1
|
Zaharija B, Bradshaw NJ. Mapping the Domain Structure and Aggregation Propensity of Proteins Using a Gateway Plasmid Vector System. Methods Mol Biol 2023; 2551:649-677. [PMID: 36310230 DOI: 10.1007/978-1-0716-2597-2_39] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Some proteins represent members of conserved families, meaning that their domain structure can be easily predicted by comparison to homologous proteins whose structures have been solved experimentally. Many other proteins, however, do not share significant detectable homology with other proteins, often as results of high amounts of coiled-coil structure and/or intrinsically unstructured regions. These proteins include many whose aggregation is linked to human disease.Here we present a refined and reliable workflow for identifying the domains of such proteins, through cloning of multiple alternative fragments, and testing whether they form soluble, folded structures when expressed as recombinant peptides in E. coli, through the use of size exclusion chromatography. By using Gateway recombination for cloning, these fragments can then be rapidly transferred to alternate vectors for testing in mammalian cells. We then specifically illustrate its use for proteins that form pathological aggregates in disease, mapping not just their basic domain structures but also the specific subdomains responsible for aggregation.
Collapse
Affiliation(s)
- Beti Zaharija
- Department of Biotechnology, University of Rijeka, Rijeka, Croatia
| | | |
Collapse
|
2
|
Bersch B, Tarbouriech N, Burmeister WP, Iseni F. Solution Structure of the C-terminal Domain of A20, the Missing Brick for the Characterization of the Interface between Vaccinia Virus DNA Polymerase and its Processivity Factor. J Mol Biol 2021; 433:167009. [PMID: 33901538 DOI: 10.1016/j.jmb.2021.167009] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 04/16/2021] [Accepted: 04/17/2021] [Indexed: 11/26/2022]
Abstract
Poxviruses are enveloped viruses with a linear, double-stranded DNA genome. Viral DNA synthesis is achieved by a functional DNA polymerase holoenzyme composed of three essential proteins. For vaccinia virus (VACV) these are E9, the catalytic subunit, a family B DNA polymerase, and the heterodimeric processivity factor formed by D4 and A20. The A20 protein links D4 to the catalytic subunit. High-resolution structures have been obtained for the VACV D4 protein in complex with an N-terminal fragment of A20 as well as for E9. In addition, biochemical studies provided evidence that a poxvirus-specific insertion (insert 3) in E9 interacts with the C-terminal residues of A20. Here, we provide solution structures of two different VACV A20 C-terminal constructs containing residues 304-426, fused at their C-terminus to either a BAP (Biotin Acceptor Peptide)-tag or a short peptide containing the helix of E9 insert 3. Together with results from titration studies, these structures shed light on the molecular interface between the catalytic subunit and the processivity factor component A20. The interface comprises hydrophobic residues conserved within the Chordopoxvirinae subfamily. Finally, we constructed a HADDOCK model of the VACV A20304-426-E9 complex, which is in excellent accordance with previous experimental data.
Collapse
Affiliation(s)
- Beate Bersch
- Institut de Biologie Structurale, Univ. Grenoble Alpes, CNRS, CEA, IBS, F-38000 Grenoble, France.
