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Barbat B, Douzi B, Ball G, Tribout M, El Karkouri K, Kellenberger C, Voulhoux R. Insights into dynamics and gating properties of T2SS secretins. SCIENCE ADVANCES 2023; 9:eadg6996. [PMID: 37792935 PMCID: PMC10550240 DOI: 10.1126/sciadv.adg6996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 09/05/2023] [Indexed: 10/06/2023]
Abstract
Secretins are outer membrane (OM) channels found in various bacterial nanomachines that secrete or assemble large extracellular structures. High-resolution 3D structures of type 2 secretion system (T2SS) secretins revealed bimodular channels with a C-module, holding a conserved central gate and an optional top gate, followed by an N-module for which multiple structural organizations have been proposed. Here, we perform a structure-driven in vivo study of the XcpD secretin, which validates one of the organizations of the N-module whose flexibility enables alternative conformations. We also show the existence of the central gate in vivo and its required flexibility, which is key for substrate passage and watertightness control. Last, functional, genomic, and phylogenetic analyses indicate that the optional top gate provides a gain of watertightness. Our data illustrate how the gating properties of T2SS secretins allow these large channels to overcome the duality between the necessity of preserving the OM impermeability while simultaneously promoting the secretion of large, folded effectors.
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Affiliation(s)
- Brice Barbat
- LCB-UMR7283, CNRS, Aix Marseille Université, IMM, Marseille, France
| | - Badreddine Douzi
- LCB-UMR7283, CNRS, Aix Marseille Université, IMM, Marseille, France
- Université de Lorraine, INRAE, DynAMic, Nancy, F-54000 France
| | - Geneviève Ball
- LCB-UMR7283, CNRS, Aix Marseille Université, IMM, Marseille, France
| | - Mathilde Tribout
- LCB-UMR7283, CNRS, Aix Marseille Université, IMM, Marseille, France
| | | | | | - Romé Voulhoux
- LCB-UMR7283, CNRS, Aix Marseille Université, IMM, Marseille, France
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2
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Thompson MK, Sharma N, Prakash A. Deciphering the orthorhombic crystal structure of a novel NEIL1 nanobody with pseudo-merohedral twinning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.07.552313. [PMID: 37609231 PMCID: PMC10441366 DOI: 10.1101/2023.08.07.552313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Nanobodies or VHHs (Variable Heavy domains of Heavy chain) are single domain antibodies that comprise three antigenic complementary determining regions (CDR). Nanobodies are used in numerous scientific applications including, bio-imaging, diagnosis, therapeutics, and macromolecular crystallography. We obtained crystals of a ∼14 kDa nanobody specific for the NEIL1 DNA glycosylase (hereafter called A5) in 0.5 M ammonium sulfate, 0.1 M sodium citrate tribasic dihydrate pH 5.6, and 1.0 M lithium sulfate monohydrate from the Crystal HT Hampton Research screen that were further optimized. Here, we describe the structure determination and refinement of the A5 crystals to a resolution of 2.1 Å. The data collected were complicated by the presence of anisotropy and twinning, and while initial space group determination pointed to a higher apparent tetragonal crystal system, the data statistics suggested twinning, placing the crystal in an orthorhombic system. Twinning was confirmed by the Padilla and Yeates test, H-test, and Britton test based on local intensity differences with a twin fraction of 0.4. Molecular replacement produced the best solution in the orthorhombic space group P2 1 2 1 2 with four molecules in the asymmetric unit and we were able to model over 96% of the residues in the electron density with a final R work and R free of 0.1988 and 0.2289 upon refinement. Synopsis The crystal structure of a specific nanobody against NEIL1 was determined to 2.1 Å. The structure was ultimately solved in an orthorhombic space group after diffraction data analysis revealed mild anisotropy as well as pseudo-merohedral twinning.
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3
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Barbat B, Douzi B, Voulhoux R. Structural lessons on bacterial secretins. Biochimie 2023; 205:110-116. [PMID: 36096236 DOI: 10.1016/j.biochi.2022.08.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/26/2022] [Accepted: 08/31/2022] [Indexed: 11/30/2022]
Abstract
To exchange and communicate with their surroundings, bacteria have evolved multiple active and passive mechanisms for trans-envelope transport. Among the pore-forming complexes found in the outer membrane of Gram-negative bacteria, secretins are distinctive homo-oligomeric channels dedicated to the active translocation of voluminous structures such as folded proteins, assembled fibers, virus particles or DNA. Members of the bacterial secretin family share a common cylinder-shaped structure with a gated pore-forming part inserted in the outer membrane, and a periplasmic channel connected to the inner membrane components of the corresponding nanomachine. In this mini-review, we will present what recently determined 3D structures have told us about the mechanisms of translocation through secretins of large substrates to the bacterial surface or in the extracellular milieu.
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Affiliation(s)
- Brice Barbat
- LCB-UMR7283, CNRS, Aix Marseille Université, IMM, 13009, Marseille, France
| | | | - Romé Voulhoux
- LCB-UMR7283, CNRS, Aix Marseille Université, IMM, 13009, Marseille, France.
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4
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Pushpker R, Bay DC, Turner RJ. Small multidrug resistance protein EmrE phenotypically associates with OmpW, DcrB and YggM for osmotic stress protection by betaine in Escherichia coli. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 36748554 DOI: 10.1099/mic.0.001287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The small multidrug resistance (SMR) protein EmrE resides in the inner membrane and provides resistance against a wide range of antiseptic quaternary cationic compounds (QCCs) for the Gram-negative bacterium Escherichia coli. We have reported previously that overexpression of the emrE gene results in the reduction of pH and osmotic tolerance, likely through EmrE-mediated biological QCC-based osmoprotectant efflux, indicating a potential physiological role for EmrE beyond providing drug resistance. EmrE is the most studied member of SMR transporter family; however, it is not known how the substrates translocated by EmrE move across the periplasm and through the outer membrane (OM). We have shown that the OM protein OmpW participates in the EmrE-mediated substrate efflux process and provided a hypothesis for the present study that additional OM and periplasmic proteins participate in the translocation process. To test the hypothesis, we conducted alkaline pH-based growth phenotype screens under emrE overexpression conditions. This screen identified 10 additional genes that appear to contribute to the EmrE-coupled osmoprotectant efflux: gspD, hofQ, yccZ, acrA, emrA, emrB, proX, osmF, dcrB and yggM. Further screening of these genes using a hyperosmotic growth phenotype assay in the presence and the absence of the osmoprotectant glycine betaine identified ompW and two periplasmic protein genes, dcrB and yggM, are mechanistically linked to EmrE.
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Affiliation(s)
- Rajnigandha Pushpker
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Denice C Bay
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Raymond J Turner
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
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5
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Moliner-Morro A, McInerney GM, Hanke L. Nanobodies in the limelight: Multifunctional tools in the fight against viruses. J Gen Virol 2022; 103. [PMID: 35579613 DOI: 10.1099/jgv.0.001731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Antibodies are natural antivirals generated by the vertebrate immune system in response to viral infection or vaccination. Unsurprisingly, they are also key molecules in the virologist's molecular toolbox. With new developments in methods for protein engineering, protein functionalization and application, smaller antibody-derived fragments are moving in focus. Among these, camelid-derived nanobodies play a prominent role. Nanobodies can replace full-sized antibodies in most applications and enable new possible applications for which conventional antibodies are challenging to use. Here we review the versatile nature of nanobodies, discuss their promise as antiviral therapeutics, for diagnostics, and their suitability as research tools to uncover novel aspects of viral infection and disease.
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Affiliation(s)
- Ainhoa Moliner-Morro
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Gerald M McInerney
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
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De Bruyn P, Prolič-Kalinšek M, Vandervelde A, Malfait M, Sterckx YGJ, Sobott F, Hadži S, Pardon E, Steyaert J, Loris R. Nanobody-aided crystallization of the transcription regulator PaaR2 from Escherichia coli O157:H7. Acta Crystallogr F Struct Biol Commun 2021; 77:374-384. [PMID: 34605442 PMCID: PMC8488858 DOI: 10.1107/s2053230x21009006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 08/30/2021] [Indexed: 11/10/2022] Open
Abstract
paaR2-paaA2-parE2 is a three-component toxin-antitoxin module found in prophage CP-993P of Escherichia coli O157:H7. Transcription regulation of this module occurs via the 123-amino-acid regulator PaaR2, which forms a large oligomeric structure. Despite appearing to be well folded, PaaR2 withstands crystallization, as does its N-terminal DNA-binding domain. Native mass spectrometry was used to screen for nanobodies that form a unique complex and stabilize the octameric structure of PaaR2. One such nanobody, Nb33, allowed crystallization of the protein. The resulting crystals belong to space group F432, with unit-cell parameter a = 317 Å, diffract to 4.0 Å resolution and are likely to contain four PaaR2 monomers and four nanobody monomers in the asymmetric unit. Crystals of two truncates containing the N-terminal helix-turn-helix domain also interact with Nb33, and the corresponding co-crystals diffracted to 1.6 and 1.75 Å resolution.
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Affiliation(s)
- Pieter De Bruyn
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
- Center for Structural Biology, VIB, Pleinlaan 2, 1050 Brussels, Belgium
| | - Maruša Prolič-Kalinšek
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
- Center for Structural Biology, VIB, Pleinlaan 2, 1050 Brussels, Belgium
| | - Alexandra Vandervelde
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
- Center for Structural Biology, VIB, Pleinlaan 2, 1050 Brussels, Belgium
| | - Milan Malfait
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Yann G.-J. Sterckx
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
- Center for Structural Biology, VIB, Pleinlaan 2, 1050 Brussels, Belgium
- Laboratory of Medical Biochemistry (LMB) and the Infla-Med Centre of Excellence, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Frank Sobott
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
- School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - San Hadži
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, 1000 Ljubljana, Slovenia
| | - Els Pardon
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
- Center for Structural Biology, VIB, Pleinlaan 2, 1050 Brussels, Belgium
| | - Jan Steyaert
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
- Center for Structural Biology, VIB, Pleinlaan 2, 1050 Brussels, Belgium
| | - Remy Loris
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
- Center for Structural Biology, VIB, Pleinlaan 2, 1050 Brussels, Belgium
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7
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Rathinaswamy MK, Fleming KD, Dalwadi U, Pardon E, Harris NJ, Yip CK, Steyaert J, Burke JE. HDX-MS-optimized approach to characterize nanobodies as tools for biochemical and structural studies of class IB phosphoinositide 3-kinases. Structure 2021; 29:1371-1381.e6. [PMID: 34348129 DOI: 10.1016/j.str.2021.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 06/07/2021] [Accepted: 07/15/2021] [Indexed: 10/20/2022]
Abstract
There is considerable interest in developing antibodies as modulators of signaling pathways. One of the most important signaling pathways in higher eukaryotes is the phosphoinositide 3-kinase (PI3K) pathway, which plays fundamental roles in growth, metabolism, and immunity. The class IB PI3K, PI3Kγ, is a heterodimeric complex composed of a catalytic p110γ subunit bound to a p101 or p84 regulatory subunit. PI3Kγ is a critical component in multiple immune signaling processes and is dependent on activation by Ras and G protein-coupled receptors (GPCRs) to mediate its cellular roles. Here we describe the rapid and efficient characterization of multiple PI3Kγ binding single-chain camelid nanobodies using hydrogen-deuterium exchange (HDX) mass spectrometry (MS) for structural and biochemical studies. We identify nanobodies that stimulated lipid kinase activity, block Ras activation, and specifically inhibited p101-mediated GPCR activation. Overall, our work reveals insight into PI3Kγ regulation and identifies sites that may be exploited for therapeutic development.
