Fadel A. Samatey Group

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サマテイ研 (日本語) Fadel A. Samatey Group (Japanese)
 Image:Flagellar hook em density 1ucu.jpg
Crystal structure of flagellar hook fitted into electron density map obtained by electron cryomicroscopy[1].

Fadel A. Samatey is Head of the Transmembrane Trafficking Unit at the Okinawa Institute of Science and Technology (OIST) (Japan). Samatey's group uses X-ray crystallography, genetic and biochemical approaches to elucidate the structures and functions of transmembrane proteins, especially type III secretion proteins in bacterial flagella.

Below are listed contributions from the Samatey Group, most recent first. This page was updated in May, 2014.

Contents

Interests and Objectives

Motility is a very important function in the living world. For this purpose, organisms such as bacteria have developed the most incredible molecular machine: the flagellar system. Bacteria such as Escherichia coli and Salmonella typhimurium swim by rotating long helical filaments called the flagellum. The flagellum is a complex structure made by the association of many different proteins. It can be divided into three parts: 1) the filament: a long, rigid, tubular structure that works as a helical propeller, 2) the hook: a short, highly flexible tubular segment that works as a universal joint, and 3) the basal body: a rotary motor embedded in the cell membrane.

During the assembly of the flagellum, all the flagellar axial proteins are exported from the cytoplasm to the flagellum distal end through a 2 -3 nm channel located at its centre. This export mechanism is regulated by a specialized protein export system located on the cytoplasmic side of the basal body. It is called the Type III Export Apparatus and is found throughout the bacterial kingdom. In the case of Salmonella, this export apparatus is made by six membrane proteins: FlhA, FlhB, FliO, FliP, FliQ, FliR, and three cytoplasmic proteins: FliI, FliH and FliJ. The export apparatus of the bacterial flagellum is homolog to the type III secretion system (T3SS) found in Gram-negative pathogenic bacteria. The T3SS role is to secrete virulence factors to host cells, leading to diverse diseases. To understand both the bacterial flagellum and its export apparatus, we have been doing structural studies on some flagellar proteins and genetic studies on the export apparatus.

Contact: f.a.samatey at oist jp

Contributions from OIST

Samatey joined OIST in 2007.

  • Barker CS, Meshcheryakova IV, Sasaki T, Roy MC, Sinha PK, Yagi T, Samatey FA. Randomly selected suppressor mutations in genes for NADH:quinone oxidoreductase-1, which rescue motility of a Salmonella ubiquinone-biosynthesis mutant strain. Microbiology. 2014 Apr 1. doi: 10.1099/mic.0.075945-0. PMID:24692644 doi:http://dx.doi.org/10.1099/mic.0.075945-0
This study showed amino acid substitutions at or near to the surface of NADH:quinone oxidoreductase-1 (NDH-1) increased growth, motility and flagellar biogenesis of mutant strains unable to synthesize the aerobic respiratory chain electron carrier ubiquinone. Therefore, NDH-1 activity in Salmonella is important for flagellar biogenesis.


 Image:3b0z-rotating.gif
FlhBc of Salmonella (3b0z). Small surface is loop 281-285. See it in interactive 3D.
  • Meshcheryakov VA, Barker CS, Kostyukova AS, Samatey FA. Function of FlhB, a membrane protein implicated in the bacterial flagellar type III secretion system. PLoS One. 2013 Jul 11;8(7):e68384. doi: 10.1371/journal.pone.0068384. Print 2013. PMID:23874605 doi:http://dx.doi.org/10.1371/journal.pone.0068384
Replacing the FlhB gene (see below) in Salmonella with that of Aquifex reduced motility. Mutations that restore motility appear to increase conformational flexibility of FlhB, providing further support for the hypothesis that such flexibility is crucial to its function.


  • Meshcheryakov VA, Kitao A, Matsunami H, Samatey FA. Inhibition of a type III secretion system by the deletion of a short loop in one of its membrane proteins. Acta Crystallogr D Biol Crystallogr. 2013 May;69(Pt 5):812-20. doi:, 10.1107/S0907444913002102. Epub 2013 Apr 11. PMID:23633590 doi:10.1107/S0907444913002102
Reports the atomic structure of the cytoplasmic domain of FlhB, a highly-conserved part of the secretion apparatus crucial to the assembly of bacterial flagella. The Salmonella typhimurium and Aquifex aeolicus structures are similar, while sequence identity is 32%. Deletion of a surface loop (281-285) that is not conserved inhibits function. This loop appears to promote crucial flexibility. See results in interactive 3D.


