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Marmont LS, Orta AK, Baileeves BWA, Sychantha D, Fernández-Galliano A, Li YE, Greene NG, Corey RA, Stansfeld PJ, Clemons WM, Bernhardt TG. Synthesis of lipid-linked precursors of the bacterial cell wall is governed by a feedback control mechanism in Pseudomonas aeruginosa. Nat Microbiol 2024; 9:763-775. [PMID: 38336881 PMCID: PMC10914600 DOI: 10.1038/s41564-024-01603-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 01/11/2024] [Indexed: 02/12/2024]
Abstract
Many bacterial surface glycans such as the peptidoglycan (PG) cell wall are built from monomeric units linked to a polyprenyl lipid carrier. How this limiting carrier is distributed among competing pathways has remained unclear. Here we describe the isolation of hyperactive variants of Pseudomonas aeruginosa MraY, the enzyme that forms the first lipid-linked PG precursor. These variants result in the elevated production of the final PG precursor lipid II in cells and are hyperactive in vitro. The activated MraY variants have substitutions that map to a cavity on the extracellular side of the dimer interface, far from the active site. Our structural and molecular dynamics results suggest that this cavity is a binding site for externalized lipid II. Overall, our results support a model in which excess externalized lipid II allosterically inhibits MraY, providing a feedback mechanism that prevents the sequestration of lipid carrier in the PG biogenesis pathway.
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Affiliation(s)
- Lindsey S Marmont
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Michael DeGroote Institute for Infectious Disease Research, David Braley Centre for Antibiotic Discovery, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Anna K Orta
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Becca W A Baileeves
- School of Life Sciences and Department of Chemistry, University of Warwick, Coventry, UK
- Warwick Medical School, University of Warwick, Coventry, UK
| | - David Sychantha
- Michael DeGroote Institute for Infectious Disease Research, David Braley Centre for Antibiotic Discovery, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Ana Fernández-Galliano
- Michael DeGroote Institute for Infectious Disease Research, David Braley Centre for Antibiotic Discovery, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Yancheng E Li
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Neil G Greene
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cell and Molecular Biology, The University of Rhode Island, Kingston, RI, USA
| | - Robin A Corey
- School of Physiology, Pharmacology, and Neuroscience, University of Bristol, Bristol, UK
| | - Phillip J Stansfeld
- School of Life Sciences and Department of Chemistry, University of Warwick, Coventry, UK
| | - William M Clemons
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Thomas G Bernhardt
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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2
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Marmont LS, Orta AK, Corey RA, Sychantha D, Galliano AF, Li YE, Baileeves BW, Greene NG, Stansfeld PJ, Clemons WM, Bernhardt TG. A feedback control mechanism governs the synthesis of lipid-linked precursors of the bacterial cell wall. bioRxiv 2023:2023.08.01.551478. [PMID: 37577621 PMCID: PMC10418202 DOI: 10.1101/2023.08.01.551478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Many bacterial surface glycans such as the peptidoglycan (PG) cell wall, O-antigens, and capsules are built from monomeric units linked to a polyprenyl lipid carrier. How this limiting lipid carrier is effectively distributed among competing pathways has remained unclear for some time. Here, we describe the isolation and characterization of hyperactive variants of Pseudomonas aeruginosa MraY, the essential and conserved enzyme catalyzing the formation of the first lipid-linked PG precursor called lipid I. These variants result in the elevated production of the final PG precursor lipid II in cells and are hyperactive in a purified system. Amino acid substitutions within the activated MraY variants unexpectedly map to a cavity on the extracellular side of the dimer interface, far from the active site. Our structural evidence and molecular dynamics simulations suggest that the cavity is a binding site for lipid II molecules that have been transported to the outer leaflet of the membrane. Overall, our results support a model in which excess externalized lipid II allosterically inhibits MraY, providing a feedback mechanism to prevent the sequestration of lipid carrier in the PG biogenesis pathway. MraY belongs to the broadly distributed polyprenyl-phosphate N-acetylhexosamine 1-phosphate transferase (PNPT) superfamily of enzymes. We therefore propose that similar feedback mechanisms may be widely employed to coordinate precursor supply with demand by polymerases, thereby optimizing the partitioning of lipid carriers between competing glycan biogenesis pathways.
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Affiliation(s)
- Lindsey S. Marmont
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115
- M.G. DeGroote Institute for Infectious Disease Research, David Braley Centre for Antibiotic Discovery, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Anna K. Orta
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, USA
| | - Robin A. Corey
- School of Physiology, Pharmacology, and Neuroscience, University of Bristol, Bristol, UK
| | - David Sychantha
- M.G. DeGroote Institute for Infectious Disease Research, David Braley Centre for Antibiotic Discovery, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Ana Fernández Galliano
- M.G. DeGroote Institute for Infectious Disease Research, David Braley Centre for Antibiotic Discovery, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Yancheng E. Li
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, USA
| | - Becca W.A. Baileeves
- School of Life Sciences and Department of Chemistry, University of Warwick, Warwick, UK
| | - Neil G. Greene
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115
| | - Phillip J. Stansfeld
- School of Life Sciences and Department of Chemistry, University of Warwick, Warwick, UK
| | - William M. Clemons
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, USA
| | - Thomas G. Bernhardt
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115
- Howard Hughes Medical Institute, Boston, United States
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3
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Orta AK, Riera N, Li YE, Tanaka S, Yun HG, Klaic L, Clemons WM. The mechanism of the phage-encoded protein antibiotic from ΦX174. Science 2023; 381:eadg9091. [PMID: 37440661 DOI: 10.1126/science.adg9091] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 05/23/2023] [Indexed: 07/15/2023]
Abstract
The historically important phage ΦX174 kills its host bacteria by encoding a 91-residue protein antibiotic called protein E. Using single-particle electron cryo-microscopy, we demonstrate that protein E bridges two bacterial proteins to form the transmembrane YES complex [MraY, protein E, sensitivity to lysis D (SlyD)]. Protein E inhibits peptidoglycan biosynthesis by obstructing the MraY active site leading to loss of lipid I production. We experimentally validate this result for two different viral species, providing a clear model for bacterial lysis and unifying previous experimental data. Additionally, we characterize the Escherichia coli MraY structure-revealing features of this essential enzyme-and the structure of the chaperone SlyD bound to a protein. Our structures provide insights into the mechanism of phage-mediated lysis and for structure-based design of phage therapeutics.
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Affiliation(s)
- Anna K Orta
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Nadia Riera
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Yancheng E Li
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Shiho Tanaka
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Hyun Gi Yun
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Lada Klaic
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - William M Clemons
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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4
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Mays A, Byars-Winston A, Hinton A, Marshall AG, Kirabo A, August A, Marlin BJ, Riggs B, Tolbert B, Wanjalla C, Womack C, Evans CS, Barnes C, Starbird C, Williams C, Reynolds C, Taabazuing C, Cameron CE, Murray DD, Applewhite D, Morton DJ, Lee D, Williams DW, Lynch D, Brady D, Lynch E, Rutaganira FUN, Silva GM, Shuler H, Saboor IA, Davis J, Dzirasa K, Hammonds-Odie L, Reyes L, Sweetwyne MT, McReynolds MR, Johnson MDL, Smith NA, Pittman N, Ajijola OA, Smith Q, Robinson RAS, Lewis SC, Murray SA, Black S, Neal SE, Andrisse S, Townsend S, Damo SM, Griffith TN, Lambert WM, Clemons WM. Juneteenth in STEMM and the barriers to equitable science. Cell 2023; 186:2510-2517. [PMID: 37295396 DOI: 10.1016/j.cell.2023.05.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 05/06/2023] [Accepted: 05/12/2023] [Indexed: 06/12/2023]
Abstract
We are 52 Black scientists. Here, we establish the context of Juneteenth in STEMM and discuss the barriers Black scientists face, the struggles they endure, and the lack of recognition they receive. We review racism's history in science and provide institutional-level solutions to reduce the burdens on Black scientists.