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Affiliation(s)
- Manoj K Rathinaswamy
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 2Y2, Canada
| | - Kaelin D Fleming
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 2Y2, Canada
| | - Udit Dalwadi
- Life Sciences Institute, Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Els Pardon
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels, Belgium; VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - Noah J Harris
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 2Y2, Canada
| | - Calvin K Yip
- Life Sciences Institute, Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Jan Steyaert
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels, Belgium; VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 2Y2, Canada; Life Sciences Institute, Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.
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8
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Horváthová L, Žárský V, Pánek T, Derelle R, Pyrih J, Motyčková A, Klápšťová V, Vinopalová M, Marková L, Voleman L, Klimeš V, Petrů M, Vaitová Z, Čepička I, Hryzáková K, Harant K, Gray MW, Chami M, Guilvout I, Francetic O, Franz Lang B, Vlček Č, Tsaousis AD, Eliáš M, Doležal P. Analysis of diverse eukaryotes suggests the existence of an ancestral mitochondrial apparatus derived from the bacterial type II secretion system. Nat Commun 2021; 12:2947. [PMID: 34011950 PMCID: PMC8134430 DOI: 10.1038/s41467-021-23046-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 03/22/2021] [Indexed: 12/14/2022] Open
Abstract
The type 2 secretion system (T2SS) is present in some Gram-negative eubacteria and used to secrete proteins across the outer membrane. Here we report that certain representative heteroloboseans, jakobids, malawimonads and hemimastigotes unexpectedly possess homologues of core T2SS components. We show that at least some of them are present in mitochondria, and their behaviour in biochemical assays is consistent with the presence of a mitochondrial T2SS-derived system (miT2SS). We additionally identified 23 protein families co-occurring with miT2SS in eukaryotes. Seven of these proteins could be directly linked to the core miT2SS by functional data and/or sequence features, whereas others may represent different parts of a broader functional pathway, possibly also involving the peroxisome. Its distribution in eukaryotes and phylogenetic evidence together indicate that the miT2SS-centred pathway is an ancestral eukaryotic trait. Our findings thus have direct implications for the functional properties of the early mitochondrion. Bacteria use the type 2 secretion system to secrete enzymes and toxins across the outer membrane to the environment. Here the authors analyse the T2SS pathway in three protist lineages and suggest that the early mitochondrion may have been capable of secreting proteins into the cytosol.
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Affiliation(s)
- Lenka Horváthová
- Faculty of Science, Department of Parasitology, Charles University, BIOCEV, Vestec, Czech Republic
| | - Vojtěch Žárský
- Faculty of Science, Department of Parasitology, Charles University, BIOCEV, Vestec, Czech Republic
| | - Tomáš Pánek
- Faculty of Science, Department of Biology and Ecology, University of Ostrava, Ostrava, Czech Republic.,Faculty of Science, Department of Zoology, Charles University, Prague 2, Czech Republic
| | - Romain Derelle
- School of Biosciences, University of Birmingham, Edgbaston, UK
| | - Jan Pyrih
- Laboratory of Molecular & Evolutionary Parasitology, RAPID group, School of Biosciences, University of Kent, Canterbury, UK.,Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Alžběta Motyčková
- Faculty of Science, Department of Parasitology, Charles University, BIOCEV, Vestec, Czech Republic
| | - Veronika Klápšťová
- Faculty of Science, Department of Parasitology, Charles University, BIOCEV, Vestec, Czech Republic
| | - Martina Vinopalová
- Faculty of Science, Department of Parasitology, Charles University, BIOCEV, Vestec, Czech Republic
| | - Lenka Marková
- Faculty of Science, Department of Parasitology, Charles University, BIOCEV, Vestec, Czech Republic
| | - Luboš Voleman
- Faculty of Science, Department of Parasitology, Charles University, BIOCEV, Vestec, Czech Republic
| | - Vladimír Klimeš
- Faculty of Science, Department of Biology and Ecology, University of Ostrava, Ostrava, Czech Republic
| | - Markéta Petrů
- Faculty of Science, Department of Parasitology, Charles University, BIOCEV, Vestec, Czech Republic
| | - Zuzana Vaitová
- Faculty of Science, Department of Parasitology, Charles University, BIOCEV, Vestec, Czech Republic
| | - Ivan Čepička
- Faculty of Science, Department of Zoology, Charles University, Prague 2, Czech Republic
| | - Klára Hryzáková
- Faculty of Science, Department of Genetics and Microbiology, Charles University, Prague 2, Czech Republic
| | - Karel Harant
- Faculty of Science, Proteomic core facility, Charles University, BIOCEV, Vestec, Czech Republic
| | - Michael W Gray
- Department of Biochemistry and Molecular Biology and Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, NS, Canada
| | - Mohamed Chami
- Center for Cellular Imaging and NanoAnalytics, University of Basel, Basel, Switzerland
| | - Ingrid Guilvout
- Biochemistry of Macromolecular Interactions Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, Paris, France
| | - Olivera Francetic
- Biochemistry of Macromolecular Interactions Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, Paris, France
| | - B Franz Lang
- Robert Cedergren Centre for Bioinformatics and Genomics, Département de Biochimie, Université de Montréal, Montreal, QC, Canada
| | - Čestmír Vlček
- Institute of Molecular Genetics, Czech Academy of Sciences, Prague 4, Czech Republic
| | - Anastasios D Tsaousis
- Laboratory of Molecular & Evolutionary Parasitology, RAPID group, School of Biosciences, University of Kent, Canterbury, UK
| | - Marek Eliáš
- Faculty of Science, Department of Biology and Ecology, University of Ostrava, Ostrava, Czech Republic.
| | - Pavel Doležal
- Faculty of Science, Department of Parasitology, Charles University, BIOCEV, Vestec, Czech Republic.
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9
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Schuler EJA, Marconi RT. The Leptospiral General Secretory Protein D (GspD), a secretin, elicits complement-independent bactericidal antibody against diverse Leptospira species and serovars. Vaccine X 2021; 7:100089. [PMID: 33733085 PMCID: PMC7941034 DOI: 10.1016/j.jvacx.2021.100089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 02/18/2021] [Accepted: 02/20/2021] [Indexed: 11/21/2022] Open
Abstract
Leptospirosis, the most common zoonotic infection worldwide, is a multi-system disorder affecting the kidney, liver, and lungs. Infections can be asymptomatic, self-limiting or progress to multi-organ system failure and pulmonary hemorrhage. The incidence of canine and human leptospirosis is steadily increasing worldwide. At least sixty-four Leptospira species and several hundred lipopolysaccharide-based serovars have been defined. Preventive vaccines are available for use in veterinary medicine and limited use in humans in some countries. All commercially available vaccines are bacterin formulations that consist of a combination of laboratory cultivated strains of different lipopolysaccharide serotypes. The development of a broadly protective subunit vaccine would represent a significant step forward in efforts to combat leptospirosis in humans, livestock, and companion animals worldwide. Here we investigate the potential of General secretory protein D (GspD; LIC11570), a secretin, to serve as a possible antigen in a multi-valent vaccine formulation. GspD is conserved, expressed in vitro, antigenic during infection and elicits antibody with complement independent bactericidal activity. Importantly, antibody to GspD is bactericidal against diverse Leptospira species of the P1 subclade. Epitope mapping localized the bactericidal epitopes to the N-terminal N0 domain of GspD. The data within support further exploration of GspD as a candidate for inclusion in a next generation multi-protein subunit vaccine.
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Affiliation(s)
- EJA. Schuler
- Department of Microbiology and Immunology, Virginia Commonwealth University Medical Center, 1112 E Clay St., Richmond, VA 23298, USA
| | - RT. Marconi
- Department of Microbiology and Immunology, Virginia Commonwealth University Medical Center, 1112 E Clay St., Richmond, VA 23298, USA
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10
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Pineau C, Guschinskaya N, Gonçalves IR, Ruaudel F, Robert X, Gouet P, Ballut L, Shevchik VE. Structure-function analysis of pectate lyase Pel3 reveals essential facets of protein recognition by the bacterial type 2 secretion system. J Biol Chem 2021; 296:100305. [PMID: 33465378 PMCID: PMC7949064 DOI: 10.1016/j.jbc.2021.100305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 01/11/2021] [Accepted: 01/14/2021] [Indexed: 12/02/2022] Open
Abstract
The type II secretion system (T2SS) transports fully folded proteins of various functions and structures through the outer membrane of Gram-negative bacteria. The molecular mechanisms of substrate recruitment by T2SS remain elusive but a prevailing view is that the secretion determinants could be of a structural nature. The phytopathogenic γ-proteobacteria, Pectobacterium carotovorum and Dickeya dadantii, secrete similar sets of homologous plant cell wall degrading enzymes, mainly pectinases, by similar T2SSs, called Out. However, the orthologous pectate lyases Pel3 and PelI from these bacteria, which share 67% of sequence identity, are not secreted by the counterpart T2SS of each bacterium, indicating a fine-tuned control of protein recruitment. To identify the related secretion determinants, we first performed a structural characterization and comparison of Pel3 with PelI using X-ray crystallography. Then, to assess the biological relevance of the observed structural variations, we conducted a loop-substitution analysis of Pel3 combined with secretion assays. We showed that there is not one element with a definite secondary structure but several distant and structurally flexible loop regions that are essential for the secretion of Pel3 and that these loop regions act together as a composite secretion signal. Interestingly, depending on the crystal contacts, one of these key secretion determinants undergoes disorder-to-order transitions that could reflect its transient structuration upon the contact with the appropriate T2SS components. We hypothesize that such T2SS-induced structuration of some intrinsically disordered zones of secretion substrates could be part of the recruitment mechanism used by T2SS.
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Affiliation(s)
- Camille Pineau
- Microbiologie Adaptation et Pathogénie, Univ Lyon, Université de Lyon 1, UMR5240 CNRS, Villeurbanne, France; Microbiologie Adaptation et Pathogénie, Univ Lyon, INSA Lyon, UMR5240, Villeurbanne, France
| | - Natalia Guschinskaya
- Microbiologie Adaptation et Pathogénie, Univ Lyon, Université de Lyon 1, UMR5240 CNRS, Villeurbanne, France; Microbiologie Adaptation et Pathogénie, Univ Lyon, INSA Lyon, UMR5240, Villeurbanne, France
| | - Isabelle R Gonçalves
- Microbiologie Adaptation et Pathogénie, Univ Lyon, Université de Lyon 1, UMR5240 CNRS, Villeurbanne, France
| | - Florence Ruaudel
- Microbiologie Adaptation et Pathogénie, Univ Lyon, Université de Lyon 1, UMR5240 CNRS, Villeurbanne, France
| | - Xavier Robert
- Molecular Microbiology and Structural Biochemistry, Univ Lyon, UMR5086 CNRS, Lyon, France
| | - Patrice Gouet
- Molecular Microbiology and Structural Biochemistry, Univ Lyon, UMR5086 CNRS, Lyon, France
| | - Lionel Ballut
- Molecular Microbiology and Structural Biochemistry, Univ Lyon, UMR5086 CNRS, Lyon, France.
| | - Vladimir E Shevchik
- Microbiologie Adaptation et Pathogénie, Univ Lyon, Université de Lyon 1, UMR5240 CNRS, Villeurbanne, France; Microbiologie Adaptation et Pathogénie, Univ Lyon, INSA Lyon, UMR5240, Villeurbanne, France.
