Fadel A. Samatey Group: Difference between revisions
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:[[Fadel_A._Samatey_Group_%28Japanese%29|サマテイ研 (日本語) Fadel A. Samatey Group (Japanese)]][[ja:Fadel A. Samatey Group (Japanese)]] | :[[Fadel_A._Samatey_Group_%28Japanese%29|サマテイ研 (日本語) Fadel A. Samatey Group (Japanese)]][[ja:Fadel A. Samatey Group (Japanese)]] | ||
<table align="right" width="260" ><tr><td rowspan="2"> </td><td>[[Image:Flagellar hook em density 1ucu.jpg]]</td></tr><tr><td><font color="#00908c">Crystal structure of flagellar hook</font> fitted into <font color="magenta">electron density map</font> obtained by electron | <table align="right" width="260" ><tr><td rowspan="2"> </td><td>[[Image:Flagellar hook em density 1ucu.jpg]]</td></tr><tr><td><font color="#00908c">Crystal structure of flagellar hook</font> fitted into <font color="magenta">electron density map</font> obtained by cryo-electron microscopy<ref name="hook1">PMID:15510139</ref>.</td></tr></table> | ||
[[User:Fadel A. Samatey|Fadel A. Samatey]] | [[User:Fadel A. Samatey|Fadel A. Samatey]] was Head of the Transmembrane Trafficking Unit at the [http://www.oist.jp Okinawa Institute of Science and Technology (OIST)] (Japan), 2007-2016. Samatey's group uses [[X-ray crystallography]], cryo-Electron microscopy, genetic, and biochemical approaches to elucidate the structures and functions of proteins, especially type III secretion proteins in [[Flagella, bacterial|bacterial flagella]]. | ||
From 1996-2007 Samatey was a member of the Keiichi Namba Group, from 1996 at Matsushita Electric, from 1997 in the [http://www.fbs.osaka-u.ac.jp/labs/namba/npn/index.html ERATO Protonic Nanomachine Project], and from 2002 at [http://www.fbs.osaka-u.ac.jp/eng/labo/09a.html Osaka University], Japan. Samatey earned his Ph.D. in 1992 at [http://www.ujf-grenoble.fr/ Université Joseph Fourier] in Grenoble, France. | |||
[[#Contributions from OIST|Below]] are listed contributions from the Samatey Group, most recent first. | [[#Contributions from OIST|Below]] are listed contributions from the Samatey Group, most recent first. | ||
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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. | 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: | '''Contact: fadel.samatey at gmail.com''' | ||
==Contributions from 2011 to Present== | |||
<ref group="xtra">PMID: 29147015</ref><references group="xtra" /> | |||
<ref group="xtra">PMID: 29105867</ref><references group="xtra" /> | |||
<ref group="xtra">PMID: 29078764</ref><references group="xtra" /> | |||
:<table style="background: #d0ffd0;padding: 6px;"><tr><td>The “ID-Rod-Stretch” is an intrinsically disordered linker found in both FlgE and FlgG, the proteins that respectively make the hook and the distal rod of the bacterial flagellum. Experiments done in FlgE of ''Salmonella enterica'' and of ''Campylobacter jejuni'' reveal the role of the ID-Rod-Stretch in the formation and stability of the flagellar hook. [https://www.youtube.com/watch?v=ZUAdpWCQD_0 See the special video abstract.] [[User:Fadel A. Samatey/FlgE III/Intrinsically Disordered Flagellar Rod Stretch| See results in interactive 3D]]. </td></tr></table> | |||
<ref group="xtra">PMID: 27811912</ref><references group="xtra" /> | |||
:<table style="background: #d0ffd0;padding: 6px;"><tr><td>The bacterial flagellar hook, which is made by the polymerization of multiple copies of FlgE protein, is a flexible segment connecting the flagellar filament to the motor. The structure presented in this article puts in evidence the complex web of interactions between FlgE molecules. These interactions stabilize the flagellar hook during its function as a universal joint.[[User:Fadel A. Samatey/FlgE II/Complete Flagellar Hook Structure| See results in interactive 3D]]. </td></tr></table> | |||