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Affiliation(s)
- Alfred Mays
- Burroughs Wellcome Fund, Durham, NC 27709, USA
| | - Angela Byars-Winston
- Department of Medicine, Institute for Diversity Science, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Antentor Hinton
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA.
| | - Andrea G Marshall
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA
| | - Annet Kirabo
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA; Department of Medicine, Division of Clinical Pharmacology, Vanderbilt University Medical Center, Vanderbilt University, Nashville, TN 37232, USA
| | - Avery August
- Department of Microbiology and Immunology, Cornell University College of Veterinary Medicine, Ithaca, NY 14853, USA
| | - Bianca J Marlin
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Department of Psychology, Columbia University, New York, NY 10032, USA; Department of Neuroscience, Columbia University, New York, NY 10027, USA
| | - Blake Riggs
- Department of Biology, San Francisco State University, San Francisco, CA 94132, USA
| | - Blanton Tolbert
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Celestine Wanjalla
- Division of Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Chad Womack
- National STEM Programs and Tech Initiatives at the education philanthropic charity, UNCF, Washington, DC 20001, USA
| | - Chantell S Evans
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27708, USA
| | | | - Chrystal Starbird
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Clintoria Williams
- Department of Neuroscience, Cell Biology & Physiology, College of Science and Mathematics, Wright State University Boonshoft School of Medicine, Dayton, OH 45435, USA
| | - Corey Reynolds
- Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA; Mouse Phenotyping Core, Baylor College of Medicine, Houston, TX 77030, USA
| | - Cornelius Taabazuing
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Craig E Cameron
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Debra D Murray
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Derrick J Morton
- Department of Biological Sciences, University of Southern California Los Angeles, Los Angeles, CA 90089, USA
| | - Dexter Lee
- Department of Physiology and Biophysics, Howard University College of Medicine, Washington, DC 20059, USA
| | - Dionna W Williams
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Donald Lynch
- Department of Medicine, Division of Cardiovascular Health and Disease, University of Cincinnati, Cincinnati, OH, USA
| | - Donita Brady
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Erin Lynch
- University of Michigan Health System, Ann Arbor, MI 48109, USA
| | - Florentine U N Rutaganira
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | - Gustavo M Silva
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Haysetta Shuler
- Winston-Salem State University Department of Biological Sciences, Winston-Salem, NC 27110, USA
| | - Ishmail Abdus Saboor
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Department of Biological Sciences, Columbia University, New York, NY 10027, USA.
| | - Jamaine Davis
- Department of Biochemistry, Cancer Biology, Neuroscience, Pharmacology, Meharry Medical College, Nashville, TN 37232, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Kafui Dzirasa
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Department of Psychiatry and Behavioral Sciences, Duke University Medical Center, Durham, NC 27710, USA; Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USA.
| | - Latanya Hammonds-Odie
- Department of Biological Sciences before School of Science and Technology, Georgia Gwinnett College, Lawrenceville, GA 30043, USA
| | - Loretta Reyes
- Division of Pediatric Nephrology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Mariya T Sweetwyne
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Melanie R McReynolds
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA; Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Michael D L Johnson
- Department of Immunobiology, University of Arizona, Tucson, AZ 85724, USA; BIO5 Institute, University of Arizona, Tucson, AZ 85724, USA; Valley Fever Center for Excellence, University of Arizona, Tucson, AZ, USA
| | - Nathan A Smith
- Del Monte Institute for Neuroscience, Department of Neuroscience, University of Rochester, School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Nikea Pittman
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Olujimi A Ajijola
- UCLA Cardiac Arrhythmia Center and Neurocardiology Research Program of Excellence, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Quinton Smith
- School of Engineering, University of California, Irvine, CA 92697-3975, USA
| | - Renã A S Robinson
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
| | - Samantha C Lewis
- Department of Molecular and Cellular Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Sandra A Murray
- Department of Cell Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 52013, USA.
| | - Sherilynn Black
- Office of the Provost and Division of Medical Education, Duke University, Durham, NC 27708, USA.
| | - Sonya E Neal
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Stanley Andrisse
- Department of Physiology and Biophysics, Howard University College of Medicine, Washington, DC 20059, USA; Department of Pediatrics, School of Medicine, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Steven Townsend
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
| | - Steven M Damo
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA; Department of Life and Physical Sciences, Fisk University, Nashville, TN 37208, USA.
| | - Theanne N Griffith
- Department of Physiology and Membrane Biology, University of California Davis, Davis, CA 95616, USA
| | - W Marcus Lambert
- Department of Epidemiology and Biostatistics, SUNY Downstate Health Sciences University, New York, NY 11203, USA
| | - William M Clemons
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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Maggiolo AO, Mahajan S, Rees DC, Clemons WM. Intradimeric Walker A ATPases: Conserved Features of A Functionally Diverse Family. J Mol Biol 2023; 435:167965. [PMID: 37330285 DOI: 10.1016/j.jmb.2023.167965] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 01/12/2023] [Indexed: 06/19/2023]
Abstract
Nucleoside-triphosphate hydrolases (NTPases) are a diverse, but essential group of enzymes found in all living organisms. NTPases that have a G-X-X-X-X-G-K-[S/T] consensus sequence (where X is any amino acid), known as the Walker A or P-loop motif, constitute a superfamily of P-loop NTPases. A subset of ATPases within this superfamily contains a modified Walker A motif, X-K-G-G-X-G-K-[S/T], wherein the first invariant lysine residue is essential to stimulate nucleotide hydrolysis. Although the proteins in this subset have vastly differing functions, ranging from electron transport during nitrogen fixation to targeting of integral membrane proteins to their correct membranes, they have evolved from a shared ancestor and have thus retained common structural features that affect their functions. These commonalities have only been disparately characterized in the context of their individual proteins systems, but have not been generally annotated as features that unite the members of this family. In this review, we report an analysis based on the sequences, structures, and functions of several members in this family that highlight their remarkable similarities. A principal feature of these proteins is their dependence on homodimerization. Since their functionalities are heavily influenced by changes that happen in conserved elements at the dimer interface, we refer to the members of this subclass as intradimeric Walker A ATPases.
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Affiliation(s)
- Ailiena O Maggiolo
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, United States
| | - Shivansh Mahajan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, United States
| | - Douglas C Rees
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, United States.
| | - William M Clemons
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, United States.
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6
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Barlow AN, Manu MS, Saladi SM, Tarr PT, Yadav Y, Thinn AMM, Zhu Y, Laganowsky AD, Clemons WM, Ramasamy S. Structures of Get3d reveal a distinct architecture associated with the emergence of photosynthesis. J Biol Chem 2023:104752. [PMID: 37100288 DOI: 10.1016/j.jbc.2023.104752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 04/16/2023] [Accepted: 04/21/2023] [Indexed: 04/28/2023] Open
Abstract
Homologs of the protein Get3 have been identified in all domains yet remain to be fully characterized. In the eukaryotic cytoplasm, Get3 delivers tail-anchored (TA) integral membrane proteins, defined by a single transmembrane helix at their C-terminus, to the endoplasmic reticulum. While most eukaryotes have a single Get3 gene, plants are notable for having multiple Get3 paralogs. Get3d is conserved across land plants and photosynthetic bacteria and includes a distinctive C-terminal α-crystallin domain. After tracing the evolutionary origin of Get3d, we solve the Arabidopsis thaliana Get3d crystal structure, identify its localization to the chloroplast, and provide evidence for a role in TA protein binding. The structure is identical to that of a cyanobacterial Get3 homolog, which is further refined here. Distinct features of Get3d include an incomplete active site, a 'closed' conformation in the apo-state, and a hydrophobic chamber. Both homologs have ATPase activity and are capable of binding TA proteins, supporting a potential role in TA protein targeting. Get3d is first found with the development of photosynthesis and conserved across 1.2 billion years into the chloroplasts of higher plants across the evolution of photosynthesis suggesting a role in the homeostasis of photosynthetic machinery.
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Affiliation(s)
- Alexandra N Barlow
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, 91125, CA, USA.
| | - M S Manu
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008, India.
| | - Shyam M Saladi
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, 91125, CA, USA
| | - Paul T Tarr
- Howard Hughes Medical Institute and Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, 91125, CA, USA
| | - Yashpal Yadav
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008, India
| | - Aye M M Thinn
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, 91125, CA, USA
| | - Yun Zhu
- Department of Chemistry, Texas A&M University, 400 Bizzell St., College Station, 77843, TX, USA
| | - Arthur D Laganowsky
- Department of Chemistry, Texas A&M University, 400 Bizzell St., College Station, 77843, TX, USA
| | - William M Clemons
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, 91125, CA, USA.
| | - Sureshkumar Ramasamy
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008, India.
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Robertson GA, Clemons WM, Griffith TN. Being Black in biophysics. Biophys J 2023; 122:E1-E3. [PMID: 36990087 PMCID: PMC10147933 DOI: 10.1016/j.bpj.2023.03.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 03/16/2023] [Accepted: 03/16/2023] [Indexed: 03/29/2023] Open
Affiliation(s)
- Gail A Robertson
- Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin
| | - William M Clemons
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California.
| | - Theanne N Griffith
- Department of Physiology and Membrane Biology, University of California Davis, Davis, California.
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8
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Li YE, Orta AK, Clemons WM. Structural basis for phage single gene lysis protein mechanisms. Biophys J 2023; 122:52a. [PMID: 36784739 DOI: 10.1016/j.bpj.2022.11.489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
Affiliation(s)
- Yancheng E Li
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Anna K Orta
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - William M Clemons
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
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9
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Mitachi K, Mingle D, Effah W, Sánchez‐Ruiz A, Hevener KE, Narayanan R, Clemons WM, Sarabia F, Kurosu M. Concise Synthesis of Tunicamycin V and Discovery of a Cytostatic DPAGT1 Inhibitor. Angew Chem Int Ed Engl 2022; 61:e202203225. [PMID: 35594368 PMCID: PMC9329268 DOI: 10.1002/anie.202203225] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Indexed: 11/11/2022]
Abstract
A short total synthesis of tunicamycin V (1), a non-selective phosphotransferase inhibitor, is achieved via a Büchner-Curtius-Schlotterbeck type reaction. Tunicamycin V can be synthesized in 15 chemical steps from D-galactal with 21 % overall yield. The established synthetic scheme is operationally very simple and flexible to introduce building blocks of interest. The inhibitory activity of one of the designed analogues 28 against human dolichyl-phosphate N-acetylglucosaminephosphotransferase 1 (DPAGT1) is 12.5 times greater than 1. While tunicamycins are cytotoxic molecules with a low selectivity, the novel analogue 28 displays selective cytostatic activity against breast cancer cell lines including a triple-negative breast cancer.