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11
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Naskar S, Hohl M, Tassinari M, Low HH. The structure and mechanism of the bacterial type II secretion system. Mol Microbiol 2020; 115:412-424. [PMID: 33283907 DOI: 10.1111/mmi.14664] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 12/03/2020] [Indexed: 12/17/2022]
Abstract
The type II secretion system (T2SS) is a multi-protein complex used by many bacteria to move substrates across their cell membrane. Substrates released into the environment serve as local and long-range effectors that promote nutrient acquisition, biofilm formation, and pathogenicity. In both animals and plants, the T2SS is increasingly recognized as a key driver of virulence. The T2SS spans the bacterial cell envelope and extrudes substrates through an outer membrane secretin channel using a pseudopilus. An inner membrane assembly platform and a cytoplasmic motor controls pseudopilus assembly. This microreview focuses on the structure and mechanism of the T2SS. Advances in cryo-electron microscopy are enabling increasingly elaborate sub-complexes to be resolved. However, key questions remain regarding the mechanism of pseudopilus extension and retraction, and how this is coupled with the choreography of the substrate moving through the secretion system. The T2SS is part of an ancient type IV filament superfamily that may have been present within the last universal common ancestor (LUCA). Overall, mechanistic principles that underlie T2SS function have implication for other closely related systems such as the type IV and tight adherence pilus systems.
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Affiliation(s)
- Souvik Naskar
- Department of Infectious Disease, Imperial College, London, UK
| | - Michael Hohl
- Department of Infectious Disease, Imperial College, London, UK
| | | | - Harry H Low
- Department of Infectious Disease, Imperial College, London, UK
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12
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Uhlemann EME, Yu CH, Patry J, Dolgova N, Lutsenko S, Muyldermans S, Dmitriev OY. Nanobodies against the metal binding domains of ATP7B as tools to study copper transport in the cell. Metallomics 2020; 12:1941-1950. [PMID: 33094790 DOI: 10.1039/d0mt00191k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Nanobodies are genetically engineered single domain antibodies derived from the unusual heavy-chain only antibodies found in llamas and camels. The small size of the nanobodies and flexible selection schemes make them uniquely versatile tools for protein biochemistry and cell biology. We have developed a panel of nanobodies against the metal binding domains of the human copper transporter ATP7B, a multidomain membrane protein with a complex regulation of enzymatic activity and intracellular localization. To enable the use of the nanobodies as tools to investigate copper transport in the cell, we characterized their binding sites and affinity by isothermal titration calorimetry and NMR. We have identified nanobodies against each of the first four metal binding domains of ATP7B, with a wide affinity range, as evidenced by dissociation constants from below 10-9 to 10-6 M. We found both the inhibitory and activating nanobodies among those tested. The diverse properties of the nanobodies make the panel useful for the structural studies of ATP7B, immunoaffinity purification of the protein, modulation of its activity in the cell, protein dynamics studies, and as mimics of copper chaperone ATOX1, the natural interaction partner of ATP7B.
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Affiliation(s)
- Eva-Maria E Uhlemann
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, Canada.
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13
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Mir MA, Mehraj U, Sheikh BA, Hamdani SS. Nanobodies: The "Magic Bullets" in therapeutics, drug delivery and diagnostics. Hum Antibodies 2020; 28:29-51. [PMID: 31322555 DOI: 10.3233/hab-190390] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Antibodies represent a well-established class of clinical diagnostics for medical applications as well as essential research and biotechnological tools. Although both polyclonal and monoclonal antibodies are indispensable reagents in basic research and diagnostics but both of them have their limitations. Hence, there is urgent need to develop strategies aimed at production of alternative scaffolds and recombinant antibodies of smaller dimensions that could be easily produced, selected and manipulated. Unlike conventional antibodies, members of Camelidae and sharks produce antibodies composed only of heavy chains with small size, high solubility, thermal stability, refolding capacity and good tissue penetration in vivo. The discovery of these naturally occurring antibodies having only heavy-chain in Camelidae family and their further development into small recombinant nanobodies represents an attractive alternative in drug delivery, diagnostics and imaging. Nanobody derivatives are soluble, stable, versatile, have unique refolding capacities, reduced aggregation tendencies and high-target binding capabilities. They can be genetically customized to target enzymes, transmembrane proteins or molecular interactions. Their ability to recognize recessed antigenic sites has been attributed to their smaller size and the ability of the extended CDR3 loop to quickly penetrate into such epitopes. With the advent of molecular engineering and phage display technology, they can be of potential use in molecular imaging, drug delivery and therapeutics for several major diseases. In this review we present the recent advances in nanobodies for modulating immune functions, for targeting cancers, viruses, toxins and microbes as well as their utility as diagnostic and biosensor tools.
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14
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Miletic S, Goessweiner-Mohr N, Marlovits TC. The Structure of the Type III Secretion System Needle Complex. Curr Top Microbiol Immunol 2020; 427:67-90. [PMID: 31667599 DOI: 10.1007/82_2019_178] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The type III secretion system (T3SS) is an essential virulence factor of many pathogenic bacterial species including Salmonella, Yersinia, Shigella and enteropathogenic Escherichia coli (EPEC). It is an intricate molecular machine that spans the bacterial membranes and injects effector proteins into target host cells, enabling bacterial infection. The T3SS needle complex comprises of proteinaceous rings supporting a needle filament which extends out into the extracellular environment. It serves as the central conduit for translocating effector proteins. Multiple laboratories have dedicated a remarkable effort to decipher the structure and function of the needle complex. A combination of structural biology techniques such as cryo-electron microscopy (cryoEM), X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy and computer modelling have been utilized to study different structural components at progressively higher resolutions. This chapter will provide an overview of the structural details of the T3SS needle complex, shedding light on this essential component of this fascinating bacterial system.
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Affiliation(s)
- Sean Miletic
- Center for Structural Systems Biology, Institute for Structural and Systems Biology, Universitätsklinikum Hamburg-Eppendorf, 85 Notkestraße, Hamburg, 22607, Germany
| | | | - Thomas C Marlovits
- Center for Structural Systems Biology, Institute for Structural and Systems Biology, Universitätsklinikum Hamburg-Eppendorf, 85 Notkestraße, Hamburg, 22607, Germany.
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15
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Silva YRDO, Contreras-Martel C, Macheboeuf P, Dessen A. Bacterial secretins: Mechanisms of assembly and membrane targeting. Protein Sci 2020; 29:893-904. [PMID: 32020694 DOI: 10.1002/pro.3835] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 01/25/2020] [Accepted: 01/28/2020] [Indexed: 12/20/2022]
Abstract
Secretion systems are employed by bacteria to transport macromolecules across membranes without compromising their integrities. Processes including virulence, colonization, and motility are highly dependent on the secretion of effector molecules toward the immediate cellular environment, and in some cases, into the host cytoplasm. In Type II and Type III secretion systems, as well as in Type IV pili, homomultimeric complexes known as secretins form large pores in the outer bacterial membrane, and the localization and assembly of such 1 MDa molecules often relies on pilotins or accessory proteins. Significant progress has been made toward understanding details of interactions between secretins and their partner proteins using approaches ranging from bacterial genetics to cryo electron microscopy. This review provides an overview of the mode of action of pilotins and accessory proteins for T2SS, T3SS, and T4PS secretins, highlighting recent near-atomic resolution cryo-EM secretin complex structures and underlining the importance of these interactions for secretin functionality.
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Affiliation(s)
- Yuri Rafael de Oliveira Silva
- Brazilian Biosciences National Laboratory (LNBio), CNPEM, Campinas, São Paulo, Brazil.,Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Carlos Contreras-Martel
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), Grenoble, France
| | - Pauline Macheboeuf
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), Grenoble, France
| | - Andréa Dessen
- Brazilian Biosciences National Laboratory (LNBio), CNPEM, Campinas, São Paulo, Brazil.,Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), Grenoble, France
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16
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Chernyatina AA, Low HH. Core architecture of a bacterial type II secretion system. Nat Commun 2019; 10:5437. [PMID: 31780649 PMCID: PMC6882859 DOI: 10.1038/s41467-019-13301-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 10/25/2019] [Indexed: 01/01/2023] Open
Abstract
Bacterial type II secretion systems (T2SSs) translocate virulence factors, toxins and enzymes across the cell outer membrane. Here we use negative stain and cryo-electron microscopy to reveal the core architecture of an assembled T2SS from the pathogen Klebsiella pneumoniae. We show that 7 proteins form a ~2.4 MDa complex that spans the cell envelope. The outer membrane complex includes the secretin PulD, with all domains modelled, and the pilotin PulS. The inner membrane assembly platform components PulC, PulE, PulL, PulM and PulN have a relative stoichiometric ratio of 2:1:1:1:1. The PulE ATPase, PulL and PulM combine to form a flexible hexameric hub. Symmetry mismatch between the outer membrane complex and assembly platform is overcome by PulC linkers spanning the periplasm, with PulC HR domains binding independently at the secretin base. Our results show that the T2SS has a highly dynamic modular architecture, with implication for pseudo-pilus assembly and substrate loading.
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Affiliation(s)
| | - Harry H Low
- Department of Life Sciences, Imperial College, London, SW7 2AZ, UK.
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17
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Abstract
The type II secretion system (T2SS) delivers toxins and a range of hydrolytic enzymes, including proteases, lipases, and carbohydrate-active enzymes, to the cell surface or extracellular space of Gram-negative bacteria. Its contribution to survival of both extracellular and intracellular pathogens as well as environmental species of proteobacteria is evident. This dynamic, multicomponent machinery spans the entire cell envelope and consists of a cytoplasmic ATPase, several inner membrane proteins, a periplasmic pseudopilus, and a secretin pore embedded in the outer membrane. Despite the trans-envelope configuration of the T2S nanomachine, proteins to be secreted engage with the system first once they enter the periplasmic compartment via the Sec or TAT export system. Thus, the T2SS is specifically dedicated to their outer membrane translocation. The many sequence and structural similarities between the T2SS and type IV pili suggest a common origin and argue for a pilus-mediated mechanism of secretion. This minireview describes the structures, functions, and interactions of the individual T2SS components and the general architecture of the assembled T2SS machinery and briefly summarizes the transport and function of a growing list of T2SS exoproteins. Recent advances in cryo-electron microscopy, which have led to an increased understanding of the structure-function relationship of the secretin channel and the pseudopilus, are emphasized.
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18
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Natarajan J, Singh N, Rapaport D. Assembly and targeting of secretins in the bacterial outer membrane. Int J Med Microbiol 2019; 309:151322. [PMID: 31262642 DOI: 10.1016/j.ijmm.2019.06.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 06/04/2019] [Accepted: 06/18/2019] [Indexed: 11/20/2022] Open
Abstract
In Gram-negative bacteria, secretion of toxins ensure the survival of the bacterium. Such toxins are secreted by sophisticated multiprotein systems. The most conserved part in some of these secretion systems are components, called secretins, which form the outer membrane ring in these systems. Recent structural studies shed some light on the oligomeric organization of secretins. However, the mechanisms by which these proteins are targeted to the outer membrane and assemble there into ring structures are still not fully understood. This review discusses the various species-specific targeting and assembly pathways that are taken by secretins in order to form their functional oligomers.
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Affiliation(s)
- Janani Natarajan
- Interfaculty Institute of Biochemistry, University of Tübingen, Hoppe-Seyler-Str. 4, 72076 Tübingen, Germany.
| | - Nidhi Singh
- Interfaculty Institute of Microbiology and Infection Medicine (IMIT), Elfriede-Aulhorn-Str.6, 72076 Tübingen, Germany
| | - Doron Rapaport
- Interfaculty Institute of Biochemistry, University of Tübingen, Hoppe-Seyler-Str. 4, 72076 Tübingen, Germany
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19
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Sgro GG, Oka GU, Souza DP, Cenens W, Bayer-Santos E, Matsuyama BY, Bueno NF, dos Santos TR, Alvarez-Martinez CE, Salinas RK, Farah CS. Bacteria-Killing Type IV Secretion Systems. Front Microbiol 2019; 10:1078. [PMID: 31164878 PMCID: PMC6536674 DOI: 10.3389/fmicb.2019.01078] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 04/29/2019] [Indexed: 01/25/2023] Open
Abstract
Bacteria have been constantly competing for nutrients and space for billions of years. During this time, they have evolved many different molecular mechanisms by which to secrete proteinaceous effectors in order to manipulate and often kill rival bacterial and eukaryotic cells. These processes often employ large multimeric transmembrane nanomachines that have been classified as types I-IX secretion systems. One of the most evolutionarily versatile are the Type IV secretion systems (T4SSs), which have been shown to be able to secrete macromolecules directly into both eukaryotic and prokaryotic cells. Until recently, examples of T4SS-mediated macromolecule transfer from one bacterium to another was restricted to protein-DNA complexes during bacterial conjugation. This view changed when it was shown by our group that many Xanthomonas species carry a T4SS that is specialized to transfer toxic bacterial effectors into rival bacterial cells, resulting in cell death. This review will focus on this special subtype of T4SS by describing its distinguishing features, similar systems in other proteobacterial genomes, and the nature of the effectors secreted by these systems and their cognate inhibitors.
