461-6
references.pmid: 22388746
references.citation: Nat Struct Mol Biol. 2009 May;16(5):477-85
references.pmid: 19396171
references.citation: FASEB J. 2013 Jul;27(7):2862-72
references.pmid: 23515444
references.citation: Structure. 2013 Jul 2;21(7):1097-1106
references.pmid: 23810695
references.citation: Proteins. 1993 Dec;17(4):412-25
references.pmid: 8108382
references.citation: J Comput Chem. 2005 Dec;26(16):1781-802
references.pmid: 16222654
references.citation: Nat Chem Biol. 2013 Oct;9(10):623-9
references.pmid: 23912165
references.citation: J Phys Chem B. 1998 Apr 30;102(18):3586-616
references.pmid: 24889800
references.citation: J Struct Biol. 2012 May;178(2):88-97
references.pmid: 22056466
references.citation: Bioinformatics. 2011 Jun 1;27(11):1575-7
references.pmid: 21471012
references.citation: Acta Crystallogr D Biol Crystallogr. 2010 Jun;66(Pt 6):709-13
references.pmid: 20516623
references.citation: Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):133-44
references.pmid: 20124693
references.citation: Nat Struct Mol Biol. 2013 Jan;20(1):99-104
references.pmid: 23222644
references.citation: J Struct Biol. 2005 Sep;151(3):250-62
references.pmid: 16125414
references.citation: Arch Virol. 2006 Mar;151(3):563-79
references.pmid: 16172841
references.citation: J Struct Biol. 2012 Nov;180(2):318-26
references.pmid: 22796867
references.citation: Methods Enzymol. 2003;374:461-91
references.pmid: 14696385
references.citation: Microb Pathog. 1987 May;2(5):367-79
references.pmid: 3507556
references.citation: Biophys J. 2011 Feb 16;100(4):L22-4
references.pmid: 21320420
references.citation: Chem Rev. 2010 Mar 10;110(3):1463-97
references.pmid: 19785456
references.citation: J Struct Biol. 2010 Jan;169(1):54-61
references.pmid: 19699799
references.citation: Nano Lett. 2011 Oct 12;11(10):4319-23
references.pmid: 21910506
references.citation: PLoS Pathog. 2010 Apr 01;6(4):e1000824
references.pmid: 20368966
references.citation: Comput Struct Biotechnol J. 2012 Jul 01;1:e201207002
references.pmid: 24688638
references.citation: Crit Rev Microbiol. 1998;24(1):23-59
references.pmid: 9561823
references.citation: Physiology (Bethesda). 2005 Oct;20:326-39
references.pmid: 16174872
references.citation: Acta Crystallogr D Biol Crystallogr. 2009 Oct;65(Pt 10):1089-97
references.pmid: 19770506
references.citation: Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):125-32
references.pmid: 20124692
references.citation: J Microsc. 2010 Jan;237(1):23-38
references.pmid: 20055916
references.citation: EMBO J. 2011 Jun 14;30(14):2972-81
references.pmid: 21673657
references.citation: Nat Struct Mol Biol. 2009 May;16(5):468-76
references.pmid: 19396170
references.citation: Acta Crystallogr D Biol Crystallogr. 2000 Feb;56(Pt 2):232-7
references.pmid: 10666615
references.citation: Acta Crystallogr D Biol Crystallogr. 2012 Mar;68(Pt 3):201-9
references.pmid: 22349221
references.citation: Virology. 2011 Sep 1;417(2):304-11
references.pmid: 21745674
references.citation: FEMS Microbiol Rev. 2005 Apr;29(2):201-29
references.pmid: 15808742
references.citation: J Struct Biol. 2012 May;178(2):139-51
references.pmid: 22245546
references.citation: Protein Sci. 2000 Sep;9(9):1753-73
references.pmid: 11045621
references.citation: J Mol Biol. 1995 Apr 28;248(2):273-93
references.pmid: 7739040
references.citation: Nature. 2005 Jun 2;435(7042):702-7
references.pmid: 15931226
references.citation: Proc Natl Acad Sci U S A. 2005 Mar 29;102(13):4729-34
references.pmid: 15774580
references.citation: J Appl Crystallogr. 2007 Aug 1;40(Pt 4):658-674
references.pmid: 19461840
references.citation: Microbiology (Reading). 2008 Feb;154(Pt 2):593-607
references.pmid: 18227263
references.citation: Cold Spring Harb Perspect Biol. 2010 Nov;2(11):a000299
references.pmid: 20926516
references.citation: Gene. 1991 Dec 20;109(1):137-41
references.pmid: 1756974
references.citation: J Bacteriol. 2011 May;193(9):2276-89
references.pmid: 21357482
references.citation: J Struct Biol. 1996 Jan-Feb;116(1):71-6
references.pmid: 8742726