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Affiliation(s)
- Katsuhiko Mitachi
- Department of Pharmaceutical Sciences College of Pharmacy University of Tennessee Health Science Center 881 Madison Avenue Memphis TN 38163 USA
| | - David Mingle
- Department of Pharmaceutical Sciences College of Pharmacy University of Tennessee Health Science Center 881 Madison Avenue Memphis TN 38163 USA
| | - Wendy Effah
- Department of Medicine University of Tennessee Health Science Center 19 S. Manassas, Room 120 Memphis TN 38103 USA
| | - Antonio Sánchez‐Ruiz
- Faculty of Pharmacy Campus de Albacete Universidad de Castilla-La Mancha Avda. Dr. José María Sánchez Ibáñez S/N 02008 Albacete Spain
| | - Kirk E. Hevener
- Department of Pharmaceutical Sciences College of Pharmacy University of Tennessee Health Science Center 881 Madison Avenue Memphis TN 38163 USA
| | - Ramesh Narayanan
- Department of Medicine University of Tennessee Health Science Center 19 S. Manassas, Room 120 Memphis TN 38103 USA
| | - William M. Clemons
- Division of Chemistry and Chemical Engineering California Institute of Technology 1200 E. California Blvd. Pasadena CA 91125 USA
| | - Francisco Sarabia
- Department of Organic Chemistry Faculty of Sciences Universidad de Málaga, Campus de Teatinos 29071 Málaga Spain
| | - Michio Kurosu
- Department of Pharmaceutical Sciences College of Pharmacy University of Tennessee Health Science Center 881 Madison Avenue Memphis TN 38163 USA
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Fry MY, Najdrová V, Maggiolo AO, Saladi SM, Doležal P, Clemons WM. Structurally derived universal mechanism for the catalytic cycle of the tail-anchored targeting factor Get3. Nat Struct Mol Biol 2022; 29:820-830. [DOI: 10.1038/s41594-022-00798-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 05/26/2022] [Indexed: 11/09/2022]
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11
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Mitachi K, Mingle D, Effah W, Sánchez-Ruiz A, Hevener KE, Narayanan R, Clemons WM, Sarabia F, Kurosu M. Concise Synthesis of Tunicamycin V and Discovery of a Cytostatic DPAGT1 Inhibitor. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202203225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Katsuhiko Mitachi
- The University of Tennessee Health Science Center College of Pharmacy Pharmacy 881 Madison AvenueROOM 557 38163 MEMPHS UNITED STATES
| | - David Mingle
- The University of Tennessee Health Science Center College of Pharmacy Pharmacy 881 MADISON AVE 38163 MEMPHS UNITED STATES
| | - Wendy Effah
- University of Tennessee College of Medicine: The University of Tennessee Health Science Center College of Medicine Medicine UNITED STATES
| | | | - Kirk E. Hevener
- UTHSC College of Pharmacy Memphis: The University of Tennessee Health Science Center College of Pharmacy Pharmacy UNITED STATES
| | - Ramesh Narayanan
- University of Tennessee College of Medicine: The University of Tennessee Health Science Center College of Medicine Medicine 19, S. Manassas 38013 Memphis UNITED STATES
| | - William M. Clemons
- Caltech: California Institute of Technology Chemistry and Chemical Engineering UNITED STATES
| | - Francisco Sarabia
- University of Malaga: Universidad de Malaga Organic Chemistry UNITED STATES
| | - Michio Kurosu
- UTHSC College of Pharmacy Memphis: The University of Tennessee Health Science Center College of Pharmacy Department of Pharmaceutical Sciences, College of Pharmacy 881 MADISON AVEROOM 557 38163 Memphis UNITED STATES
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12
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Fry MY, Saladi SM, Cunha A, Clemons WM. Sequence-based features that are determinant for tail-anchored membrane protein sorting in eukaryotes. Traffic 2021; 22:306-318. [PMID: 34288289 PMCID: PMC8380732 DOI: 10.1111/tra.12809] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 07/15/2021] [Accepted: 07/18/2021] [Indexed: 11/29/2022]
Abstract
The correct targeting and insertion of tail-anchored (TA) integral membrane proteins is critical for cellular homeostasis. TA proteins are defined by a hydrophobic transmembrane domain (TMD) at their C-terminus and are targeted to either the ER or mitochondria. Derived from experimental measurements of a few TA proteins, there has been little examination of the TMD features that determine localization. As a result, the localization of many TA proteins are misclassified by the simple heuristic of overall hydrophobicity. Because ER-directed TMDs favor arrangement of hydrophobic residues to one side, we sought to explore the role of geometric hydrophobic properties. By curating TA proteins with experimentally determined localizations and assessing hypotheses for recognition, we bioinformatically and experimentally verify that a hydrophobic face is the most accurate singular metric for separating ER and mitochondria-destined yeast TA proteins. A metric focusing on an 11 residue segment of the TMD performs well when classifying human TA proteins. The most inclusive predictor uses both hydrophobicity and C-terminal charge in tandem. This work provides context for previous observations and opens the door for more detailed mechanistic experiments to determine the molecular factors driving this recognition.
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Affiliation(s)
- Michelle Y. Fry
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, USA
| | - Shyam M. Saladi
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, USA
| | - Alexandre Cunha
- Division of Biology and Biological Engineering, Center for Advanced Methods in Biological Image Analysis, Beckman Institute, Pasadena, California, USA
| | - William M. Clemons
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, USA
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13
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Fry MY, Saladi SM, Clemons WM. The STI1-domain is a flexible alpha-helical fold with a hydrophobic groove. Protein Sci 2021; 30:882-898. [PMID: 33620121 PMCID: PMC7980504 DOI: 10.1002/pro.4049] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/17/2021] [Accepted: 02/18/2021] [Indexed: 01/05/2023]
Abstract
STI1-domains are present in a variety of co-chaperone proteins and are required for the transfer of hydrophobic clients in various cellular processes. The domains were first identified in the yeast Sti1 protein where they were referred to as DP1 and DP2. Based on hidden Markov model searches, this domain had previously been found in other proteins including the mammalian co-chaperone SGTA, the DNA damage response protein Rad23, and the chloroplast import protein Tic40. Here, we refine the domain definition and carry out structure-based sequence alignment of STI1-domains showing conservation of five amphipathic helices. Upon examinations of these identified domains, we identify a preceding helix 0 and unifying sequence properties, determine new molecular models, and recognize that STI1-domains nearly always occur in pairs. The similarity at the sequence, structure, and molecular levels likely supports a unified functional role.
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Affiliation(s)
- Michelle Y. Fry
- Division of Chemistry and Chemical EngineeringCalifornia Institute of TechnologyPasadenaCaliforniaUSA
| | - Shyam M. Saladi
- Division of Chemistry and Chemical EngineeringCalifornia Institute of TechnologyPasadenaCaliforniaUSA
| | - William M. Clemons
- Division of Chemistry and Chemical EngineeringCalifornia Institute of TechnologyPasadenaCaliforniaUSA
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14
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Lin KF, Fry MY, Saladi SM, Clemons WM. Molecular basis of tail-anchored integral membrane protein recognition by the cochaperone Sgt2. J Biol Chem 2021; 296:100441. [PMID: 33610544 PMCID: PMC8010706 DOI: 10.1016/j.jbc.2021.100441] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 02/04/2021] [Accepted: 02/17/2021] [Indexed: 02/08/2023] Open
Abstract
The targeting and insertion of tail-anchored (TA) integral membrane proteins (IMPs) into the correct membrane is critical for cellular homeostasis. The fungal protein Sgt2, and its human homolog SGTA, is the entry point for clients to the guided entry of tail-anchored protein (GET) pathway, which targets endoplasmic reticulum-bound TA IMPs. Consisting of three structurally independent domains, the C terminus of Sgt2 binds to the hydrophobic transmembrane domain (TMD) of clients. However, the exact binding interface within Sgt2 and molecular details that underlie its binding mechanism and client preference are not known. Here, we reveal the mechanism of Sgt2 binding to hydrophobic clients, including TA IMPs. Through sequence analysis, biophysical characterization, and a series of capture assays, we establish that the Sgt2 C-terminal domain is flexible but conserved and sufficient for client binding. A molecular model for this domain reveals a helical hand forming a hydrophobic groove approximately 15 Å long that is consistent with our observed higher affinity for client TMDs with a hydrophobic face and a minimal length of 11 residues. This work places Sgt2 into a broader family of TPR-containing cochaperone proteins, demonstrating structural and sequence-based similarities to the DP domains in the yeast Hsp90 and Hsp70 coordinating protein, Sti1.