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Affiliation(s)
- Germán G. Sgro
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Gabriel U. Oka
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Diorge P. Souza
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - William Cenens
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Ethel Bayer-Santos
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Bruno Y. Matsuyama
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Natalia F. Bueno
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | | | - Cristina E. Alvarez-Martinez
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, University of Campinas (UNICAMP), Campinas, Brazil
| | - Roberto K. Salinas
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Chuck S. Farah
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
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20
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van Beusekom B, Heidebrecht T, Adamopoulos A, Fish A, Pardon E, Steyaert J, Joosten RP, Perrakis A. Characterization and structure determination of a llama-derived nanobody targeting the J-base binding protein 1. Acta Crystallogr F Struct Biol Commun 2018; 74:690-695. [PMID: 30387773 PMCID: PMC6213982 DOI: 10.1107/s2053230x18010282] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 07/16/2018] [Indexed: 01/06/2023] Open
Abstract
J-base binding protein 1 (JBP1) contributes to the biosynthesis and maintenance of base J (β-D-glucosylhydroxymethyluracil), a modification of thymidine confined to some protozoa. Camelid (llama) single-domain antibody fragments (nanobodies) targeting JBP1 were produced for use as crystallization chaperones. Surface plasmon resonance screening identified Nb6 as a strong binder, recognizing JBP1 with a 1:1 stoichiometry and high affinity (Kd = 30 nM). Crystallization trials of JBP1 in complex with Nb6 yielded crystals that diffracted to 1.47 Å resolution. However, the dimensions of the asymmetric unit and molecular replacement with a nanobody structure clearly showed that the crystals of the expected complex with JBP1 were of the nanobody alone. Nb6 crystallizes in space group P31 with two molecules in the asymmetric unit; its crystal structure was refined to a final resolution of 1.64 Å. Ensemble refinement suggests that in the ligand-free state one of the complementarity-determining regions (CDRs) is flexible, while the other two adopt well defined conformations.
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Affiliation(s)
- Bart van Beusekom
- Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Tatjana Heidebrecht
- Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Athanassios Adamopoulos
- Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Alexander Fish
- Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Els Pardon
- VIB–VUB Center for Structural Biology, VIB, Pleinlaan 2, 1050 Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Jan Steyaert
- VIB–VUB Center for Structural Biology, VIB, Pleinlaan 2, 1050 Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Robbie P. Joosten
- Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Anastassis Perrakis
- Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
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21
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Ahlstrand T, Torittu A, Elovaara H, Välimaa H, Pöllänen MT, Kasvandik S, Högbom M, Ihalin R. Interactions between the Aggregatibacter actinomycetemcomitans secretin HofQ and host cytokines indicate a link between natural competence and interleukin-8 uptake. Virulence 2018; 9:1205-1223. [PMID: 30088437 PMCID: PMC6086316 DOI: 10.1080/21505594.2018.1499378] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Naturally competent bacteria acquire DNA from their surroundings to survive in nutrient-poor environments and incorporate DNA into their genomes as new genes for improved survival. The secretin HofQ from the oral pathogen Aggregatibacter actinomycetemcomitans has been associated with DNA uptake. Cytokine sequestering is a potential virulence mechanism in various bacteria and may modulate both host defense and bacterial physiology. The objective of this study was to elucidate a possible connection between natural competence and cytokine uptake in A. actinomycetemcomitans. The extramembranous domain of HofQ (emHofQ) was shown to interact with various cytokines, of which IL-8 exhibited the strongest interaction. The dissociation constant between emHofQ and IL-8 was 43 nM in static settings and 2.4 μM in dynamic settings. The moderate binding affinity is consistent with the hypothesis that emHofQ recognizes cytokines before transporting them into the cells. The interaction site was identified via crosslinking and mutational analysis. By structural comparison, relateda type I KH domain with a similar interaction site was detected in the Neisseria meningitidis secretin PilQ, which has been shown to participate in IL-8 uptake. Deletion of hofQ from the A. actinomycetemcomitans genome decreased the overall biofilm formation of this organism, abolished the response to cytokines, i.e., decreased eDNA levels in the presence of cytokines, and increased the susceptibility of the biofilm to tested β-lactams. Moreover, we showed that recombinant IL-8 interacted with DNA. These results can be used in further studies on the specific role of cytokine uptake in bacterial virulence without interfering with natural-competence-related DNA uptake.
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Affiliation(s)
- Tuuli Ahlstrand
- a Department of Biochemistry , University of Turku , Turku , Finland
| | - Annamari Torittu
- a Department of Biochemistry , University of Turku , Turku , Finland
| | - Heli Elovaara
- a Department of Biochemistry , University of Turku , Turku , Finland
| | - Hannamari Välimaa
- b Department of Virology , University of Helsinki , Helsinki , Finland.,c Department of Oral and Maxillofacial Surgery , Helsinki University Hospital , Helsinki , Finland
| | - Marja T Pöllänen
- d Institute of Dentistry , University of Turku , Turku , Finland
| | - Sergo Kasvandik
- e Institute of Technology , University of Tartu , Tartu , Estonia
| | - Martin Högbom
- f Department of Biochemistry and Biophysics , Stockholm University , Stockholm , Sweden
| | - Riikka Ihalin
- a Department of Biochemistry , University of Turku , Turku , Finland
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22
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Majewski DD, Worrall LJ, Strynadka NCJ. Secretins revealed: structural insights into the giant gated outer membrane portals of bacteria. Curr Opin Struct Biol 2018; 51:61-72. [DOI: 10.1016/j.sbi.2018.02.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 02/28/2018] [Indexed: 01/19/2023]
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23
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Structural insight into the assembly of the type II secretion system pilotin–secretin complex from enterotoxigenic Escherichia coli. Nat Microbiol 2018; 3:581-587. [DOI: 10.1038/s41564-018-0148-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 03/07/2018] [Indexed: 12/29/2022]
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24
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Yerabham ASK, Müller-Schiffmann A, Ziehm T, Stadler A, Köber S, Indurkhya X, Marreiros R, Trossbach SV, Bradshaw NJ, Prikulis I, Willbold D, Weiergräber OH, Korth C. Biophysical insights from a single chain camelid antibody directed against the Disrupted-in-Schizophrenia 1 protein. PLoS One 2018; 13:e0191162. [PMID: 29324815 PMCID: PMC5764400 DOI: 10.1371/journal.pone.0191162] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 12/31/2017] [Indexed: 01/17/2023] Open
Abstract
Accumulating evidence suggests an important role for the Disrupted-in-Schizophrenia 1 (DISC1) protein in neurodevelopment and chronic mental illness. In particular, the C-terminal 300 amino acids of DISC1 have been found to mediate important protein-protein interactions and to harbor functionally important phosphorylation sites and disease-associated polymorphisms. However, long disordered regions and oligomer-forming subdomains have so far impeded structural analysis. VHH domains derived from camelid heavy chain only antibodies are minimal antigen binding modules with appreciable solubility and stability, which makes them well suited for the stabilizing proteins prior to structural investigation. Here, we report on the generation of a VHH domain derived from an immunized Lama glama, displaying high affinity for the human DISC1 C region (aa 691-836), and its characterization by surface plasmon resonance, size exclusion chromatography and immunological techniques. The VHH-DISC1 (C region) complex was also used for structural investigation by small angle X-ray scattering analysis. In combination with molecular modeling, these data support predictions regarding the three-dimensional fold of this DISC1 segment as well as its steric arrangement in complex with our VHH antibody.
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Affiliation(s)
- Antony S. K. Yerabham
- Department of Neuropathology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | | | - Tamar Ziehm
- Institute of Complex Systems (ICS-6: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
| | - Andreas Stadler
- Jülich Centre for Neutron Science JCNS and Institute for Complex Systems ICS, Forschungszentrum Jülich, Jülich, Germany
| | - Sabrina Köber
- Department of Neuropathology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Xela Indurkhya
- Department of Neuropathology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Rita Marreiros
- Department of Neuropathology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Svenja V. Trossbach
- Department of Neuropathology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Nicholas J. Bradshaw
- Department of Neuropathology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Ingrid Prikulis
- Department of Neuropathology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Dieter Willbold
- Institute of Complex Systems (ICS-6: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
- Institute for Physical Biology and BMFZ, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Oliver H. Weiergräber
- Institute of Complex Systems (ICS-6: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
| | - Carsten Korth
- Department of Neuropathology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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25
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Ereño-Orbea J, Sicard T, Cui H, Carson J, Hermans P, Julien JP. Structural Basis of Enhanced Crystallizability Induced by a Molecular Chaperone for Antibody Antigen-Binding Fragments. J Mol Biol 2017; 430:322-336. [PMID: 29277294 DOI: 10.1016/j.jmb.2017.12.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Revised: 11/30/2017] [Accepted: 12/13/2017] [Indexed: 12/20/2022]
Abstract
Monoclonal antibodies constitute one of the largest groups of drugs to treat cancers and immune disorders, and are guiding the design of vaccines against infectious diseases. Fragments antigen-binding (Fabs) have been preferred over monoclonal antibodies for the structural characterization of antibody-antigen complexes due to their relatively low flexibility. Nonetheless, Fabs often remain challenging to crystallize because of the surface characteristics of complementary determining regions and the residual flexibility in the hinge region between the variable and constant domains. Here, we used a variable heavy-chain (VHH) domain specific for the human kappa light chain to assist in the structure determination of three therapeutic Fabs that were recalcitrant to crystallization on their own. We show that this ligand alters the surface properties of the antibody-ligand complex and lowers its aggregation temperature to favor crystallization. The VHH crystallization chaperone also restricts the flexible hinge of Fabs to a narrow range of angles, and so independently of the variable region. Our findings contribute a valuable approach to antibody structure determination and provide biophysical insight into the principles that govern the crystallization of macromolecules.
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Affiliation(s)
- June Ereño-Orbea
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, Canada M5G 0A4
| | - Taylor Sicard
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, Canada M5G 0A4; Department of Biochemistry, University of Toronto, Toronto, ON, Canada M5S 1A8
| | - Hong Cui
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, Canada M5G 0A4
| | - Jacob Carson
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, Canada M5G 0A4
| | - Pim Hermans
- BAC, BV, part of Thermo Fisher Scientific, Leiden, the Netherlands
| | - Jean-Philippe Julien
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, Canada M5G 0A4; Department of Biochemistry, University of Toronto, Toronto, ON, Canada M5S 1A8; Department of Immunology, University of Toronto, Toronto, ON, Canada M5S 1A8.