Salmonella that synthesized a recombinant FlhB protein, made of the transmembrane region of Aquifex FlhB fused to the cytoplasmic domain of Salmonella FlhB, produced very few flagella. Suppressor mutations reducing the synthesis of ubiquinone for the respiratory chain or in the flhA gene increased flagella numbers, demonstrating a genetic interaction between FlhB and respiratory chain activity, and FlhB and FlhA.


  • Matsunami H, Samatey FA, Nagashima S, Imada K, Namba K. Crystallization and preliminary X-ray analysis of FlgA, a periplasmic protein essential for flagellar P-ring assembly. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2012 Mar 1;68(Pt 3):310-3. Epub, 2012 Feb 23. PMID:22442230 doi:10.1107/S1744309112001327


 
Crystals of the flagellar hook protein FlgE from C. jejuni produced in the Samatey lab[2].
  • Kido Y, Yoon YH, Samatey FA. Crystallization of a 79 kDa fragment of the hook protein FlgE from Campylobacter jejuni. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2011 Dec 1;67(Pt, 12):1653-7. Epub 2011 Nov 30. PMID:22139190 doi:10.1107/S1744309111043272


 Image:3azd-rotating.gif
Coiled-coil of N-termini of chimeric non-muscle tropomyosin (3azd).
  • Meshcheryakov VA, Krieger I, Kostyukova AS, Samatey FA. Structure of a tropomyosin N-terminal fragment at 0.98 A resolution. Acta Crystallogr D Biol Crystallogr. 2011 Sep;67(Pt 9):822-5. Epub 2011, Aug 9. PMID:21904035 doi:10.1107/S090744491102645X
A high resolution atomic model of a chimeric (rat + yeast) N-terminal fragment of non-muscle tropomyosin confirms prior NMR results, but gives more accurate side-chain positions in the coiled-coil dimer.


  • Meshcheryakov VA, Samatey FA. Purification, crystallization and preliminary X-ray crystallographic analysis of the C-terminal cytoplasmic domain of FlhB from Salmonella typhimurium. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2011 Jul 1;67(Pt, 7):808-11. Epub 2011 Jun 30. PMID:21795800 doi:10.1107/S1744309111018938


  • Meshcheryakov VA, Yoon YH, Samatey FA. Purification, crystallization and preliminary X-ray crystallographic analysis of the C-terminal cytoplasmic domain of FlhB from Aquifex aeolicus. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2011 Feb 1;67(Pt, 2):280-2. Epub 2011 Jan 27. PMID:21301106 doi:10.1107/S1744309110052942


  • Barker CS, Meshcheryakova IV, Kostyukova AS, Samatey FA. FliO regulation of FliP in the formation of the Salmonella enterica flagellum. PLoS Genet. 2010 Sep 30;6(9). pii: e1001143. PMID:20941389 doi:10.1371/journal.pgen.1001143
The membrane topology of FliO was determined and it has a small cytoplasmic domain whose overexpression partially bypassed the function of full-length FliO. Also, a fliO deletion mutant strain was almost non-motile, but motility was somewhat rescued by suppressor mutations in the fliP gene suggesting that FliO and FliP interact.

Samatey Contributions Prior to OIST

Before joining OIST, from 1996-2007 Samatey was a member of the Keiichi Namba Group, from 1996 at Matsushita Electric, from 1997 in the ERATO Protonic Nanomachine Project, and from 2002 at Osaka University, Japan. Samatey earned his Ph.D. in 1992 at Université Joseph Fourier in Grenoble, France.


 Image:Flagellar hook 3.gif
Simplified model of the rotating bacterial flagellar hook.
  • Furuta T, Samatey FA, Matsunami H, Imada K, Namba K, Kitao A. Gap compression/extension mechanism of bacterial flagellar hook as the molecular universal joint. J Struct Biol. 2007 Mar;157(3):481-90. Epub 2006 Oct 20. PMID:17142059 doi:10.1016/j.jsb.2006.10.006
Analyses the mechanism by which monomers of the flagellar hook slide against each other during hook rotation, to permit bending while transmitting torque.


  • Kitao A, Yonekura K, Maki-Yonekura S, Samatey FA, Imada K, Namba K, Go N. Switch interactions control energy frustration and multiple flagellar filament structures. Proc Natl Acad Sci U S A. 2006 Mar 28;103(13):4894-9. Epub 2006 Mar 20. PMID:16549789 doi:10.1073/pnas.0510285103
Describes a massive molecular dynamics simulation that successfully accounts for polymorphic supercoiling in the bacterial flagellar filament. Interactions between protein monomer chains are dissected into permanent, sliding, and switch categories.