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Affiliation(s)
- Ku-Feng Lin
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, USA
| | - Michelle Y Fry
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, USA
| | - Shyam M Saladi
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, USA
| | - William M Clemons
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, USA.
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15
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Mitachi K, Kansal RG, Hevener KE, Gillman CD, Hussain SM, Yun HG, Miranda-Carboni GA, Glazer ES, Clemons WM, Kurosu M. DPAGT1 Inhibitors of Capuramycin Analogues and Their Antimigratory Activities of Solid Tumors. J Med Chem 2020; 63:10855-10878. [PMID: 32886511 DOI: 10.1021/acs.jmedchem.0c00545] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Capuramycin displays a narrow spectrum of antibacterial activity by targeting bacterial translocase I (MraY). In our program of development of new N-acetylglucosaminephosphotransferase1 (DPAGT1) inhibitors, we have identified that a capuramycin phenoxypiperidinylbenzylamide analogue (CPPB) inhibits DPAGT1 enzyme with an IC50 value of 200 nM. Despite a strong DPAGT1 inhibitory activity, CPPB does not show cytotoxicity against normal cells and a series of cancer cell lines. However, CPPB inhibits migrations of several solid cancers including pancreatic cancers that require high DPAGT1 expression in order for tumor progression. DPAGT1 inhibition by CPPB leads to a reduced expression level of Snail but does not reduce E-cadherin expression level at the IC50 (DPAGT1) concentration. CPPB displays a strong synergistic effect with paclitaxel against growth-inhibitory action of a patient-derived pancreatic adenocarcinoma, PD002: paclitaxel (IC50: 1.25 μM) inhibits growth of PD002 at 0.0024-0.16 μM in combination with 0.10-2.0 μM CPPB (IC50: 35 μM).
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Affiliation(s)
- Katsuhiko Mitachi
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, 881 Madison Avenue, Memphis, Tennessee 38163, United States
| | - Rita G Kansal
- Department of Surgery and Center for Cancer Research, College of Medicine, University of Tennessee Health Science Center, 910 Madison St., Suite 300, Memphis, Tennessee 38163, United States
| | - Kirk E Hevener
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, 881 Madison Avenue, Memphis, Tennessee 38163, United States
| | - Cody D Gillman
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, California 91125, United States
| | - Syed M Hussain
- Department of Surgery and Center for Cancer Research, College of Medicine, University of Tennessee Health Science Center, 910 Madison St., Suite 300, Memphis, Tennessee 38163, United States
| | - Hyun Gi Yun
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, California 91125, United States
| | - Gustavo A Miranda-Carboni
- Department of Medicine, Division of Hematology-Oncology, University of Tennessee Health Science Center, 19 S. Manassas Avenue, Memphis, Tennessee 38163, United States
| | - Evan S Glazer
- Department of Surgery and Center for Cancer Research, College of Medicine, University of Tennessee Health Science Center, 910 Madison St., Suite 300, Memphis, Tennessee 38163, United States
| | - William M Clemons
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, California 91125, United States
| | - Michio Kurosu
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, 881 Madison Avenue, Memphis, Tennessee 38163, United States
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16
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Mitachi K, Yun HG, Gillman CD, Skorupinska-Tudek K, Swiezewska E, Clemons WM, Kurosu M. Substrate Tolerance of Bacterial Glycosyltransferase MurG: Novel Fluorescence-Based Assays. ACS Infect Dis 2020; 6:1501-1516. [PMID: 31769280 DOI: 10.1021/acsinfecdis.9b00242] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
MurG (uridine diphosphate-N-acetylglucosamine/N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase) is an essential bacterial glycosyltransferase that catalyzes the N-acetylglucosamine (GlcNAc) transformation of lipid I to lipid II during peptidoglycan biosynthesis. Park's nucleotide has been a convenient biochemical tool to study the function of MraY (phospho-MurNAc-(pentapeptide) translocase) and MurG; however, no fluorescent probe has been developed to differentiate individual processes in the biotransformation of Park's nucleotide to lipid II via lipid I. Herein, we report a robust assay of MurG using either the membrane fraction of a M. smegmatis strain or a thermostable MraY and MurG of Hydrogenivirga sp. as enzyme sources, along with Park's nucleotide or Park's nucleotide-Nε-C6-dansylthiourea and uridine diphosphate (UDP)-GlcN-C6-FITC as acceptor and donor substrates. Identification of both the MraY and MurG products can be performed simultaneously by HPLC in dual UV mode. Conveniently, the generated lipid II fluorescent analogue can also be quantitated via UV-Vis spectrometry without the separation of the unreacted lipid I derivative. The microplate-based assay reported here is amenable to high-throughput MurG screening. A preliminary screening of a collection of small molecules has demonstrated the robustness of the assays and resulted in rediscovery of ristocetin A as a strong antimycobacterial MurG and MraY inhibitor.
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Affiliation(s)
- Katsuhiko Mitachi
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, 881 Madison Avenue, Memphis, Tennessee 38163, United States
| | - Hyun Gi Yun
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, California 91125, United States
| | - Cody D. Gillman
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, California 91125, United States
| | - Karolina Skorupinska-Tudek
- Department of Lipid Biochemistry, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warszawa, Poland
| | - Ewa Swiezewska
- Department of Lipid Biochemistry, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warszawa, Poland
| | - William M. Clemons
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, California 91125, United States
| | - Michio Kurosu
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, 881 Madison Avenue, Memphis, Tennessee 38163, United States
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17
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Mitachi K, Kurosu SM, Gillman CD, Yun HG, Clemons WM, Kurosu M. A practical synthesis of a novel DPAGT1 inhibitor, aminouridyl phenoxypiperidinbenzyl butanamide (APPB) for in vivo studies. MethodsX 2019; 6:2305-2321. [PMID: 31667130 PMCID: PMC6812346 DOI: 10.1016/j.mex.2019.09.031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 09/23/2019] [Indexed: 01/17/2023] Open
Abstract
Immunotherapy that targets N-linked glycans has not yet been developed due in large part to the lack of specificity of N-linked glycans between normal and malignant cells. N-Glycan chains are synthesized by the sequential action of glycosyl transferases in the Golgi apparatus. It is an overwhelming task to discover drug-like inhibitors of glycosyl transferases that block the synthesis of specific branching processes in cancer cells, killing tumor cells selectively. It has long been known that N-glycan biosynthesis can be inhibited by disruption of the first committed enzyme, dolichyl-phosphate N-acetylglucosaminephosphotransferase 1 (DPAGT1). Selective DPAGT1 inhibitors have the promising therapeutic potential for certain solid cancers that require increased branching of N-linked glycans in their growth progressions. Recently, we discovered that an anti-Clostridium difficile molecule, aminouridyl phenoxypiperidinbenzyl butanamide (APPB) showed DPAGT1 inhibitory activity with the IC50 value of 0.25 μM. It was confirmed that APPB inhibits N-glycosylation of β-catenin at 2.5 nM concentration. A sharp difference between APPB and tunicamycin was that the hemolytic activity of APPB is significantly attenuated (IC50 > 200 μM RBC). Water solubility of APPB is >350-times greater than that of tunicamycin (78.8 mg/mL for APPB, <0.2 mg/mL for tunicamycin). A novel DPAGT1 inhibitor, APPB selectively inhibits growth of the solid tumors (e.g. KB, LoVo, SK-OV-3, MDA-MB-432S, HCT116, Panc-1, and AsPC-1) at low μM concentrations, but does not inhibit growth of a leukemia cell (L1210) and the healthy cells (Vero and HPNE) at these concentrations. In vitro metabolic stability using rat liver microsomes indicated that a half-life (t1/2) of APPB is sufficiently long (>60 min) for in vivo studies (PK/PD, safety profiles, and in vivo efficacy) using animal models. We have refined all steps in the previously reported synthesis for APPB for larger-scale. This article summarizes protocols of gram-scale synthesis of APPB and its physicochemical data, and a convenient DPAGT1 assay. Remember that the abstract is what readers see first in electronic abstracting & indexing services. This is the advertisement of your article. Make it interesting, and easy to be understood. Be accurate and specific, keep it as brief as possible.
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Affiliation(s)
- Katsuhiko Mitachi
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, 881 Madison Avenue, Memphis, TN 38163, United States
| | - Shou M Kurosu
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, 881 Madison Avenue, Memphis, TN 38163, United States
| | - Cody D Gillman
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, United States
| | - Hyun Gi Yun
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, United States
| | - William M Clemons
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, United States
| | - Michio Kurosu
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, 881 Madison Avenue, Memphis, TN 38163, United States
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18
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Mitachi K, Kurosu SM, Eslamimehr S, Lemieux MR, Ishizaki Y, Clemons WM, Kurosu M. Semisynthesis of an Anticancer DPAGT1 Inhibitor from a Muraymycin Biosynthetic Intermediate. Org Lett 2019; 21:876-879. [PMID: 30698984 PMCID: PMC6447083 DOI: 10.1021/acs.orglett.8b03716] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We have explored a method to convert a muraymycin biosynthetic intermediate 3 to an anticancer drug lead 2 for in vivo and thorough preclinical studies. Cu(OAc)2 forms a stable complex with the amide 4 and prevents electrophilic reactions at the 2-((3-aminopropyl)amino)acetamide moiety. Under the present conditions, the desired 5″-primary amine was selectively protected with (Boc)2O to yield 6. The intermediate 6 was converted to 2 in two steps with 90% yield.