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26
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Koromyslova AD, Hansman GS. Nanobodies targeting norovirus capsid reveal functional epitopes and potential mechanisms of neutralization. PLoS Pathog 2017; 13:e1006636. [PMID: 29095961 PMCID: PMC5667739 DOI: 10.1371/journal.ppat.1006636] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 09/08/2017] [Indexed: 11/18/2022] Open
Abstract
Norovirus is the leading cause of gastroenteritis worldwide. Despite recent developments in norovirus propagation in cell culture, these viruses are still challenging to grow routinely. Moreover, little is known on how norovirus infects the host cells, except that histo-blood group antigens (HBGAs) are important binding factors for infection and cell entry. Antibodies that bind at the HBGA pocket and block attachment to HBGAs are believed to neutralize the virus. However, additional neutralization epitopes elsewhere on the capsid likely exist and impeding the intrinsic structural dynamics of the capsid could be equally important. In the current study, we investigated a panel of Nanobodies in order to probe functional epitopes that could trigger capsid rearrangement and/ or interfere with HBGA binding interactions. The precise binding sites of six Nanobodies (Nano-4, Nano-14, Nano-26, Nano-27, Nano-32, and Nano-42) were identified using X-ray crystallography. We showed that these Nanobodies bound on the top, side, and bottom of the norovirus protruding domain. The impact of Nanobody binding on norovirus capsid morphology was analyzed using electron microscopy and dynamic light scattering. We discovered that distinct Nanobody epitopes were associated with varied changes in particle structural integrity and assembly. Interestingly, certain Nanobody-induced capsid morphological changes lead to the capsid protein degradation and viral RNA exposure. Moreover, Nanobodies employed multiple inhibition mechanisms to prevent norovirus attachment to HBGAs, which included steric obstruction (Nano-14), allosteric interference (Nano-32), and violation of normal capsid morphology (Nano-26 and Nano-85). Finally, we showed that two Nanobodies (Nano-26 and Nano-85) not only compromised capsid integrity and inhibited VLPs attachment to HBGAs, but also recognized a broad panel of norovirus genotypes with high affinities. Consequently, Nano-26 and Nano-85 have a great potential to function as novel therapeutic agents against human noroviruses. We determined the binding sites of six novel human norovirus specific Nanobodies (Nano-4, Nano-14, Nano-26, Nano-27, Nano-32, and Nano-42) using X-ray crystallography. The unique Nanobody recognition epitopes were correlated with their potential neutralizing capacities. We showed that one Nanobody (Nano-26) bound numerous genogroup II genotypes and interacted with highly conserved capsid residues. Four Nanobodies (Nano-4, Nano-26, Nano-27, and Nano-42) bound to occluded regions on the intact particles and impaired normal capsid morphology and particle integrity. One Nanobody (Nano-14) bound contiguous to the HBGA pocket and interacted with several residues involved in binding HBGAs. We found that the Nanobodies delivered multiple inhibition mechanisms, which included steric obstruction, allosteric interference, and disruption of the capsid stability. Our data suggested that the HBGA pocket might not be an ideal target for drug development, since the surrounding region is highly variable and inherently suffers from lack of conservation among the genetically diverse genotypes. Instead, we showed that the capsid contained other highly susceptible regions that could be targeted for virus inhibition.
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Affiliation(s)
- Anna D. Koromyslova
- Schaller Research Group at the University of Heidelberg and the DKFZ, Heidelberg, Germany
- Department of Infectious Diseases, Virology, University of Heidelberg, Heidelberg, Germany
- * E-mail: (ADK); (GSH)
| | - Grant S. Hansman
- Schaller Research Group at the University of Heidelberg and the DKFZ, Heidelberg, Germany
- Department of Infectious Diseases, Virology, University of Heidelberg, Heidelberg, Germany
- * E-mail: (ADK); (GSH)
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Unraveling the Self-Assembly of the Pseudomonas aeruginosa XcpQ Secretin Periplasmic Domain Provides New Molecular Insights into Type II Secretion System Secreton Architecture and Dynamics. mBio 2017; 8:mBio.01185-17. [PMID: 29042493 PMCID: PMC5646246 DOI: 10.1128/mbio.01185-17] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The type II secretion system (T2SS) releases large folded exoproteins across the envelope of many Gram-negative pathogens. This secretion process therefore requires specific gating, interacting, and dynamics properties mainly operated by a bipartite outer membrane channel called secretin. We have a good understanding of the structure-function relationship of the pore-forming C-terminal domain of secretins. In contrast, the high flexibility of their periplasmic N-terminal domain has been an obstacle in obtaining the detailed structural information required to uncover its molecular function. In Pseudomonas aeruginosa, the Xcp T2SS plays an important role in bacterial virulence by its capacity to deliver a large panel of toxins and degradative enzymes into the surrounding environment. Here, we revealed that the N-terminal domain of XcpQ secretin spontaneously self-assembled into a hexamer of dimers independently of its C-terminal domain. Furthermore, and by using multidisciplinary approaches, we elucidate the structural organization of the XcpQ N domain and demonstrate that secretin flexibility at interdimer interfaces is mandatory for its function. Bacterial secretins are large homooligomeric proteins constituting the outer membrane pore-forming element of several envelope-embedded nanomachines essential in bacterial survival and pathogenicity. They comprise a well-defined membrane-embedded C-terminal domain and a modular periplasmic N-terminal domain involved in substrate recruitment and connection with inner membrane components. We are studying the XcpQ secretin of the T2SS present in the pathogenic bacterium Pseudomonas aeruginosa. Our data highlight the ability of the XcpQ N-terminal domain to spontaneously oligomerize into a hexamer of dimers. Further in vivo experiments revealed that this domain adopts different conformations essential for the T2SS secretion process. These findings provide new insights into the functional understanding of bacterial T2SS secretins.
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Holcomb J, Spellmon N, Zhang Y, Doughan M, Li C, Yang Z. Protein crystallization: Eluding the bottleneck of X-ray crystallography. AIMS BIOPHYSICS 2017; 4:557-575. [PMID: 29051919 PMCID: PMC5645037 DOI: 10.3934/biophy.2017.4.557] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
To date, X-ray crystallography remains the gold standard for the determination of macromolecular structure and protein substrate interactions. However, the unpredictability of obtaining a protein crystal remains the limiting factor and continues to be the bottleneck in determining protein structures. A vast amount of research has been conducted in order to circumvent this issue with limited success. No single method has proven to guarantee the crystallization of all proteins. However, techniques using antibody fragments, lipids, carrier proteins, and even mutagenesis of crystal contacts have been implemented to increase the odds of obtaining a crystal with adequate diffraction. In addition, we review a new technique using the scaffolding ability of PDZ domains to facilitate nucleation and crystal lattice formation. Although in its infancy, such technology may be a valuable asset and another method in the crystallography toolbox to further the chances of crystallizing problematic proteins.
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Affiliation(s)
- Joshua Holcomb
- Department of Microbiology, Immunology, and Biochemistry, Wayne State University School of Medicine, Detroit, MI, USA
| | - Nicholas Spellmon
- Department of Microbiology, Immunology, and Biochemistry, Wayne State University School of Medicine, Detroit, MI, USA
| | - Yingxue Zhang
- Department of Microbiology, Immunology, and Biochemistry, Wayne State University School of Medicine, Detroit, MI, USA
| | - Maysaa Doughan
- Department of Microbiology, Immunology, and Biochemistry, Wayne State University School of Medicine, Detroit, MI, USA
| | - Chunying Li
- Center for Molecular and Translational Medicine, Georgia State University, Atlanta, GA, USA
| | - Zhe Yang
- Department of Microbiology, Immunology, and Biochemistry, Wayne State University School of Medicine, Detroit, MI, USA
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Near-atomic resolution cryoelectron microscopy structure of the 30-fold homooligomeric SpoIIIAG channel essential to spore formation in Bacillus subtilis. Proc Natl Acad Sci U S A 2017; 114:E7073-E7081. [PMID: 28784753 DOI: 10.1073/pnas.1704310114] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Bacterial sporulation allows starving cells to differentiate into metabolically dormant spores that can survive extreme conditions. Following asymmetric division, the mother cell engulfs the forespore, surrounding it with two bilayer membranes. During the engulfment process, an essential channel, the so-called feeding tube apparatus, is thought to cross both membranes to create a direct conduit between the mother cell and the forespore. At least nine proteins are required to create this channel, including SpoIIQ and SpoIIIAA-AH. Here, we present the near-atomic resolution structure of one of these proteins, SpoIIIAG, determined by single-particle cryo-EM. A 3D reconstruction revealed that SpoIIIAG assembles into a large and stable 30-fold symmetric complex with a unique mushroom-like architecture. The complex is collectively composed of three distinctive circular structures: a 60-stranded vertical β-barrel that forms a large inner channel encircled by two concentric rings, one β-mediated and the other formed by repeats of a ring-building motif (RBM) common to the architecture of various dual membrane secretion systems of distinct function. Our near-atomic resolution structure clearly shows that SpoIIIAG exhibits a unique and dramatic adaptation of the RBM fold with a unique β-triangle insertion that assembles into the prominent channel, the dimensions of which suggest the potential passage of large macromolecules between the mother cell and forespore during the feeding process. Indeed, mutation of residues located at key interfaces between monomers of this RBM resulted in severe defects both in vivo and in vitro, providing additional support for this unprecedented structure.
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Gu S, Shevchik VE, Shaw R, Pickersgill RW, Garnett JA. The role of intrinsic disorder and dynamics in the assembly and function of the type II secretion system. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1255-1266. [PMID: 28733198 DOI: 10.1016/j.bbapap.2017.07.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 07/02/2017] [Accepted: 07/17/2017] [Indexed: 10/19/2022]
Abstract
Many Gram-negative commensal and pathogenic bacteria use a type II secretion system (T2SS) to transport proteins out of the cell. These exported proteins or substrates play a major role in toxin delivery, maintaining biofilms, replication in the host and subversion of host immune responses to infection. We review the current structural and functional work on this system and argue that intrinsically disordered regions and protein dynamics are central for assembly, exo-protein recognition, and secretion competence of the T2SS. The central role of intrinsic disorder-order transitions in these processes may be a particular feature of type II secretion.
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Affiliation(s)
- Shuang Gu
- Queen Mary University of London, School of Biological and Chemical Sciences, London E1 4NS, United Kingdom
| | - Vladimir E Shevchik
- Université de Lyon, F-69003, Université Lyon 1, Lyon, F-69622, INSA-Lyon, Villeurbanne F-69621, CNRS, UMR5240, Microbiologie Adaptation et Pathogénie, Lyon F-69622, France
| | - Rosie Shaw
- Queen Mary University of London, School of Biological and Chemical Sciences, London E1 4NS, United Kingdom
| | - Richard W Pickersgill
- Queen Mary University of London, School of Biological and Chemical Sciences, London E1 4NS, United Kingdom.
| | - James A Garnett
- Queen Mary University of London, School of Biological and Chemical Sciences, London E1 4NS, United Kingdom.