  • Shaikh TR, Thomas DR, Chen JZ, Samatey FA, Matsunami H, Imada K, Namba K, Derosier DJ. A partial atomic structure for the flagellar hook of Salmonella typhimurium. Proc Natl Acad Sci U S A. 2005 Jan 25;102(4):1023-8. Epub 2005 Jan 18. PMID:15657146
Free Full Text


 Image:Samatey hook copyright nature 2004.gif
Bacterial flagellar hook, a molecular universal joint.
  • Samatey FA, Matsunami H, Imada K, Nagashima S, Shaikh TR, Thomas DR, Chen JZ, Derosier DJ, Kitao A, Namba K. Structure of the bacterial flagellar hook and implication for the molecular universal joint mechanism. Nature. 2004 Oct 28;431(7012):1062-8. PMID:15510139 doi:http://dx.doi.org/10.1038/nature02997
Reports the first structure of a major fragment of the protein monomer that assembles into the bacterial flagellar hook (1wlg, 1.8 Å resolution). Fits the monomer into an electron cryomicroscopic density map, resulting in straight and curved models of the hook, including a rotating model.


  • Samatey FA, Matsunami H, Imada K, Nagashima S, Namba K. Crystallization of a core fragment of the flagellar hook protein FlgE. Acta Crystallogr D Biol Crystallogr. 2004 Nov;60(Pt 11):2078-80. Epub 2004, Oct 20. PMID:15502333 doi:10.1107/S0907444904022735


 Image:1io1-rotating.gif
Monomer of the Salmonella flagellar filament, 1io1.
  • Samatey FA, Imada K, Nagashima S, Vonderviszt F, Kumasaka T, Yamamoto M, Namba K. Structure of the bacterial flagellar protofilament and implications for a switch for supercoiling. Nature. 2001 Mar 15;410(6826):331-7. PMID:11268201 doi:10.1038/35066504
Reports, for the first time, the atomic structure of a major fragment of the protein chain monomer that assembles into the bacterial flagellar filament (1io1, 2.0 Å resolution). The crystal contained chains of monomers, which revealed how the monomer protein chains fit together into protofilaments. Theoretical simulation revealed a possible mechanism for how the filament reverses direction, a mechanism crucial to how bacteria swim towards food or away from harm by reversing the flagellar motor.


  • Samatey FA, Imada K, Vonderviszt F, Shirakihara Y, Namba K. Crystallization of the F41 fragment of flagellin and data collection from extremely thin crystals. J Struct Biol. 2000 Nov;132(2):106-11. PMID:11162732 doi:10.1006/jsbi.2000.4312


1990's

  • Samatey FA, Xu C, Popot JL. On the distribution of amino acid residues in transmembrane alpha-helix bundles. Proc Natl Acad Sci U S A. 1995 May 9;92(10):4577-81. PMID:7753846
  • Claros MG, Perea J, Shu Y, Samatey FA, Popot JL, Jacq C. Limitations to in vivo import of hydrophobic proteins into yeast mitochondria. The case of a cytoplasmically synthesized apocytochrome b. Eur J Biochem. 1995 Mar 15;228(3):762-71. PMID:7737175
  • Lazzaroni JC, Vianney A, Popot JL, Benedetti H, Samatey F, Lazdunski C, Portalier R, Geli V. Transmembrane alpha-helix interactions are required for the functional assembly of the Escherichia coli Tol complex. J Mol Biol. 1995 Feb 10;246(1):1-7. PMID:7853390 doi:http://dx.doi.org/10.1006/jmbi.1994.0058
  • Samatey FA, Zaccai G, Engelman DM, Etchebest C, Popot JL. Rotational orientation of transmembrane alpha-helices in bacteriorhodopsin. A neutron diffraction study. J Mol Biol. 1994 Mar 4;236(4):1093-104. PMID:8120889

See Also

References


  1. Samatey FA, Matsunami H, Imada K, Nagashima S, Shaikh TR, Thomas DR, Chen JZ, Derosier DJ, Kitao A, Namba K. Structure of the bacterial flagellar hook and implication for the molecular universal joint mechanism. Nature. 2004 Oct 28;431(7012):1062-8. PMID:15510139 doi:http://dx.doi.org/10.1038/nature02997
  2. Kido Y, Yoon YH, Samatey FA. Crystallization of a 79 kDa fragment of the hook protein FlgE from Campylobacter jejuni. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2011 Dec 1;67(Pt, 12):1653-7. Epub 2011 Nov 30. PMID:22139190 doi:10.1107/S1744309111043272

Animation Credits
Animation of the full backbone trace of the flagellar hook is by Fadel Samatey. The simplified flagellar hook animation is by Eric Martz using RasMol. Animations of 3b0z, 3azd, and 1io1 were generated by Eric Martz using Alexey Porollo's Polyview-3D server, which makes its output in PyMOL.

Proteopedia Page Contributors and Editors (what is this?)

Eric Martz, Fadel A. Samatey

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