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Affiliation(s)
- Katsuhiko Mitachi
- Department of Pharmaceutical Sciences, College of Pharmacy , University of Tennessee Health Science Center , 881 Madison Avenue , Memphis , Tennessee 38163 , United States
| | - Shou M Kurosu
- Department of Pharmaceutical Sciences, College of Pharmacy , University of Tennessee Health Science Center , 881 Madison Avenue , Memphis , Tennessee 38163 , United States
| | - Shakiba Eslamimehr
- Department of Pharmaceutical Sciences, College of Pharmacy , University of Tennessee Health Science Center , 881 Madison Avenue , Memphis , Tennessee 38163 , United States
| | - Maddie R Lemieux
- Department of Pharmaceutical Sciences, College of Pharmacy , University of Tennessee Health Science Center , 881 Madison Avenue , Memphis , Tennessee 38163 , United States
| | - Yoshimasa Ishizaki
- Laboratory of Microbiology , Institute of Microbial Chemistry (BIKAKEN) , 3-14-23, Kamiosaki , Shinagawa-ku, Tokyo 141-0021 , Japan
| | - William M Clemons
- Division of Chemistry and Chemical Engineering , California Institute of Technology , 1200 E. California Boulevard , Pasadena , California 91125 , United States
| | - Michio Kurosu
- Department of Pharmaceutical Sciences, College of Pharmacy , University of Tennessee Health Science Center , 881 Madison Avenue , Memphis , Tennessee 38163 , United States
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19
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Saladi SM, Javed N, Müller A, Clemons WM. A statistical model for improved membrane protein expression using sequence-derived features. J Biol Chem 2018; 293:4913-4927. [PMID: 29378850 PMCID: PMC5880134 DOI: 10.1074/jbc.ra117.001052] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 01/22/2018] [Indexed: 11/06/2022] Open
Abstract
The heterologous expression of integral membrane proteins (IMPs) remains a major bottleneck in the characterization of this important protein class. IMP expression levels are currently unpredictable, which renders the pursuit of IMPs for structural and biophysical characterization challenging and inefficient. Experimental evidence demonstrates that changes within the nucleotide or amino acid sequence for a given IMP can dramatically affect expression levels, yet these observations have not resulted in generalizable approaches to improve expression levels. Here, we develop a data-driven statistical predictor named IMProve that, using only sequence information, increases the likelihood of selecting an IMP that expresses in Escherichia coli The IMProve model, trained on experimental data, combines a set of sequence-derived features resulting in an IMProve score, where higher values have a higher probability of success. The model is rigorously validated against a variety of independent data sets that contain a wide range of experimental outcomes from various IMP expression trials. The results demonstrate that use of the model can more than double the number of successfully expressed targets at any experimental scale. IMProve can immediately be used to identify favorable targets for characterization. Most notably, IMProve demonstrates for the first time that IMP expression levels can be predicted directly from sequence.
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Affiliation(s)
- Shyam M Saladi
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125
| | - Nauman Javed
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125
| | - Axel Müller
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125
| | - William M Clemons
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125.
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Mitachi K, Yun HG, Kurosu SM, Eslamimehr S, Lemieux MR, Klaić L, Clemons WM, Kurosu M. Novel FR-900493 Analogues That Inhibit the Outgrowth of Clostridium difficile Spores. ACS Omega 2018; 3:1726-1739. [PMID: 29503973 PMCID: PMC5830699 DOI: 10.1021/acsomega.7b01740] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 01/26/2018] [Indexed: 05/08/2023]
Abstract
The spectrum of antibacterial activity for the nucleoside antibiotic FR-900493 (1) can be extended by chemical modifications. We have generated a small focused library based on the structure of 1 and identified UT-17415 (9), UT-17455 (10), UT-17460 (11), and UT-17465 (12), which exhibit anti-Clostridium difficile growth inhibitory activity. These analogues also inhibit the outgrowth of C. difficile spores at 2× minimum inhibitory concentration. One of these analogues, 11, relative to 1 exhibits over 180-fold and 15-fold greater activity against the enzymes, phospho-MurNAc-pentapeptide translocase (MraY) and polyprenyl phosphate-GlcNAc-1-phosphate transferase (WecA), respectively. The phosphotransferase inhibitor 11 displays antimicrobial activity against several tested bacteria including Bacillus subtilis, Clostridium spp., and Mycobacterium smegmatis, but no growth inhibitory activity is observed against the other Gram-positive and Gram-negative bacteria. The selectivity index (Vero cell cytotoxicity/C. difficileantimicrobial activity) of 11 is approximately 17, and 11 does not induce hemolysis even at a 100 μM concentration.
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Affiliation(s)
- Katsuhiko Mitachi
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, 881 Madison Avenue, Memphis, Tennessee 38163, United States
| | - Hyun Gi Yun
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, 1200 E. California Blvd, Pasadena, California 91125, United States
| | - Sara M. Kurosu
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, 881 Madison Avenue, Memphis, Tennessee 38163, United States
| | - Shakiba Eslamimehr
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, 881 Madison Avenue, Memphis, Tennessee 38163, United States
| | - Maddie R. Lemieux
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, 881 Madison Avenue, Memphis, Tennessee 38163, United States
| | - Lada Klaić
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, 1200 E. California Blvd, Pasadena, California 91125, United States
| | - William M. Clemons
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, 1200 E. California Blvd, Pasadena, California 91125, United States
| | - Michio Kurosu
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, 881 Madison Avenue, Memphis, Tennessee 38163, United States
- E-mail: . Phone: 901-448-1045. Fax: 901-448-6940 (M.K.)
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21
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22
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Niesen MJM, Marshall SS, Miller TF, Clemons WM. Improving membrane protein expression by optimizing integration efficiency. J Biol Chem 2017; 292:19537-19545. [PMID: 28918393 DOI: 10.1074/jbc.m117.813469] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 09/12/2017] [Indexed: 12/22/2022] Open
Abstract
The heterologous overexpression of integral membrane proteins in Escherichia coli often yields insufficient quantities of purifiable protein for applications of interest. The current study leverages a recently demonstrated link between co-translational membrane integration efficiency and protein expression levels to predict protein sequence modifications that improve expression. Membrane integration efficiencies, obtained using a coarse-grained simulation approach, robustly predicted effects on expression of the integral membrane protein TatC for a set of 140 sequence modifications, including loop-swap chimeras and single-residue mutations distributed throughout the protein sequence. Mutations that improve simulated integration efficiency were 4-fold enriched with respect to improved experimentally observed expression levels. Furthermore, the effects of double mutations on both simulated integration efficiency and experimentally observed expression levels were cumulative and largely independent, suggesting that multiple mutations can be introduced to yield higher levels of purifiable protein. This work provides a foundation for a general method for the rational overexpression of integral membrane proteins based on computationally simulated membrane integration efficiencies.
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Affiliation(s)
- Michiel J M Niesen
- From the Department of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125
| | - Stephen S Marshall
- From the Department of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125
| | - Thomas F Miller
- From the Department of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125
| | - William M Clemons
- From the Department of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125
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Saladi S, Chu AE, Clemons WM. Statistical Models Robustly Predict Membrane Protein Expression in E. Coli. Biophys J 2017. [DOI: 10.1016/j.bpj.2016.11.1929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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24
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Chu AE, Saladi SM, Bradbury N, Clemons WM. Towards a Universal Characterization of the Membrane Protein Expression Landscape. Biophys J 2017. [DOI: 10.1016/j.bpj.2016.11.1046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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Marshall SS, Niesen MJM, Müller A, Tiemann K, Saladi SM, Galimidi RP, Zhang B, Clemons WM, Miller TF. A Link between Integral Membrane Protein Expression and Simulated Integration Efficiency. Cell Rep 2016; 16:2169-2177. [PMID: 27524616 DOI: 10.1016/j.celrep.2016.07.042] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 06/09/2016] [Accepted: 07/16/2016] [Indexed: 01/16/2023] Open
Abstract
Integral membrane proteins (IMPs) control the flow of information and nutrients across cell membranes, yet IMP mechanistic studies are hindered by difficulties in expression. We investigate this issue by addressing the connection between IMP sequence and observed expression levels. For homologs of the IMP TatC, observed expression levels vary widely and are affected by small changes in protein sequence. The effect of sequence changes on experimentally observed expression levels strongly correlates with the simulated integration efficiency obtained from coarse-grained modeling, which is directly confirmed using an in vivo assay. Furthermore, mutations that improve the simulated integration efficiency likewise increase the experimentally observed expression levels. Demonstration of these trends in both Escherichia coli and Mycobacterium smegmatis suggests that the results are general to other expression systems. This work suggests that IMP integration is a determinant for successful expression, raising the possibility of controlling IMP expression via rational design.