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Thomassin JL, Santos Moreno J, Guilvout I, Tran Van Nhieu G, Francetic O. The trans-envelope architecture and function of the type 2 secretion system: new insights raising new questions. Mol Microbiol 2017; 105:211-226. [DOI: 10.1111/mmi.13704] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/04/2017] [Indexed: 12/21/2022]
Affiliation(s)
- Jenny-Lee Thomassin
- Department of structural biology and chemistry, Biochemistry of Macromolecular Interactions Unit; Institut Pasteur; 28 rue du Dr Roux 75724 Paris Cedex 15 France
- Centre National de la Recherche Scientifique (CNRS); ERL6002 75724 Paris France
| | - Javier Santos Moreno
- Université Paris Diderot (Paris 7) Sorbonne Paris Cité; Paris France
- Laboratory of Intercellular Communication and Microbial Infections; CIRB, Collège de France; 11 Place Marcelin Berthelot 75005 Paris France
- Institut National de la Santé et de la Recherche Médicale (Inserm) U1050; 75005 Paris France
- Centre National de la Recherche Scientifique (CNRS), UMR7241; 75005 Paris France
- MEMOLIFE Laboratory of Excellence and Paris Sciences et Lettres; 75005 Paris France
| | - Ingrid Guilvout
- Department of structural biology and chemistry, Biochemistry of Macromolecular Interactions Unit; Institut Pasteur; 28 rue du Dr Roux 75724 Paris Cedex 15 France
- Centre National de la Recherche Scientifique (CNRS); ERL6002 75724 Paris France
| | - Guy Tran Van Nhieu
- Laboratory of Intercellular Communication and Microbial Infections; CIRB, Collège de France; 11 Place Marcelin Berthelot 75005 Paris France
- Institut National de la Santé et de la Recherche Médicale (Inserm) U1050; 75005 Paris France
- Centre National de la Recherche Scientifique (CNRS), UMR7241; 75005 Paris France
- MEMOLIFE Laboratory of Excellence and Paris Sciences et Lettres; 75005 Paris France
| | - Olivera Francetic
- Department of structural biology and chemistry, Biochemistry of Macromolecular Interactions Unit; Institut Pasteur; 28 rue du Dr Roux 75724 Paris Cedex 15 France
- Centre National de la Recherche Scientifique (CNRS); ERL6002 75724 Paris France
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Crystallographic and biochemical characterization of the dimeric architecture of site-2 protease. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:1859-1871. [PMID: 28502790 DOI: 10.1016/j.bbamem.2017.05.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 05/08/2017] [Accepted: 05/10/2017] [Indexed: 11/23/2022]
Abstract
Regulated intramembrane proteolysis by members of the site-2 protease family (S2P) is an essential signal transduction mechanism conserved from bacteria to humans. There is some evidence that extra-membranous domains, like PDZ and CBS domains, regulate the proteolytic activity of S2Ps and that some members act as dimers. Here we report the crystal structure of the regulatory CBS domain pair of S2P from Archaeoglobus fulgidus, AfS2P, in the apo and nucleotide-bound form in complex with a specific nanobody from llama. Cross-linking and SEC-MALS analyses show for the first time the dimeric architecture of AfS2P both in the membrane and in detergent micelles. The CBS domain pair dimer (CBS module) displays an unusual head-to-tail configuration and nucleotide binding triggers no major conformational changes in the magnesium-free state. In solution, MgATP drives monomerization of the CBS module. We propose a model of the so far unknown architecture of the transmembrane domain dimer and for a regulatory mechanism of AfS2P that involves the interaction of positively charged arginine residues located at the cytoplasmic face of the transmembrane domain with the negatively charged phosphate groups of ATP moieties bound to the CBS domain pairs. Binding of MgATP could promote opening of the CBS module to allow lateral access of the globular cytoplasmic part of the substrate.
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Alterations in Peptidoglycan Cross-Linking Suppress the Secretin Assembly Defect Caused by Mutation of GspA in the Type II Secretion System. J Bacteriol 2017; 199:JB.00617-16. [PMID: 28138102 DOI: 10.1128/jb.00617-16] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Accepted: 01/23/2017] [Indexed: 12/22/2022] Open
Abstract
In Gram-negative bacteria, the peptidoglycan (PG) cell wall is a significant structural barrier for outer membrane protein assembly. In Aeromonas hydrophila, outer membrane multimerization of the type II secretion system (T2SS) secretin ExeD requires the function of the inner membrane assembly factor complex ExeAB. The putative mechanism of the complex involves the reorganization of PG and localization of ExeD, whereby ExeA functions by interacting with PG to form a site for secretin assembly and ExeB forms an interaction with ExeD. This mechanism led us to hypothesize that increasing the pore size of PG would circumvent the requirement for ExeA in the assembly of the ExeD secretin. Growth of A. hydrophila in 270 mM Gly reduced PG cross-links by approximately 30% and led to the suppression of secretin assembly defects in exeA strains and in those expressing ExeA mutants by enabling localization of the secretin in the outer membrane. We also established a heterologous ExeD assembly system in Escherichia coli and showed that ExeAB and ExeC are the only A. hydrophila proteins required for the assembly of the ExeD secretin in E. coli and that ExeAB-independent assembly of ExeD can occur upon overexpression of the d,d-carboxypeptidase PBP 5. These results support an assembly model in which, upon binding to PG, ExeA induces multimerization and pore formation in the sacculus, which enables ExeD monomers to interact with ExeB and assemble into a secretin that both is inserted in the outer membrane and crosses the PG layer to interact with the inner membrane platform of the T2SS.IMPORTANCE The PG layer imposes a strict structural impediment for the assembly of macromolecular structures that span the cell envelope and serve as virulence factors in Gram-negative species. This work revealed that by decreasing PG cross-linking by growth in Gly, the absolute requirement for the PG-binding activity of ExeA in the assembly of the ExeD secretin was alleviated in A. hydrophila In a heterologous assembly model in E. coli, expression of the carboxypeptidase PBP 5 could relieve the requirement for ExeAB in the assembly of the ExeD secretin. These results provide some mechanistic details of the ExeAB assembly complex function, in which the PG-binding and oligomerization functions of ExeAB are used to create a pore in the PG that is required for secretin assembly.
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Abstract
Type IVa pili (T4aP) are ubiquitous microbial appendages used for adherence, twitching motility, DNA uptake, and electron transfer. Many of these functions depend on dynamic assembly and disassembly of the pilus by a megadalton-sized, cell envelope-spanning protein complex located at the poles of rod-shaped bacteria. How the T4aP assembly complex becomes integrated into the cell envelope in the absence of dedicated peptidoglycan (PG) hydrolases is unknown. After ruling out the potential involvement of housekeeping PG hydrolases in the installation of the T4aP machinery in Pseudomonas aeruginosa, we discovered that key components of inner (PilMNOP) and outer (PilQ) membrane subcomplexes are recruited to future sites of cell division. Midcell recruitment of a fluorescently tagged alignment subcomplex component, mCherry-PilO, depended on PilQ secretin monomers—specifically, their N-terminal PG-binding AMIN domains. PilP, which connects PilO to PilQ, was required for recruitment, while PilM, which is structurally similar to divisome component FtsA, was not. Recruitment preceded secretin oligomerization in the outer membrane, as loss of the PilQ pilotin PilF had no effect on localization. These results were confirmed in cells chemically blocked for cell division prior to outer membrane invagination. The hub protein FimV and a component of the polar organelle coordinator complex—PocA—were independently required for midcell recruitment of PilO and PilQ. Together, these data suggest an integrated, energy-efficient strategy for the targeting and preinstallation—rather than retrofitting—of the T4aP system into nascent poles, without the need for dedicated PG-remodeling enzymes. The peptidoglycan (PG) layer of bacterial cell envelopes has limited porosity, representing a physical barrier to the insertion of large protein complexes involved in secretion and motility. Many systems include dedicated PG hydrolase components that create space for their insertion, but the ubiquitous type IVa pilus (T4aP) system lacks such an enzyme. Instead, we found that components of the T4aP system are recruited to future sites of cell division, where they could be incorporated into the cell envelope during the formation of new poles, eliminating the need for PG hydrolases. Targeting depends on the presence of septal PG-binding motifs in specific components, as removal of those motifs causes delocalization. This preinstallation strategy for the T4aP assembly system would ensure that both daughter cells are poised to extrude pili from new poles as soon as they separate from one another.
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Comor L, Dolinska S, Bhide K, Pulzova L, Jiménez-Munguía I, Bencurova E, Flachbartova Z, Potocnakova L, Kanova E, Bhide M. Joining the in vitro immunization of alpaca lymphocytes and phage display: rapid and cost effective pipeline for sdAb synthesis. Microb Cell Fact 2017; 16:13. [PMID: 28114943 PMCID: PMC5259998 DOI: 10.1186/s12934-017-0630-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Accepted: 01/17/2017] [Indexed: 12/13/2022] Open
Abstract
Background Camelids possess unique functional heavy chain antibodies, which can be produced and modified in vitro as a single domain antibody (sdAb or nanobody) with full antigen binding ability. Production of sdAb in conventional manner requires active immunization of Camelidae animal, which is laborious, time consuming, costly and in many cases not feasible (e.g. in case of highly toxic or infectious antigens). Results In this study, we describe an alternative pipeline that includes in vitro stimulation of naïve alpaca B-lymphocytes by antigen of interest (in this case endothelial cell binding domain of OspA of Borrelia) in the presence of recombinant alpaca interleukins 2 and 4, construction of sdAb phage library, selection of antigen specific sdAb expressed on phages (biopanning) and confirmation of binding ability of sdAb to the antigen. By joining the in vitro immunization and the phage display ten unique phage clones carrying sdAb were selected. Out of ten, seven sdAb showed strong antigen binding ability in phage ELISA. Furthermore, two soluble forms of sdAb were produced and their differential antigen binding affinity was measured with bio-layer interferometry. Conclusion A proposed pipeline has potential to reduce the cost substantially required for maintenance of camelid herd for active immunization. Furthermore, in vitro immunization can be achieved within a week to enrich mRNA copies encoding antigen-specific sdAbs in B cell. This rapid and cost effective pipeline can help researchers to develop efficiently sdAb for diagnostic and therapeutic purposes.
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Affiliation(s)
- Lubos Comor
- Laboratory of Biomedical Microbiology and Immunology, University of Veterinary Medicine and Pharmacy, 73, 04181, Kosice, Slovakia
| | - Saskia Dolinska
- Laboratory of Biomedical Microbiology and Immunology, University of Veterinary Medicine and Pharmacy, 73, 04181, Kosice, Slovakia
| | - Katarina Bhide
- Laboratory of Biomedical Microbiology and Immunology, University of Veterinary Medicine and Pharmacy, 73, 04181, Kosice, Slovakia
| | - Lucia Pulzova
- Laboratory of Biomedical Microbiology and Immunology, University of Veterinary Medicine and Pharmacy, 73, 04181, Kosice, Slovakia
| | - Irene Jiménez-Munguía
- Laboratory of Biomedical Microbiology and Immunology, University of Veterinary Medicine and Pharmacy, 73, 04181, Kosice, Slovakia
| | - Elena Bencurova
- Laboratory of Biomedical Microbiology and Immunology, University of Veterinary Medicine and Pharmacy, 73, 04181, Kosice, Slovakia
| | - Zuzana Flachbartova
- Laboratory of Biomedical Microbiology and Immunology, University of Veterinary Medicine and Pharmacy, 73, 04181, Kosice, Slovakia
| | - Lenka Potocnakova
- Laboratory of Biomedical Microbiology and Immunology, University of Veterinary Medicine and Pharmacy, 73, 04181, Kosice, Slovakia
| | - Evelina Kanova
- Laboratory of Biomedical Microbiology and Immunology, University of Veterinary Medicine and Pharmacy, 73, 04181, Kosice, Slovakia
| | - Mangesh Bhide
- Laboratory of Biomedical Microbiology and Immunology, University of Veterinary Medicine and Pharmacy, 73, 04181, Kosice, Slovakia. .,Institute of Neuroimunnology, Slovak Academy of Sciences, Bratislava, Slovakia.