<ref group="xtra">PMID: 27759043</ref><references group="xtra" /> | |||
:<table style="background: #d0ffd0;padding: 6px;"><tr><td>The assembly of about a hundred molecules of FlgE protein makes the bacterial flagellar hook. FlgE has a high variability in amino acid residues composition and in molecular weight. Our study shows that FlgE can be divided in two distinct parts. The first part comprises domains that are found in all FlgE proteins and will make the basic structure of the hook common to all flagellated bacteria. The second part, hyper-variable both in size and structure, will be bacteria dependent and will give to the hook additional and specific properties to the bacterium its belong to.[[User:Fadel A. Samatey/FlgE I| See results in interactive 3D]]. </td></tr></table> | |||
<table align="right" width="240" ><tr><td rowspan="2"> </td><td>[[Image:Samatey-FlgA-Align02a-321px-sh.gif]]</td></tr><tr><td> Superposition of the different domains of the open and closed forms of FlgA. See it in [[User:Fadel_A._Samatey/FlgA_I|interactive 3D]].</td></tr></table> | |||
<ref group="xtra">PMID: 27273476</ref><references group="xtra" /> | |||
:<table style="background: #d0ffd0;padding: 6px;"><tr><td>The bacterial flagellar P-ring is located in the periplasm and is important for the externalization of the bacterial flagellum in Gram-negative bacteria. FlgA is a protein that regulates the assembly of the P-ring. Deletion of ''flgA'' gene leads to non-flagellated cells. This study showed that it is possible, by reducing the flexibility of FlgA, to block the formation of the flagellum.[[User:Fadel_A._Samatey/FlgA_I| See results in interactive 3D]]. </td></tr></table> | |||
== | <ref group="xtra">PMID: 26691662</ref><references group="xtra" /> | ||
:<table style="background: #d0ffd0;padding: 6px;"><tr><td>FlhA is the largest membrane protein of the Type III export apparatus and is homologous to the large family of FHIPEP export proteins. FHIPEP proteins contain a highly-conserved cytoplasmic domain. This study suggested that the FHIPEP region of FlhA is part of the gate regulating substrate entry into the export apparatus pore.</td></tr></table> | |||
<ref group="xtra">PMID: 25201947</ref><references group="xtra" /> | |||
:<table style="background: #d0ffd0;padding: 6px;"><tr><td>Deletion of the fliO gene creates a mutant strain that is poorly motile; however, suppressor mutations in the fliP gene can partially rescue motility. Here we found a missense mutation that localized to the clpP gene, which encodes the ClpP subunit of the ClpXP protease, and a synonymous mutation that localized to the fliA gene, which encodes the flagellar sigma factor, σ(28) also could partially rescue motility of fliO mutant strains. Combining these suppressor mutations with mutations in the fliP gene fully rescued flagellar biosynthesis and motility for fliO deletion mutant strains. The suppressor mutations in the fliP gene had the greatest effect. This suggests that the function of FliO is closely associated with regulation of FliP during assembly of the flagellum.</td></tr></table> | |||
<ref group="xtra">PMID: 25195895 </ref><references group="xtra" /> | |||
<ref group="xtra">PMID: 24692644</ref><references group="xtra" /> | |||
:<table style="background: #d0ffd0;padding: 6px;"><tr><td>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.</td></tr></table> | |||
<ref group="xtra">PMID: 24415724 </ref><references group="xtra" /> | |||
<ref group="xtra">PMID: 24209861 </ref><references group="xtra" /> | |||
<table align="right" width="240" ><tr><td rowspan="2"> </td><td>[[Image:3b0z-rotating.gif]]</td></tr><tr><td>FlhBc of ''Salmonella'' ([[3b0z]]). Small surface is <font color="magenta">loop 281-285</font>. See it in [[User:Fadel A. Samatey/FlhBc I|interactive 3D]].</td></tr></table> | |||