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Affiliation(s)
- Stephen S Marshall
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Michiel J M Niesen
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Axel Müller
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Katrin Tiemann
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Shyam M Saladi
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Rachel P Galimidi
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Bin Zhang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - William M Clemons
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
| | - Thomas F Miller
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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26
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Saladi SM, Javed N, Müller A, Clemons WM. A Machine Learning Approach to Heterologous Membrane Protein Overexpression. Biophys J 2016. [DOI: 10.1016/j.bpj.2015.11.278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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27
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Lin KF, Clemons WM. Promiscuous Binding of Membrane Proteins on Flexible Co-Chaperones, Yeast Sgt2 and Human SGTA. Biophys J 2016. [DOI: 10.1016/j.bpj.2015.11.2994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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28
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Gristick HB, Rome ME, Chartron JW, Rao M, Hess S, Shan SO, Clemons WM. Mechanism of Assembly of a Substrate Transfer Complex during Tail-anchored Protein Targeting. J Biol Chem 2015; 290:30006-17. [PMID: 26451041 DOI: 10.1074/jbc.m115.677328] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Indexed: 11/06/2022] Open
Abstract
Tail-anchored (TA) proteins, defined as having a single transmembrane helix at their C terminus, are post-translationally targeted to the endoplasmic reticulum membrane by the guided entry of TA proteins (GET) pathway. In yeast, the handover of TA substrates is mediated by the heterotetrameric Get4/Get5 complex (Get4/5), which tethers the co-chaperone Sgt2 to the targeting factor, the Get3 ATPase. Binding of Get4/5 to Get3 is critical for efficient TA targeting; however, questions remain about the formation of the Get3·Get4/5 complex. Here we report crystal structures of a Get3·Get4/5 complex from Saccharomyces cerevisiae at 2.8 and 6.0 Å that reveal a novel interface between Get3 and Get4 dominated by electrostatic interactions. Kinetic and mutational analyses strongly suggest that these structures represent an on-pathway intermediate that rapidly assembles and then rearranges to the final Get3·Get4/5 complex. Furthermore, we provide evidence that the Get3·Get4/5 complex is dominated by a single Get4/5 heterotetramer bound to one monomer of a Get3 dimer, uncovering an intriguing asymmetry in the Get4/5 heterotetramer upon Get3 binding. Ultrafast diffusion-limited electrostatically driven Get3·Get4/5 association enables Get4/5 to rapidly sample and capture Get3 at different stages of the GET pathway.
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Affiliation(s)
| | - Michael E Rome
- From the Division of Chemistry and Chemical Engineering and
| | | | - Meera Rao
- From the Division of Chemistry and Chemical Engineering and
| | - Sonja Hess
- The Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, California 91125
| | - Shu-ou Shan
- From the Division of Chemistry and Chemical Engineering and
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29
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Abstract
High-resolution structures provide new insights into how an RNA-protein complex recognizes the signal that targets membrane proteins to the endoplasmic reticulum before they aggregate.
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Affiliation(s)
- Jee-Young Mock
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, United States
| | - William M Clemons
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, United States
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30
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Jang KS, Nani RR, Kalli A, Levin S, Müller A, Hess S, Reisman SE, Clemons WM. A cationic cysteine-hydrazide as an enrichment tool for the mass spectrometric characterization of bacterial free oligosaccharides. Anal Bioanal Chem 2015; 407:6181-90. [PMID: 26100547 DOI: 10.1007/s00216-015-8798-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 05/07/2015] [Accepted: 05/21/2015] [Indexed: 10/23/2022]
Abstract
In Campylobacterales and related ε-proteobacteria with N-linked glycosylation (NLG) pathways, free oligosaccharides (fOS) are released into the periplasmic space from lipid-linked precursors by the bacterial oligosaccharyltransferase (PglB). This hydrolysis results in the same molecular structure as the oligosaccharide that is transferred to a protein to be glycosylated. This allowed for the general elucidation of the fOS-branched structures and monosaccharides from a number of species using standard enrichment and mass spectrometry methods. To aid characterization of fOS, hydrazide chemistry has often been used for chemical modification of the reducing part of oligosaccharides resulting in better selectivity and sensitivity in mass spectrometry; however, the removal of the unreacted reagents used for the modification often causes the loss of the sample. Here, we develop a more robust method for fOS purification and characterize glycostructures using complementary tandem mass spectrometry (MS/MS) analysis. A cationic cysteine hydrazide derivative was synthesized to selectively isolate fOS from periplasmic fractions of bacteria. The cysteine hydrazide nicotinamide (Cyhn) probe possesses both thiol and cationic moieties. The former enables reversible conjugation to a thiol-activated solid support, while the latter improves the ionization signal during MS analysis. This enrichment was validated on the well-studied Campylobacter jejuni by identifying fOS from the periplasmic extracts. Using complementary MS/MS analysis, we approximated data of a known structure of the fOS from Campylobacter concisus. This versatile enrichment technique allows for the exploration of a diversity of protein glycosylation pathways.
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Affiliation(s)
- Kyoung-Soon Jang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, M/C 114-96 1200 E California Blvd, Pasadena, CA, 91125, USA
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31
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Abstract
Peptidoglycan (PG) is unique to bacteria, and thus, the enzymes responsible for its biosynthesis are promising antibacterial drug targets. The membrane-embedded enzymes in PG remain significant challenges in studying their mechanisms due to the fact that preparations of suitable enzymatic substrates require time-consuming biological transformations or chemical synthesis. Lipid I (prenyl diphosphoryl-MurNAc-pentapeptide) is an important PG biosynthesis intermediate to study the central enzymes, translocase I (MraY/MurX) and MurG. Lipid I isolated from nature contains the C50-or C55-prenyl unit that shows extremely poor water-solubility that renders studies of translocase I and MurG enzymes difficult. We have studied biological transformation of water soluble lipid I fluorescent probes using bacterial membrane fractions and purified MraY enzymes. In our investigation of the minimum structural requirements of the prenyl phosphates in MraY-catalyzed lipid I synthesis, we found that (2Z,6E)-farnesyl phosphate (C15-phosphate) can be recognized by E. coli MraY to generate the water-soluble lipid I fluorescent probes in high-yield. Under the optimized conditions, the same reaction was performed by using the purified MraY from Hydrogenivirga spp. to afford the lipid I analog with high-yield in a short reaction time.
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Affiliation(s)
- Katsuhiko Mitachi
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, 881 Madison Avenue, Memphis, TN 38163, USA
| | - Shajila Siricilla
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, 881 Madison Avenue, Memphis, TN 38163, USA
| | - Lada Klaic
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Bld. Pasadena, CA 91125, USA
| | - William M. Clemons
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Bld. Pasadena, CA 91125, USA
| | - Michio Kurosu
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, 881 Madison Avenue, Memphis, TN 38163, USA
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32
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Müller A, Beeby M, McDowall AW, Chow J, Jensen GJ, Clemons WM. Ultrastructure and complex polar architecture of the human pathogen Campylobacter jejuni. Microbiologyopen 2014; 3:702-10. [PMID: 25065852 PMCID: PMC4234261 DOI: 10.1002/mbo3.200] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 06/17/2014] [Accepted: 06/27/2014] [Indexed: 12/12/2022] Open
Abstract
Campylobacter jejuni is one of the most successful food-borne human pathogens. Here we use electron cryotomography to explore the ultrastructure of C. jejuni cells in logarithmically growing cultures. This provides the first look at this pathogen in a near-native state at macromolecular resolution (~5 nm). We find a surprisingly complex polar architecture that includes ribosome exclusion zones, polyphosphate storage granules, extensive collar-shaped chemoreceptor arrays, and elaborate flagellar motors.
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Affiliation(s)
- Axel Müller
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, California, 91125
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33
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Gristick HB, Rao M, Chartron JW, Rome ME, Shan SO, Clemons WM. Crystal structure of ATP-bound Get3-Get4-Get5 complex reveals regulation of Get3 by Get4. Nat Struct Mol Biol 2014; 21:437-42. [PMID: 24727835 PMCID: PMC4386898 DOI: 10.1038/nsmb.2813] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Accepted: 03/24/2014] [Indexed: 11/16/2022]
Abstract
Correct localization of membrane proteins is essential to all cells. Chaperone cascades coordinate the capture and handover of substrate proteins from the ribosome to their target membrane; yet the mechanistic and structural details of these processes remain unclear. Here we investigate the conserved GET pathway, in which the Get4-Get5 complex mediates the handover of tail-anchor (TA) substrates from the co-chaperone Sgt2 to the Get3 ATPase, the central targeting factor. We present a crystal structure of a yeast Get3-Get4-Get5 complex in an ATP-bound state, and show how Get4 primes Get3 into the optimal configuration for substrate capture. Structure-guided biochemical analyses demonstrate that Get4-mediated regulation of ATP hydrolysis by Get3 is essential to efficient TA protein targeting. Analogous regulation of other chaperones or targeting factors could provide a general mechanism for ensuring effective substrate capture during protein biogenesis.