| | - Nicolas Tarbouriech
- Institut de Biologie Structurale, Univ. Grenoble Alpes, CNRS, CEA, IBS, F-38000 Grenoble, France
| | - Wim P Burmeister
- Institut de Biologie Structurale, Univ. Grenoble Alpes, CNRS, CEA, IBS, F-38000 Grenoble, France
| | - Frédéric Iseni
- Unité de Virologie, Institut de Recherche Biomédicale des Armées, BP73, F-91223 Brétigny-sur-Orge Cedex, France
| |
Collapse
|
3
|
Giachin G, Jessop M, Bouverot R, Acajjaoui S, Saïdi M, Chretien A, Bacia‐Verloop M, Signor L, Mas PJ, Favier A, Borel Meneroud E, Hons M, Hart DJ, Kandiah E, Boeri Erba E, Buisson A, Leonard G, Gutsche I, Soler‐Lopez M. Assembly of The Mitochondrial Complex I Assembly Complex Suggests a Regulatory Role for Deflavination. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202011548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Gabriele Giachin
- Structural Biology Group European Synchrotron Radiation Facility (ESRF) 71 avenue des Martyrs 38043 Grenoble France
| | - Matthew Jessop
- Institut de Biologie Structurale (IBS) CNRS, CEA Université Grenoble Alpes 71 avenue des Martyrs 38044 Grenoble France
| | - Romain Bouverot
- Structural Biology Group European Synchrotron Radiation Facility (ESRF) 71 avenue des Martyrs 38043 Grenoble France
| | - Samira Acajjaoui
- Structural Biology Group European Synchrotron Radiation Facility (ESRF) 71 avenue des Martyrs 38043 Grenoble France
| | - Melissa Saïdi
- Structural Biology Group European Synchrotron Radiation Facility (ESRF) 71 avenue des Martyrs 38043 Grenoble France
| | - Anaïs Chretien
- Structural Biology Group European Synchrotron Radiation Facility (ESRF) 71 avenue des Martyrs 38043 Grenoble France
| | - Maria Bacia‐Verloop
- Institut de Biologie Structurale (IBS) CNRS, CEA Université Grenoble Alpes 71 avenue des Martyrs 38044 Grenoble France
| | - Luca Signor
- Institut de Biologie Structurale (IBS) CNRS, CEA Université Grenoble Alpes 71 avenue des Martyrs 38044 Grenoble France
| | - Philippe J. Mas
- Integrated Structural Biology Grenoble (ISBG) CNRS CEA, Université Grenoble Alpes 71 avenue des Martyrs 38042 Grenoble France
| | - Adrien Favier
- Institut de Biologie Structurale (IBS) CNRS, CEA Université Grenoble Alpes 71 avenue des Martyrs 38044 Grenoble France
| | - Eve Borel Meneroud
- Grenoble Institut des Neurosciences (GIN) Centre Inserm U1216 Equipe Neuropathologies et Dysfonctions Synaptiques Université Grenoble Alpes 31 Chemin Fortuné Ferrini 38700 La Tronche France
| | - Michael Hons
- European Molecular Biology Laboratory (EMBL) Grenoble Outstation 71 avenue des Martyrs 38042 Grenoble France
| | - Darren J. Hart
- Institut de Biologie Structurale (IBS) CNRS, CEA Université Grenoble Alpes 71 avenue des Martyrs 38044 Grenoble France
| | - Eaazhisai Kandiah
- Structural Biology Group European Synchrotron Radiation Facility (ESRF) 71 avenue des Martyrs 38043 Grenoble France
| | - Elisabetta Boeri Erba
- Institut de Biologie Structurale (IBS) CNRS, CEA Université Grenoble Alpes 71 avenue des Martyrs 38044 Grenoble France
| | - Alain Buisson
- Grenoble Institut des Neurosciences (GIN) Centre Inserm U1216 Equipe Neuropathologies et Dysfonctions Synaptiques Université Grenoble Alpes 31 Chemin Fortuné Ferrini 38700 La Tronche France
| | - Gordon Leonard
- Structural Biology Group European Synchrotron Radiation Facility (ESRF) 71 avenue des Martyrs 38043 Grenoble France
| | - Irina Gutsche
- Institut de Biologie Structurale (IBS) CNRS, CEA Université Grenoble Alpes 71 avenue des Martyrs 38044 Grenoble France
| | - Montserrat Soler‐Lopez
- Structural Biology Group European Synchrotron Radiation Facility (ESRF) 71 avenue des Martyrs 38043 Grenoble France
| |
Collapse
|
4
|
Giachin G, Jessop M, Bouverot R, Acajjaoui S, Saïdi M, Chretien A, Bacia-Verloop M, Signor L, Mas PJ, Favier A, Borel Meneroud E, Hons M, Hart DJ, Kandiah E, Boeri Erba E, Buisson A, Leonard G, Gutsche I, Soler-Lopez M. Assembly of The Mitochondrial Complex I Assembly Complex Suggests a Regulatory Role for Deflavination. Angew Chem Int Ed Engl 2021; 60:4689-4697. [PMID: 33320993 PMCID: PMC7986633 DOI: 10.1002/anie.202011548] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Indexed: 01/01/2023]
Abstract
Fatty acid β‐oxidation (FAO) and oxidative phosphorylation (OXPHOS) are mitochondrial redox processes that generate ATP. The biogenesis of the respiratory Complex I, a 1 MDa multiprotein complex that is responsible for initiating OXPHOS, is mediated by assembly factors including the mitochondrial complex I assembly (MCIA) complex. However, the organisation and the role of the MCIA complex are still unclear. Here we show that ECSIT functions as the bridging node of the MCIA core complex. Furthermore, cryo‐electron microscopy together with biochemical and biophysical experiments reveal that the C‐terminal domain of ECSIT directly binds to the vestigial dehydrogenase domain of the FAO enzyme ACAD9 and induces its deflavination, switching ACAD9 from its role in FAO to an MCIA factor. These findings provide the structural basis for the MCIA complex architecture and suggest a unique molecular mechanism for coordinating the regulation of the FAO and OXPHOS pathways to ensure an efficient energy production.