<ref group="xtra">PMID: 23874605</ref><references group="xtra" /> | |||
:<table style="background: #d0ffd0;padding: 6px;"><tr><td>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.</td></tr></table> | |||
<ref group="xtra">PMID: 23633590</ref><references group="xtra" /> | |||
:<table style="background: #d0ffd0;padding: 6px;"><tr><td>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. [[User:Fadel_A._Samatey/FlhBc_I|See results in interactive 3D]]. </td></tr></table> | |||
<ref group="xtra">PMID: 22952860</ref><references group="xtra" /> | |||
:<table style="background: #d0ffd0;padding: 6px;"><tr><td>''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.</td></tr></table> | |||
<ref group="xtra">PMID: 22442230</ref><references group="xtra" /> | |||
<table width="200" align="right"><tr><td>[[Image:Protein crystals samatey.png|200px]]</td><td> </td></tr><tr><td>Crystals of the [[Flagellar hook of bacteria|flagellar hook protein]] FlgE from ''C. jejuni'' produced in the Samatey lab<ref>PMID:22139190</ref>.</td></tr></table> | |||
<ref group="xtra">PMID: 22139190</ref><references group="xtra" /> | <ref group="xtra">PMID: 22139190</ref><references group="xtra" /> | ||
<table align="right" width="240" ><tr><td rowspan="2"> </td><td>[[Image:3azd-rotating.gif]]</td></tr><tr><td>Coiled-coil of N-termini of chimeric non-muscle tropomyosin ([[3azd]]).</td></tr></table> | |||
<ref group="xtra">PMID: 21904035</ref><references group="xtra" /> | <ref group="xtra">PMID: 21904035</ref><references group="xtra" /> | ||
:<table style="background: #d0ffd0;padding: 6px;"><tr><td>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.</td></tr></table> | |||
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<ref group="xtra">PMID: 21301106</ref><references group="xtra" /> | <ref group="xtra">PMID: 21301106</ref><references group="xtra" /> | ||
==Contributions from 2001 to 2010== | |||
<ref group="xtra">PMID: 20941389</ref><references group="xtra" /> | <ref group="xtra">PMID: 20941389</ref><references group="xtra" /> | ||
:<table style="background: #fff0d0;padding: 6px;"><tr><td>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.</td></tr></table> | |||
<!-- 1994-6, not yet with Namba [http://pfwww.kek.jp/ Photon Factory] in Tsukuba, Japan --> | <!-- 1994-6, not yet with Namba [http://pfwww.kek.jp/ Photon Factory] in Tsukuba, Japan --> | ||
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<ref group="xtra">PMID: 17142059</ref><references group="xtra" /> | <ref group="xtra">PMID: 17142059</ref><references group="xtra" /> | ||
:<table style="background: # | :<table style="background: #fff0d0;padding: 6px;"><tr><td>Analyses the mechanism by which monomers of the '''[[Flagellar hook of bacteria|flagellar hook]]''' slide against each other during hook rotation, to permit bending while transmitting torque.</td></tr></table> | ||
<ref group="xtra">PMID: 16549789</ref><references group="xtra" /> | <ref group="xtra">PMID: 16549789</ref><references group="xtra" /> | ||
:<table style="background: # | :<table style="background: #fff0d0;padding: 6px;"><tr><td>Describes a massive molecular dynamics simulation that successfully accounts for polymorphic supercoiling in the '''[[Flagellar filament of bacteria|bacterial flagellar filament]]'''. Interactions between protein monomer chains are dissected into ''permanent'', ''sliding'', and ''switch'' categories.</td></tr></table> | ||