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Three-Dimensional Structure of the Ultraoligotrophic Marine Bacterium "Candidatus Pelagibacter ubique". Appl Environ Microbiol 2017; 83:AEM.02807-16. [PMID: 27836840 DOI: 10.1128/aem.02807-16] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Accepted: 11/09/2016] [Indexed: 11/20/2022] Open
Abstract
SAR11 bacteria are small, heterotrophic, marine alphaproteobacteria found throughout the oceans. They thrive at the low nutrient concentrations typical of open ocean conditions, although the adaptations required for life under those conditions are not well understood. To illuminate this issue, we used cryo-electron tomography to study "Candidatus Pelagibacter ubique" strain HTCC1062, a member of the SAR11 clade. Our results revealed its cellular dimensions and details of its intracellular organization. Frozen-hydrated cells, which were preserved in a life-like state, had an average cell volume (enclosed by the outer membrane) of 0.037 ± 0.011 μm3 Strikingly, the periplasmic space occupied ∼20% to 50% of the total cell volume in log-phase cells and ∼50% to 70% in stationary-phase cells. The nucleoid occupied the convex side of the crescent-shaped cells and the ribosomes predominantly occupied the concave side, at a relatively high concentration of 10,000 to 12,000 ribosomes/μm3 Outer membrane pore complexes, likely composed of PilQ, were frequently observed in both log-phase and stationary-phase cells. Long filaments, most likely type IV pili, were found on dividing cells. The physical dimensions, intracellular organization, and morphological changes throughout the life cycle of "Ca. Pelagibacter ubique" provide structural insights into the functional adaptions of these oligotrophic ultramicrobacteria to their habitat. IMPORTANCE Bacterioplankton of the SAR11 clade (Pelagibacterales) are of interest because of their global biogeochemical significance and because they appear to have been molded by unusual evolutionary circumstances that favor simplicity and efficiency. They have adapted to an ecosystem in which nutrient concentrations are near the extreme limits at which transport systems can function adequately, and they have evolved streamlined genomes to execute only functions essential for life. However, little is known about the actual size limitations and cellular features of living oligotrophic ultramicrobacteria. In this study, we have used cryo-electron tomography to obtain accurate physical information about the cellular architecture of "Candidatus Pelagibacter ubique," the first cultivated member of the SAR11 clade. These results provide foundational information for answering questions about the cell architecture and functions of these ultrasmall oligotrophic bacteria.
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Yan Z, Yin M, Xu D, Zhu Y, Li X. Structural insights into the secretin translocation channel in the type II secretion system. Nat Struct Mol Biol 2017; 24:177-183. [DOI: 10.1038/nsmb.3350] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Accepted: 12/06/2016] [Indexed: 12/31/2022]
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Abstract
Ligand-induced activation of G protein-coupled receptors (GPCRs) is a key mechanism permitting communication between cells and organs. Enormous progress has recently elucidated the structural and dynamic features of GPCR transmembrane signaling. Nanobodies, the recombinant antigen-binding fragments of camelid heavy-chain-only antibodies, have emerged as important research tools to lock GPCRs in particular conformational states. Active-state stabilizing nanobodies have elucidated several agonist-bound structures of hormone-activated GPCRs and have provided insight into the dynamic character of receptors. Nanobodies have also been used to stabilize transient GPCR transmembrane signaling complexes, yielding the first structural insights into GPCR signal transduction across the cellular membrane. Beyond their in vitro uses, nanobodies have served as conformational biosensors in living systems and have provided novel ways to modulate GPCR function. Here, we highlight several examples of how nanobodies have enabled the study of GPCR function and give insights into potential future uses of these important tools.
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Affiliation(s)
- Aashish Manglik
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, California 94305; ,
| | - Brian K Kobilka
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, California 94305; ,
| | - Jan Steyaert
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium;
- VIB Structural Biology Research Center, Vrije Universiteit Brussel, 1050 Brussels, Belgium
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The "Sticky Patch" Model of Crystallization and Modification of Proteins for Enhanced Crystallizability. Methods Mol Biol 2017; 1607:77-115. [PMID: 28573570 DOI: 10.1007/978-1-4939-7000-1_4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Crystallization of macromolecules has long been perceived as a stochastic process, which cannot be predicted or controlled. This is consistent with another popular notion that the interactions of molecules within the crystal, i.e., crystal contacts, are essentially random and devoid of specific physicochemical features. In contrast, functionally relevant surfaces, such as oligomerization interfaces and specific protein-protein interaction sites, are under evolutionary pressures so their amino acid composition, structure, and topology are distinct. However, current theoretical and experimental studies are significantly changing our understanding of the nature of crystallization. The increasingly popular "sticky patch" model, derived from soft matter physics, describes crystallization as a process driven by interactions between select, specific surface patches, with properties thermodynamically favorable for cohesive interactions. Independent support for this model comes from various sources including structural studies and bioinformatics. Proteins that are recalcitrant to crystallization can be modified for enhanced crystallizability through chemical or mutational modification of their surface to effectively engineer "sticky patches" which would drive crystallization. Here, we discuss the current state of knowledge of the relationship between the microscopic properties of the target macromolecule and its crystallizability, focusing on the "sticky patch" model. We discuss state-of-the-art in silico methods that evaluate the propensity of a given target protein to form crystals based on these relationships, with the objective to design variants with modified molecular surface properties and enhanced crystallization propensity. We illustrate this discussion with specific cases where these approaches allowed to generate crystals suitable for structural analysis.
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Worrall LJ, Hong C, Vuckovic M, Deng W, Bergeron JRC, Majewski DD, Huang RK, Spreter T, Finlay BB, Yu Z, Strynadka NCJ. Near-atomic-resolution cryo-EM analysis of the Salmonella T3S injectisome basal body. Nature 2016; 540:597-601. [DOI: 10.1038/nature20576] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 10/25/2016] [Indexed: 12/17/2022]
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Guilvout I, Brier S, Chami M, Hourdel V, Francetic O, Pugsley AP, Chamot-Rooke J, Huysmans GHM. Prepore Stability Controls Productive Folding of the BAM-independent Multimeric Outer Membrane Secretin PulD. J Biol Chem 2016; 292:328-338. [PMID: 27903652 DOI: 10.1074/jbc.m116.759498] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 11/21/2016] [Indexed: 12/19/2022] Open
Abstract
Members of a group of multimeric secretion pores that assemble independently of any known membrane-embedded insertase in Gram-negative bacteria fold into a prepore before membrane-insertion occurs. The mechanisms and the energetics that drive the folding of these proteins are poorly understood. Here, equilibrium unfolding and hydrogen/deuterium exchange monitored by mass spectrometry indicated that a loss of 4-5 kJ/mol/protomer in the N3 domain that is peripheral to the membrane-spanning C domain in the dodecameric secretin PulD, the founding member of this class, prevents pore formation by destabilizing the prepore into a poorly structured dodecamer as visualized by electron microscopy. Formation of native PulD-multimers by mixing protomers that differ in N3 domain stability, suggested that the N3 domain forms a thermodynamic seal onto the prepore. This highlights the role of modest free energy changes in the folding of pre-integration forms of a hyperstable outer membrane complex and reveals a key driving force for assembly independently of the β-barrel assembly machinery.
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Affiliation(s)
- Ingrid Guilvout
- From the Molecular Genetics Unit, CNRS ERL 3526.,Laboratory of Macromolecular Systems and Signaling and
| | - Sébastien Brier
- Structural Mass Spectrometry and Proteomics Unit, CNRS UMR 3528, Institut Pasteur, 75724 Paris Cedex 15, France and
| | - Mohamed Chami
- the BioEM lab, Biozentrum, University of Basel, CH 4058 Basel, Switzerland
| | - Véronique Hourdel
- Structural Mass Spectrometry and Proteomics Unit, CNRS UMR 3528, Institut Pasteur, 75724 Paris Cedex 15, France and
| | - Olivera Francetic
- From the Molecular Genetics Unit, CNRS ERL 3526.,Laboratory of Macromolecular Systems and Signaling and
| | | | - Julia Chamot-Rooke
- Structural Mass Spectrometry and Proteomics Unit, CNRS UMR 3528, Institut Pasteur, 75724 Paris Cedex 15, France and
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Glanville J, D'Angelo S, Khan TA, Reddy ST, Naranjo L, Ferrara F, Bradbury ARM. Deep sequencing in library selection projects: what insight does it bring? Curr Opin Struct Biol 2016; 33:146-60. [PMID: 26451649 DOI: 10.1016/j.sbi.2015.09.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 08/19/2015] [Accepted: 09/17/2015] [Indexed: 11/17/2022]
Abstract
High throughput sequencing is poised to change all aspects of the way antibodies and other binders are discovered and engineered. Millions of available sequence reads provide an unprecedented sampling depth able to guide the design and construction of effective, high quality naïve libraries containing tens of billions of unique molecules. Furthermore, during selections, high throughput sequencing enables quantitative tracing of enriched clones and position-specific guidance to amino acid variation under positive selection during antibody engineering. Successful application of the technologies relies on specific PCR reagent design, correct sequencing platform selection, and effective use of computational tools and statistical measures to remove error, identify antibodies, estimate diversity, and extract signatures of selection from the clone down to individual structural positions. Here we review these considerations and discuss some of the remaining challenges to the widespread adoption of the technology.
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Affiliation(s)
- J Glanville
- Program in Computational and Systems Immunology, Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - S D'Angelo
- University of New Mexico Comprehensive Cancer Center, and Division of Molecular Medicine, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - T A Khan
- ETH Zurich, Department of Biosystems Science and Engineering, Basel, Switzerland
| | - S T Reddy
- ETH Zurich, Department of Biosystems Science and Engineering, Basel, Switzerland
| | - L Naranjo
- Bioscience division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - F Ferrara
- University of New Mexico Comprehensive Cancer Center, and Division of Molecular Medicine, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - A R M Bradbury
- Bioscience division, Los Alamos National Laboratory, Los Alamos, NM, USA.
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Wang Y, Fan Z, Shao L, Kong X, Hou X, Tian D, Sun Y, Xiao Y, Yu L. Nanobody-derived nanobiotechnology tool kits for diverse biomedical and biotechnology applications. Int J Nanomedicine 2016; 11:3287-303. [PMID: 27499623 PMCID: PMC4959585 DOI: 10.2147/ijn.s107194] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Owing to peculiar properties of nanobody, including nanoscale size, robust structure, stable and soluble behaviors in aqueous solution, reversible refolding, high affinity and specificity for only one cognate target, superior cryptic cleft accessibility, and deep tissue penetration, as well as a sustainable source, it has been an ideal research tool for the development of sophisticated nanobiotechnologies. Currently, the nanobody has been evolved into versatile research and application tool kits for diverse biomedical and biotechnology applications. Various nanobody-derived formats, including the nanobody itself, the radionuclide or fluorescent-labeled nanobodies, nanobody homo- or heteromultimers, nanobody-coated nanoparticles, and nanobody-displayed bacteriophages, have been successfully demonstrated as powerful nanobiotechnological tool kits for basic biomedical research, targeting drug delivery and therapy, disease diagnosis, bioimaging, and agricultural and plant protection. These applications indicate a special advantage of these nanobody-derived technologies, already surpassing the “me-too” products of other equivalent binders, such as the full-length antibodies, single-chain variable fragments, antigen-binding fragments, targeting peptides, and DNA-based aptamers. In this review, we summarize the current state of the art in nanobody research, focusing on the nanobody structural features, nanobody production approach, nanobody-derived nanobiotechnology tool kits, and the potentially diverse applications in biomedicine and biotechnology. The future trends, challenges, and limitations of the nanobody-derived nanobiotechnology tool kits are also discussed.