Collapse
Affiliation(s)
- Gabriele Giachin
- Structural Biology Group, European Synchrotron Radiation Facility (ESRF), 71 avenue des Martyrs, 38043, Grenoble, France
| | - Matthew Jessop
- Institut de Biologie Structurale (IBS), CNRS, CEA, Université Grenoble Alpes, 71 avenue des Martyrs, 38044, Grenoble, France
| | - Romain Bouverot
- Structural Biology Group, European Synchrotron Radiation Facility (ESRF), 71 avenue des Martyrs, 38043, Grenoble, France
| | - Samira Acajjaoui
- Structural Biology Group, European Synchrotron Radiation Facility (ESRF), 71 avenue des Martyrs, 38043, Grenoble, France
| | - Melissa Saïdi
- Structural Biology Group, European Synchrotron Radiation Facility (ESRF), 71 avenue des Martyrs, 38043, Grenoble, France
| | - Anaïs Chretien
- Structural Biology Group, European Synchrotron Radiation Facility (ESRF), 71 avenue des Martyrs, 38043, Grenoble, France
| | - Maria Bacia-Verloop
- Institut de Biologie Structurale (IBS), CNRS, CEA, Université Grenoble Alpes, 71 avenue des Martyrs, 38044, Grenoble, France
| | - Luca Signor
- Institut de Biologie Structurale (IBS), CNRS, CEA, Université Grenoble Alpes, 71 avenue des Martyrs, 38044, Grenoble, France
| | - Philippe J Mas
- Integrated Structural Biology Grenoble (ISBG) CNRS, CEA, Université Grenoble Alpes, 71 avenue des Martyrs, 38042, Grenoble, France
| | - Adrien Favier
- Institut de Biologie Structurale (IBS), CNRS, CEA, Université Grenoble Alpes, 71 avenue des Martyrs, 38044, Grenoble, France
| | - Eve Borel Meneroud
- Grenoble Institut des Neurosciences (GIN), Centre Inserm U1216, Equipe Neuropathologies et Dysfonctions Synaptiques, Université Grenoble Alpes, 31 Chemin Fortuné Ferrini, 38700, La Tronche, France
| | - Michael Hons
- European Molecular Biology Laboratory (EMBL), Grenoble Outstation, 71 avenue des Martyrs, 38042, Grenoble, France
| | - Darren J Hart
- Institut de Biologie Structurale (IBS), CNRS, CEA, Université Grenoble Alpes, 71 avenue des Martyrs, 38044, Grenoble, France
| | - Eaazhisai Kandiah
- Structural Biology Group, European Synchrotron Radiation Facility (ESRF), 71 avenue des Martyrs, 38043, Grenoble, France
| | - Elisabetta Boeri Erba
- Institut de Biologie Structurale (IBS), CNRS, CEA, Université Grenoble Alpes, 71 avenue des Martyrs, 38044, Grenoble, France
| | - Alain Buisson
- Grenoble Institut des Neurosciences (GIN), Centre Inserm U1216, Equipe Neuropathologies et Dysfonctions Synaptiques, Université Grenoble Alpes, 31 Chemin Fortuné Ferrini, 38700, La Tronche, France
| | - Gordon Leonard
- Structural Biology Group, European Synchrotron Radiation Facility (ESRF), 71 avenue des Martyrs, 38043, Grenoble, France
| | - Irina Gutsche
- Institut de Biologie Structurale (IBS), CNRS, CEA, Université Grenoble Alpes, 71 avenue des Martyrs, 38044, Grenoble, France
| | - Montserrat Soler-Lopez
- Structural Biology Group, European Synchrotron Radiation Facility (ESRF), 71 avenue des Martyrs, 38043, Grenoble, France
| |
Collapse
|
5
|
Klingl S, Kordes S, Schmid B, Gerlach RG, Hensel M, Muller YA. Recombinant protein production and purification of SiiD, SiiE and SiiF - Components of the SPI4-encoded type I secretion system from Salmonella Typhimurium. Protein Expr Purif 2020; 172:105632. [PMID: 32251835 DOI: 10.1016/j.pep.2020.105632] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 03/20/2020] [Accepted: 03/29/2020] [Indexed: 12/15/2022]
Abstract
In humans, Salmonella enterica infections are responsible for a plethora of medical conditions. These include intestinal inflammation and typhoid fever. The initial contact between Salmonella and polarized epithelial cells is established by the SPI4-encoded type I secretion system (T1SS), which secretes SiiE, a giant non-fimbrial adhesin. We have recombinantly produced various domains of this T1SS from Salmonella enterica serovar Typhimurium in Escherichia coli for further experimental characterization. We purified three variants of SiiD, the periplasmic adapter protein spanning the space between the inner and outer membrane, two variants of the SiiE N-terminal region and the N-terminal domain of the SiiF ATP-binding cassette (ABC) transporter. In all three proteins, at least one variant yielded high amounts of pure soluble protein. Secondary structure content and cooperative unfolding were investigated by circular dichroism (CD) spectroscopy. Secondary structure contents were in good agreement with estimates derived from SiiD and SiiF homology models or, in case of the SiiE N-terminal region, a secondary structure prediction. For one SiiD variant, protein crystals could be obtained that diffracted X-rays to approximately 4 Å resolution.