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<table align="right" width="200" ><tr><td rowspan="2"> </td><td>[[Image:Samatey hook copyright nature 2004.gif]]</td></tr><tr><td> [[Flagellar hook of bacteria|Bacterial flagellar hook]].</td></tr></table> | <table align="right" width="200" ><tr><td rowspan="2"> </td><td>[[Image:Samatey hook copyright nature 2004.gif]]</td></tr><tr><td> [[Flagellar hook of bacteria|Bacterial flagellar hook]], a molecular [http://en.wikipedia.org/wiki/Universal_joint universal joint].</td></tr></table> | ||
<Structure size='200' frame='true' align='right' caption='[[Flagellar hook of bacteria|Flagellar hook]] monomer, [[1wlg]].' scene='User:Eric_Martz/Workbench/Samatey_Group/1wlg_monomer/1' /> | <!--<Structure size='200' frame='true' align='right' caption='[[Flagellar hook of bacteria|Flagellar hook]] monomer, [[1wlg]].' scene='User:Eric_Martz/Workbench/Samatey_Group/1wlg_monomer/1' />--> | ||
<ref group="xtra">PMID: 15510139</ref><references group="xtra" /> | <ref group="xtra">PMID: 15510139</ref><references group="xtra" /> | ||
:<table style="background: # | :<table style="background: #fff0d0;padding: 6px;"><tr><td>Reports the first structure of a major fragment of the protein monomer that assembles into the '''[[Flagellar hook of bacteria|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.</td></tr></table> | ||
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<Structure size='200' frame='true' align='right' caption='[[Flagellar filament of bacteria|Flagellar filament]] monomer, [[1io1]].' scene='User:Eric_Martz/Workbench/Samatey_Group/Flag_fil_monomer/1' /> | <!--<Structure size='200' frame='true' align='right' caption='[[Flagellar filament of bacteria|Flagellar filament]] monomer, [[1io1]].' scene='User:Eric_Martz/Workbench/Samatey_Group/Flag_fil_monomer/1' />--> | ||
{{Clear}} | |||
<table align="right" width="250" ><tr><td rowspan="2"> </td><td>[[Image:1io1-rotating.gif]]</td></tr><tr><td>Monomer of the ''Salmonella'' [[Flagella, bacterial|flagellar]] filament, [[1io1]].</td></tr></table> | |||
<ref group="xtra">PMID: 11268201</ref><references group="xtra" /> | <ref group="xtra">PMID: 11268201</ref><references group="xtra" /> | ||
:<table style="background: # | :<table style="background: #fff0d0;padding: 6px;"><tr><td>Reports, for the first time, the atomic structure of a major fragment of the protein chain monomer that assembles into the '''[[Flagellar filament of bacteria|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.</td></tr></table> | ||
< | <!--<center><table width="450"><tr><td>[[Image:Protein crystals samatey.png]]</td><td> </td><td>Crystals of the [[Flagellar hook of bacteria|flagellar hook protein]] FlgE from ''C. jejuni'' produced in the Samatey lab<ref>PMID:22139190</ref>.</td></tr></table></center>--> | ||
==Contributions from 1990 to 2000== | |||
< | <ref group="xtra">PMID: 11162732</ref><references group="xtra" /> | ||
<ref group="xtra">PMID: 7753846</ref><references group="xtra" /> | <ref group="xtra">PMID: 7753846</ref><references group="xtra" /> | ||
<ref group="xtra">PMID: 7737175</ref><references group="xtra" /> | <ref group="xtra">PMID: 7737175</ref><references group="xtra" /> | ||
<ref group="xtra">PMID: 7853390</ref><references group="xtra" /> | <ref group="xtra">PMID: 7853390</ref><references group="xtra" /> | ||
<ref group="xtra">PMID: 8120889</ref><references group="xtra" /> | <ref group="xtra">PMID: 8120889</ref><references group="xtra" /> | ||
==See Also== | ==See Also== | ||
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*[[Flagellar hook of bacteria]] | *[[Flagellar hook of bacteria]] | ||
= | <span style="font-size:150%">References</span> | ||
---- | |||
<references /> | <references /> | ||
---- | |||
<span style="font-size:140%">Animation Credits</span><br> | |||
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 [http://polyview.cchmc.org/polyview3d.html Polyview-3D server], which makes its output in [[PyMOL]]. | |||