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Affiliation(s)
- Yongzhong Wang
- School of Life Sciences, Collaborative Innovation Center of Modern Bio-manufacture, Anhui University, Hefei, People's Republic of China
| | - Zhen Fan
- Department of Biomedical Engineering, The Ohio State University, Columbus, OH, USA
| | - Lei Shao
- State Key Laboratory of New Drugs and Pharmaceutical Process, Shanghai Institute of Pharmaceutical Industry, Shanghai
| | - Xiaowei Kong
- School of Life Sciences, Collaborative Innovation Center of Modern Bio-manufacture, Anhui University, Hefei, People's Republic of China
| | - Xianjuan Hou
- School of Life Sciences, Collaborative Innovation Center of Modern Bio-manufacture, Anhui University, Hefei, People's Republic of China
| | - Dongrui Tian
- School of Life Sciences, Collaborative Innovation Center of Modern Bio-manufacture, Anhui University, Hefei, People's Republic of China
| | - Ying Sun
- School of Life Sciences, Collaborative Innovation Center of Modern Bio-manufacture, Anhui University, Hefei, People's Republic of China
| | - Yazhong Xiao
- School of Life Sciences, Collaborative Innovation Center of Modern Bio-manufacture, Anhui University, Hefei, People's Republic of China
| | - Li Yu
- Department of Microbiology and Parasitology, Anhui Provincial Laboratory of Microbiology and Parasitology, Anhui Key Laboratory of Zoonoses, Anhui Medical University, Hefei, People's Republic of China
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Figueroa M, Sleutel M, Vandevenne M, Parvizi G, Attout S, Jacquin O, Vandenameele J, Fischer AW, Damblon C, Goormaghtigh E, Valerio-Lepiniec M, Urvoas A, Durand D, Pardon E, Steyaert J, Minard P, Maes D, Meiler J, Matagne A, Martial JA, Van de Weerdt C. The unexpected structure of the designed protein Octarellin V.1 forms a challenge for protein structure prediction tools. J Struct Biol 2016; 195:19-30. [PMID: 27181418 DOI: 10.1016/j.jsb.2016.05.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 04/19/2016] [Accepted: 05/12/2016] [Indexed: 12/26/2022]
Abstract
Despite impressive successes in protein design, designing a well-folded protein of more 100 amino acids de novo remains a formidable challenge. Exploiting the promising biophysical features of the artificial protein Octarellin V, we improved this protein by directed evolution, thus creating a more stable and soluble protein: Octarellin V.1. Next, we obtained crystals of Octarellin V.1 in complex with crystallization chaperons and determined the tertiary structure. The experimental structure of Octarellin V.1 differs from its in silico design: the (αβα) sandwich architecture bears some resemblance to a Rossman-like fold instead of the intended TIM-barrel fold. This surprising result gave us a unique and attractive opportunity to test the state of the art in protein structure prediction, using this artificial protein free of any natural selection. We tested 13 automated webservers for protein structure prediction and found none of them to predict the actual structure. More than 50% of them predicted a TIM-barrel fold, i.e. the structure we set out to design more than 10years ago. In addition, local software runs that are human operated can sample a structure similar to the experimental one but fail in selecting it, suggesting that the scoring and ranking functions should be improved. We propose that artificial proteins could be used as tools to test the accuracy of protein structure prediction algorithms, because their lack of evolutionary pressure and unique sequences features.
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Affiliation(s)
- Maximiliano Figueroa
- GIGA-Research, Molecular Biomimetics and Protein Engineering, University of Liège, Liège, Belgium.
| | - Mike Sleutel
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Marylene Vandevenne
- GIGA-Research, Molecular Biomimetics and Protein Engineering, University of Liège, Liège, Belgium
| | - Gregory Parvizi
- GIGA-Research, Molecular Biomimetics and Protein Engineering, University of Liège, Liège, Belgium
| | - Sophie Attout
- GIGA-Research, Molecular Biomimetics and Protein Engineering, University of Liège, Liège, Belgium
| | - Olivier Jacquin
- GIGA-Research, Molecular Biomimetics and Protein Engineering, University of Liège, Liège, Belgium
| | - Julie Vandenameele
- Laboratoire d'Enzymologie et Repliement des Protéines, Centre for Protein Engineering, University of Liège, Liège, Belgium
| | - Axel W Fischer
- Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN, United States
| | | | - Erik Goormaghtigh
- Laboratory for the Structure and Function of Biological Membranes, Center for Structural Biology and Bioinformatics, Université Libre de Bruxelles, Brussels, Belgium
| | - Marie Valerio-Lepiniec
- Institute for Integrative Biology of the Cell (I2BC), UMT 9198, CEA, CNRS, Université Paris-Sud, Orsay, France
| | - Agathe Urvoas
- Institute for Integrative Biology of the Cell (I2BC), UMT 9198, CEA, CNRS, Université Paris-Sud, Orsay, France
| | - Dominique Durand
- Institute for Integrative Biology of the Cell (I2BC), UMT 9198, CEA, CNRS, Université Paris-Sud, Orsay, France
| | - Els Pardon
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium
| | - Jan Steyaert
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium
| | - Philippe Minard
- Institute for Integrative Biology of the Cell (I2BC), UMT 9198, CEA, CNRS, Université Paris-Sud, Orsay, France
| | - Dominique Maes
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Jens Meiler
- Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN, United States
| | - André Matagne
- Laboratoire d'Enzymologie et Repliement des Protéines, Centre for Protein Engineering, University of Liège, Liège, Belgium
| | - Joseph A Martial
- GIGA-Research, Molecular Biomimetics and Protein Engineering, University of Liège, Liège, Belgium
| | - Cécile Van de Weerdt
- GIGA-Research, Molecular Biomimetics and Protein Engineering, University of Liège, Liège, Belgium.
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Salzer R, D'Imprima E, Gold VAM, Rose I, Drechsler M, Vonck J, Averhoff B. Topology and Structure/Function Correlation of Ring- and Gate-forming Domains in the Dynamic Secretin Complex of Thermus thermophilus. J Biol Chem 2016; 291:14448-56. [PMID: 27226590 DOI: 10.1074/jbc.m116.724153] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Indexed: 11/06/2022] Open
Abstract
Secretins are versatile outer membrane pores used by many bacteria to secrete proteins, toxins, or filamentous phages; extrude type IV pili (T4P); or take up DNA. Extrusion of T4P and natural transformation of DNA in the thermophilic bacterium Thermus thermophilus requires a unique secretin complex comprising six stacked rings, a membrane-embedded cone structure, and two gates that open and close a central channel. To investigate the role of distinct domains in ring and gate formation, we examined a set of deletion derivatives by cryomicroscopy techniques. Here we report that maintaining the N0 ring in the deletion derivatives led to stable PilQ complexes. Analyses of the variants unraveled that an N-terminal domain comprising a unique βββαβ fold is essential for the formation of gate 2. Furthermore, we identified four βαββα domains essential for the formation of the N2 to N5 rings. Mutant studies revealed that deletion of individual ring domains significantly reduces piliation. The N1, N2, N4, and N5 deletion mutants were significantly impaired in T4P-mediated twitching motility, whereas the motility of the N3 mutant was comparable with that of wild-type cells. This indicates that the deletion of the N3 ring leads to increased pilus dynamics, thereby compensating for the reduced number of pili of the N3 mutant. All mutants exhibit a wild-type natural transformation phenotype, leading to the conclusion that DNA uptake is independent of functional T4P.
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Affiliation(s)
- Ralf Salzer
- From Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main and
| | - Edoardo D'Imprima
- the Department of Structural Biology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Vicki A M Gold
- the Department of Structural Biology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Ilona Rose
- From Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main and
| | - Moritz Drechsler
- From Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main and
| | - Janet Vonck
- the Department of Structural Biology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Beate Averhoff
- From Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main and
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Kubori T, Nagai H. The Type IVB secretion system: an enigmatic chimera. Curr Opin Microbiol 2016; 29:22-9. [DOI: 10.1016/j.mib.2015.10.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2015] [Revised: 10/14/2015] [Accepted: 10/15/2015] [Indexed: 10/22/2022]
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Development and Validation of a Small Single-domain Antibody That Effectively Inhibits Matrix Metalloproteinase 8. Mol Ther 2016; 24:890-902. [PMID: 26775809 DOI: 10.1038/mt.2016.2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 12/31/2015] [Indexed: 12/15/2022] Open
Abstract
A detrimental role for matrix metalloproteinase 8 (MMP8) has been identified in several pathological conditions, e.g., lethal hepatitis and the systemic inflammatory response syndrome. Since matrix MMP8-deficient mice are protected in the above-mentioned diseases, specific MMP8 inhibitors could be of clinical value. However, targeting a specific matrix metalloproteinase remains challenging due to the strong structural homology of matrix metalloproteinases, which form a family of 25 members in mammals. Single-domain antibodies, called nanobodies, offer a range of possibilities toward therapy since they are easy to generate, express, produce, and modify, e.g., by linkage to nanobodies directed against other target molecules. Hence, we generated small MMP8-binding nanobodies, and established a proof-of-principle for developing nanobodies that inhibit matrix metalloproteinase activity. Also, we demonstrated for the first time the possibility of expressing nanobodies systemically by in vivo electroporation of the muscle and its relevance as a potential therapy in inflammatory diseases.
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Bieli D, Alborelli I, Harmansa S, Matsuda S, Caussinus E, Affolter M. Development and Application of Functionalized Protein Binders in Multicellular Organisms. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2016; 325:181-213. [DOI: 10.1016/bs.ircmb.2016.02.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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Dmitriev OY, Lutsenko S, Muyldermans S. Nanobodies as Probes for Protein Dynamics in Vitro and in Cells. J Biol Chem 2015; 291:3767-75. [PMID: 26677230 DOI: 10.1074/jbc.r115.679811] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Nanobodies are the recombinant antigen-recognizing domains of the minimalistic heavy chain-only antibodies produced by camels and llamas. Nanobodies can be easily generated, effectively optimized, and variously derivatized with standard molecular biology protocols. These properties have triggered the recent explosion in the nanobody use in basic and clinical research. This review focuses on the emerging use of nanobodies for understanding and monitoring protein dynamics on the scales ranging from isolated protein domains to live cells, from nanoseconds to hours. The small size and high solubility make nanobodies uniquely suited for studying protein dynamics by NMR. The ability to produce conformation-sensitive nanobodies in cells enables studies that link structural dynamics of a target protein to its cellular behavior. The link between in vitro and in-cell dynamics, afforded by nanobodies, brings the analysis of such important events as receptor signaling, membrane protein trafficking, and protein interactions to the next level of resolution.
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Affiliation(s)
- Oleg Y Dmitriev
- From the Department of Biochemistry, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada,
| | - Svetlana Lutsenko
- the Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, and
| | - Serge Muyldermans
- the Unit of Cellular and Molecular Immunology, Vrije Universiteit Brussel, 1050, Brussels, Belgium
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Lipids assist the membrane insertion of a BAM-independent outer membrane protein. Sci Rep 2015; 5:15068. [PMID: 26463896 PMCID: PMC4604470 DOI: 10.1038/srep15068] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 09/14/2015] [Indexed: 02/04/2023] Open
Abstract
Like several other large, multimeric bacterial outer membrane proteins (OMPs), the assembly of the Klebsiella oxytoca OMP PulD does not rely on the universally conserved β-barrel assembly machinery (BAM) that catalyses outer membrane insertion. The only other factor known to interact with PulD prior to or during outer membrane targeting and assembly is the cognate chaperone PulS. Here, in vitro translation-transcription coupled PulD folding demonstrated that PulS does not act during the membrane insertion of PulD, and engineered in vivo site-specific cross-linking between PulD and PulS showed that PulS binding does not prevent membrane insertion. In vitro folding kinetics revealed that PulD is atypical compared to BAM-dependent OMPs by inserting more rapidly into membranes containing E. coli phospholipids than into membranes containing lecithin. PulD folding was fast in diC14:0-phosphatidylethanolamine liposomes but not diC14:0-phosphatidylglycerol liposomes, and in diC18:1-phosphatidylcholine liposomes but not in diC14:1-phosphatidylcholine liposomes. These results suggest that PulD efficiently exploits the membrane composition to complete final steps in insertion and explain how PulD can assemble independently of any protein-assembly machinery. Lipid-assisted assembly in this manner might apply to other large OMPs whose assembly is BAM-independent.
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