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Affiliation(s)
- Harry B Gristick
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, USA
| | - Meera Rao
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, USA
| | - Justin W Chartron
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, USA
| | - Michael E Rome
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, USA
| | - Shu-Ou Shan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, USA
| | - William M Clemons
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, USA
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34
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Abstract
Physiological adaptation to proteotoxic stress in the endoplasmic reticulum (ER) requires retrotranslocation of misfolded proteins into the cytoplasm for ubiquitination and elimination by ER-associated degradation (ERAD). A surprising paradox emerging from recent studies is that ubiquitin ligases (E3s) and deubiquitinases (DUBs), enzymes with opposing activities, can both promote ERAD. Here we demonstrate that the ERAD E3 gp78 can ubiquitinate not only ERAD substrates, but also the machinery protein Ubl4A, a key component of the Bag6 chaperone complex. Remarkably, instead of targeting Ubl4A for degradation, polyubiquitination is associated with irreversible proteolytic processing and inactivation of Bag6. Importantly, we identify USP13 as a gp78-associated DUB that eliminates ubiquitin conjugates from Ubl4A to maintain the functionality of Bag6. Our study reveals an unexpected paradigm in which a DUB prevents undesired ubiquitination to sharpen substrate specificity for an associated ubiquitin ligase partner and to promote ER quality control. DOI: http://dx.doi.org/10.7554/eLife.01369.001.
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Affiliation(s)
- Yanfen Liu
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, United States
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35
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Jang KS, Sweredoski MJ, Graham RLJ, Hess S, Clemons WM. Comprehensive proteomic profiling of outer membrane vesicles from Campylobacter jejuni. J Proteomics 2013; 98:90-8. [PMID: 24382552 DOI: 10.1016/j.jprot.2013.12.014] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Revised: 12/05/2013] [Accepted: 12/17/2013] [Indexed: 10/25/2022]
Abstract
UNLABELLED Gram-negative bacteria constitutively release outer membrane vesicles (OMVs) during cell growth that play significant roles in bacterial survival, virulence and pathogenesis. In this study, comprehensive proteomic analysis of OMVs from a human gastrointestinal pathogen Campylobacter jejuni NCTC11168 was performed using high-resolution mass spectrometry. The OMVs of C. jejuni NCTC11168 were isolated from culture supernatants then characterized using electron microscopy and dynamic light scattering revealing spherical OMVs of an average diameter of 50nm. We then identified 134 vesicular proteins using high-resolution LTQ-Orbitrap mass spectrometry. Subsequent functional analysis of the genes revealed the relationships of the vesicular proteins. Furthermore, known N-glycoproteins were identified from the list of the vesicular proteome, implying the potential role of the OMVs as a delivery means for biologically relevant bacterial glycoproteins. These results enabled us to elucidate the overall proteome profile of pathogenic bacterium C. jejuni and to speculate on the function of OMVs in bacterial infections and communication. BIOLOGICAL SIGNIFICANCE This work demonstrates the importance of understanding vesicular proteomes from a human pathogen Campylobacter jejuni. From the secreted outer membrane vesicles (OMVs) of C. jejuni NCTC11168, we found a variety of virulence factors and essential proteins for bacterial survival. Bioinformatics analysis of these proteins predicted functional enrichment and localization. The most highly enriched were redox enzymes, which are considered to be essential for survival in oxygen-limiting environments and are predicted to be on the twin-arginine translocation (Tat) pathway suggesting a role for this pathway in the biogenesis of OMVs. This study additionally implicates a biological role for N-linked glycoproteins in OMVs. These approaches allow for a better understanding of the physiology of this important human pathogen.
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Affiliation(s)
- Kyoung-Soon Jang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Michael J Sweredoski
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Robert L J Graham
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Sonja Hess
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - William M Clemons
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA.
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36
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Rao M, Rome ME, Clemons WM, Shan SO. Precise Timing of ATPase Activation Drives Targeting of Tail-Anchored Proteins. Biophys J 2013. [DOI: 10.1016/j.bpj.2012.11.3178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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37
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Abstract
The DNA phage ΦX174 encodes the integral membrane protein E whose expression leads to host cell lysis by inhibition of the peptidoglycan synthesis enzyme MraY. Here we use mutagenesis to characterize the molecular details of the E lysis mechanism. We find that a minimal 18-residue region with the modified wild-type sequences of the conserved transmembrane helix of E is sufficient to lyse host cells and that specific residues within and at the boundaries of this helix are important for activity. This suggests that positioning of the helix in the membrane is critical for interactions with MraY. We further characterize the interaction site of the transmembrane helix with MraY demonstrating E forms a stable complex with MraY. Triggering cell lysis by peptidoglycan synthesis inhibition is a traditional route for antimicrobial strategies. Understanding the mechanism of bacterial cell lysis by E will provide insights into new antimicrobial strategies using re-engineered E peptides.
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Affiliation(s)
- Shiho Tanaka
- Division of Chemistry and Chemical Engineering, California Institute of Technology, M/C 114-96, Pasadena, CA 91125, USA
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38
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Chartron JW, Clemons WM. Structural investigations of the Get4/Get5/Sgt2 complex. FASEB J 2012. [DOI: 10.1096/fasebj.26.1_supplement.749.4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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39
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Chartron JW, Clemons WM, Suloway CJM. The complex process of GETting tail-anchored membrane proteins to the ER. Curr Opin Struct Biol 2012; 22:217-24. [PMID: 22444563 DOI: 10.1016/j.sbi.2012.03.001] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2012] [Accepted: 03/01/2012] [Indexed: 10/28/2022]
Abstract
Biosynthesis of membrane proteins requires that hydrophobic transmembrane (TM) regions be shielded from the cytoplasm while being directed to the correct membrane. Tail-anchored (TA) membrane proteins, characterized by a single C-terminal TM, pose an additional level of complexity because they must be post-translationally targeted. In eukaryotes, the GET pathway shuttles TA-proteins to the endoplasmic reticulum. The key proteins required in yeast (Sgt2 and Get1-5) have been under extensive structural and biochemical investigation during recent years. The central protein Get3 utilizes nucleotide linked conformational changes to facilitate substrate loading and targeting. Here we analyze this complex process from a structural perspective, as understood in yeast, and further postulate on similar pathways in other domains of life.
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Affiliation(s)
- Justin W Chartron
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, United States
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40
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Chartron JW, VanderVelde DG, Rao M, Clemons WM. Get5 carboxyl-terminal domain is a novel dimerization motif that tethers an extended Get4/Get5 complex. J Biol Chem 2012; 287:8310-7. [PMID: 22262836 DOI: 10.1074/jbc.m111.333252] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Tail-anchored trans-membrane proteins are targeted to membranes post-translationally. The proteins Get4 and Get5 form an obligate complex that catalyzes the transfer of tail-anchored proteins destined to the endoplasmic reticulum from Sgt2 to the cytosolic targeting factor Get3. Get5 forms a homodimer mediated by its carboxyl domain. We show here that a conserved motif exists within the carboxyl domain. A high resolution crystal structure and solution NMR structures of this motif reveal a novel and stable helical dimerization domain. We additionally determined a solution NMR structure of a divergent fungal homolog, and comparison of these structures allows annotation of specific stabilizing interactions. Using solution x-ray scattering and the structures of all folded domains, we present a model of the full-length Get4/Get5 complex.
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Affiliation(s)
- Justin W Chartron
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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41
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Chartron JW, Gonzalez GM, Clemons WM. A structural model of the Sgt2 protein and its interactions with chaperones and the Get4/Get5 complex. J Biol Chem 2011; 286:34325-34. [PMID: 21832041 PMCID: PMC3190793 DOI: 10.1074/jbc.m111.277798] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Revised: 07/18/2011] [Indexed: 11/06/2022] Open
Abstract
The insertion of tail-anchored transmembrane (TA) proteins into the appropriate membrane is a post-translational event that requires stabilization of the transmembrane domain and targeting to the proper destination. Sgt2 is a heat-shock protein cognate (HSC) co-chaperone that preferentially binds endoplasmic reticulum-destined TA proteins and directs them to the GET pathway via Get4 and Get5. Here, we present the crystal structure from a fungal Sgt2 homolog of the tetratrico-repeat (TPR) domain and part of the linker that connects to the C-terminal domain. The linker extends into the two-carboxylate clamp of the TPR domain from a symmetry-related molecule mimicking the binding to HSCs. Based on this structure, we provide biochemical evidence that the Sgt2 TPR domain has the ability to directly bind multiple HSC family members. The structure allows us to propose features involved in this lower specificity relative to other TPR containing co-chaperones. We further show that a dimer of Sgt2 binds a single Get5 and use small angle x-ray scattering to characterize the domain arrangement of Sgt2 in solution. These results allow us to present a structural model of the Sgt2-Get4/Get5-HSC complex.
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Affiliation(s)
- Justin W. Chartron
- From the Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125
| | - Grecia M. Gonzalez
- From the Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125
| | - William M. Clemons
- From the Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125
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42
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Ramasamy SK, Clemons WM. Structure of the twin-arginine signal-binding protein DmsD from Escherichia coli. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:746-50. [PMID: 19652330 DOI: 10.1107/s1744309109023811] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2009] [Accepted: 06/21/2009] [Indexed: 11/10/2022]
Abstract
The translocation of folded proteins via the twin-arginine translocation (Tat) pathway is regulated to prevent the futile export of inactive substrate. DmsD is part of a class of cytoplasmic chaperones that play a role in preventing certain redox proteins from premature transport. DmsD from Escherichia coli has been crystallized in space group P4(1)2(1)2, with unit-cell parameters a = b = 97.45, c = 210.04 A, in the presence of a small peptide. The structure has been solved by molecular replacement to a resolution of 2.4 A and refined to an R factor of 19.4%. There are four molecules in the asymmetric unit that may mimic a higher order structure in vivo. There appears to be density for the peptide in a predicted binding pocket, which lends support to its role as the signal-recognition surface for this class of proteins.
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Affiliation(s)
- Suresh Kumar Ramasamy
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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43
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Ménétret JF, Schaletzky J, Clemons WM, Osborne AR, Skånland SS, Denison C, Gygi SP, Kirkpatrick DS, Park E, Ludtke SJ, Rapoport TA, Akey CW. Ribosome binding of a single copy of the SecY complex: implications for protein translocation. Mol Cell 2008; 28:1083-92. [PMID: 18158904 DOI: 10.1016/j.molcel.2007.10.034] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2007] [Revised: 08/03/2007] [Accepted: 10/04/2007] [Indexed: 12/29/2022]
Abstract
The SecY complex associates with the ribosome to form a protein translocation channel in the bacterial plasma membrane. We have used cryo-electron microscopy and quantitative mass spectrometry to show that a nontranslating E. coli ribosome binds to a single SecY complex. The crystal structure of an archaeal SecY complex was then docked into the electron density maps. In the resulting model, two cytoplasmic loops of SecY extend into the exit tunnel near proteins L23, L29, and L24. The loop between transmembrane helices 8 and 9 interacts with helices H59 and H50 in the large subunit RNA, while the 6/7 loop interacts with H7. We also show that point mutations of basic residues within either loop abolish ribosome binding. We suggest that SecY binds to this primary site on the ribosome and subsequently captures and translocates the nascent chain.
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Affiliation(s)
- Jean-François Ménétret
- Department of Physiology and Biophysics, Boston University School of Medicine, 700 Albany Street, Boston, MA 02118-2526, USA
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44
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Abstract
The apparatus responsible for translocation of proteins across bacterial membranes is the conserved SecY complex, consisting of SecY, SecE, and SecG. Prior genetic analysis provided insight into the mechanisms of protein export, as well as the interactions between the component proteins. In particular, the prl suppressor alleles of secE and secY, which allow export of secretory proteins with defective signal sequences, have proven particularly useful. Here, we report the isolation of novel mutations in secE and secY, as well as the phenotypic effects of combinations of prl mutations. These new alleles, as well as previously characterized prl mutations, were analyzed in light of the recently published crystal structure of the archaeal SecY complex. Our results support and expand a model of Prl suppressor activity that proposes that all of the prlA and prlG alleles either destabilize the closed state of the channel or stabilize the open form. These mutants thus allow channel opening to occur without the triggering event of signal sequence binding that is required in a wild-type complex.
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Affiliation(s)
- Margaret A Smith
- Department of Microbiology and Immunology, University of North Dakota School of Medicine and Health Sciences, Grand Forks, North Dakota 58202-9037, USA
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Cannon KS, Or E, Clemons WM, Shibata Y, Rapoport TA. Disulfide bridge formation between SecY and a translocating polypeptide localizes the translocation pore to the center of SecY. ACTA ACUST UNITED AC 2005; 169:219-25. [PMID: 15851514 PMCID: PMC2171872 DOI: 10.1083/jcb.200412019] [Citation(s) in RCA: 135] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
During their biosynthesis, many proteins pass through the membrane via a hydrophilic channel formed by the heterotrimeric Sec61/SecY complex. Whether this channel forms at the interface of multiple copies of Sec61/SecY or is intrinsic to a monomeric complex, as suggested by the recently solved X-ray structure of the Methanococcus jannaschii SecY complex, is a matter of contention. By introducing a single cysteine at various positions in Escherichia coli SecY and testing its ability to form a disulfide bond with a single cysteine in a translocating chain, we provide evidence that translocating polypeptides pass through the center of the SecY complex. The strongest cross-links were observed with residues that would form a constriction in an hourglass-shaped pore. This suggests that the channel makes only limited contact with a translocating polypeptide, thus minimizing the energy required for translocation.
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Affiliation(s)
- Kurt S Cannon
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
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Abstract
A structurally conserved protein translocation channel is formed by the heterotrimeric Sec61 complex in eukaryotes, and SecY complex in archaea and bacteria. Electron microscopy studies suggest that the channel may function as an oligomeric assembly of Sec61 or SecY complexes. Remarkably, the recently determined X-ray structure of an archaeal SecY complex indicates that the pore is located at the center of a single molecule of the complex. This structure suggests how the pore opens perpendicular to the plane of the membrane to allow the passage of newly synthesized secretory proteins across the membrane and opens laterally to allow transmembrane segments of nascent membrane proteins to enter the lipid bilayer. The electron microscopy and X-ray results together suggest that only one copy of the SecY or Sec61 complex within an oligomer translocates a polypeptide chain at any given time.
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Affiliation(s)
- William M Clemons
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
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Abstract
The ATPase SecA mediates the posttranslational translocation of a wide range of polypeptide substrates through the SecY channel in the cytoplasmic membrane of bacteria. We have determined the crystal structure of a monomeric form of Bacillus subtilis SecA at a 2.2-A resolution. A comparison with the previously determined structures of SecA reveals a nucleotide-independent, large conformational change that opens a deep groove similar to that in other proteins that interact with diverse polypeptides. We propose that the open form of SecA represents an activated state.
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Affiliation(s)
- Andrew R Osborne
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
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Abstract
The mechanisms by which hydrophobic molecules, such as long-chain fatty acids, enter cells are poorly understood. In Gram-negative bacteria, the lipopolysaccharide layer in the outer membrane is an efficient barrier for fatty acids and aromatic hydrocarbons destined for biodegradation. We report crystal structures of the long-chain fatty acid transporter FadL from Escherichia coli at 2.6 and 2.8 angstrom resolution. FadL forms a 14-stranded beta barrel that is occluded by a central hatch domain. The structures suggest that hydrophobic compounds bind to multiple sites in FadL and use a transport mechanism that involves spontaneous conformational changes in the hatch.
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Affiliation(s)
- Bert van den Berg
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA.
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Van den Berg B, Clemons WM, Collinson I, Modis Y, Hartmann E, Harrison SC, Rapoport TA. X-ray structure of a protein-conducting channel. Nature 2003; 427:36-44. [PMID: 14661030 DOI: 10.1038/nature02218] [Citation(s) in RCA: 927] [Impact Index Per Article: 44.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2003] [Accepted: 11/19/2003] [Indexed: 11/09/2022]
Abstract
A conserved heterotrimeric membrane protein complex, the Sec61 or SecY complex, forms a protein-conducting channel, allowing polypeptides to be transferred across or integrated into membranes. We report the crystal structure of the complex from Methanococcus jannaschii at a resolution of 3.2 A. The structure suggests that one copy of the heterotrimer serves as a functional translocation channel. The alpha-subunit has two linked halves, transmembrane segments 1-5 and 6-10, clamped together by the gamma-subunit. A cytoplasmic funnel leading into the channel is plugged by a short helix. Plug displacement can open the channel into an 'hourglass' with a ring of hydrophobic residues at its constriction. This ring may form a seal around the translocating polypeptide, hindering the permeation of other molecules. The structure also suggests mechanisms for signal-sequence recognition and for the lateral exit of transmembrane segments of nascent membrane proteins into lipid, and indicates binding sites for partners that provide the driving force for translocation.
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Affiliation(s)
- Bert Van den Berg
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, USA
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Brodersen DE, Clemons WM, Carter AP, Wimberly BT, Ramakrishnan V. Phasing the 30S ribosomal subunit structure. Acta Crystallogr D Biol Crystallogr 2003; 59:2044-50. [PMID: 14573961 DOI: 10.1107/s0907444903017669] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2003] [Accepted: 08/07/2003] [Indexed: 11/11/2022]
Abstract
The methods involved in determining the 850 kDa structure of the 30S ribosomal subunit from Thermus thermophilus were in many ways identical to those that are generally used in standard protein crystallography. This paper reviews and analyses the methods that can be used in phasing such large structures and shows that the anomalous signal collected from heavy-atom compounds bound to the RNA is both necessary and sufficient for ab initio structure determination at high resolution. In addition, measures to counter problems with non-isomorphism and radiation decay are described.
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Affiliation(s)
- D E Brodersen
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, England
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