Collapse
Affiliation(s)
- Stefan Klingl
- Division of Biotechnology, Department of Biology, Friedrich-Alexander-University Erlangen-Nürnberg, D-91052, Erlangen, Germany
| | - Sina Kordes
- Division of Biotechnology, Department of Biology, Friedrich-Alexander-University Erlangen-Nürnberg, D-91052, Erlangen, Germany
| | - Benedikt Schmid
- Division of Biotechnology, Department of Biology, Friedrich-Alexander-University Erlangen-Nürnberg, D-91052, Erlangen, Germany
| | | | - Michael Hensel
- Abt. Mikrobiologie and CellNanOs, Universität Osnabrück, Osnabrück, Germany
| | - Yves A Muller
- Division of Biotechnology, Department of Biology, Friedrich-Alexander-University Erlangen-Nürnberg, D-91052, Erlangen, Germany.
| |
Collapse
|
6
|
Simonini S, Mas PJ, Mas CMVS, Østergaard L, Hart DJ. Auxin sensing is a property of an unstructured domain in the Auxin Response Factor ETTIN of Arabidopsis thaliana. Sci Rep 2018; 8:13563. [PMID: 30202032 PMCID: PMC6131142 DOI: 10.1038/s41598-018-31634-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 08/04/2018] [Indexed: 11/18/2022] Open
Abstract
The plant hormone auxin regulates numerous aspects of the plant life cycle. Auxin signalling is mediated by auxin response factors (ARFs) that dimerise with modulating Aux/IAA repressors. ARF3 (ETTIN or ETT) is atypical as it does not interact with Aux/IAA repressors. It is proposed to be a non-canonical auxin sensor, regulating diverse functions essential for development. This sensing ability relies on a unique C-terminal ETT specific domain (ES domain). Alignments of ETT orthologues across the angiosperm phylum revealed that the length and sequence identities of ES domains are poorly conserved. Computational predictors suggested the ES domains to be intrinsically disordered, explaining their tolerance of insertions, deletions and mutations during evolution. Nevertheless, five highly conserved short linear motifs were identified suggesting functional significance. High-throughput library screening identified an almost full-length soluble ES domain that did not bind auxin directly, but exhibited a dose-dependent response in a yeast two-hybrid system against the Arabidopsis INDEHISCENT (IND) transcription factor. Circular dichroism confirmed the domain was disordered. The identification and purification of this domain opens the way to the future characterisation of the ETT auxin-sensing mechanism in planta and an improved understanding of auxin-mediated regulation.
Collapse
Affiliation(s)
- Sara Simonini
- Crop Genetics Department, John Innes Centre, Norwich Research Park, Colney Lane, NR4 7UH, Norwich, UK
- Department of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, CH-8008, Zürich, Switzerland
| | - Philippe J Mas
- Integrated Structural Biology Grenoble (ISBG) CNRS, CEA, Université Grenoble Alpes, EMBL, 71 avenue des Martyrs, F-38042, Grenoble, France
| | - Caroline M V S Mas
- Integrated Structural Biology Grenoble (ISBG) CNRS, CEA, Université Grenoble Alpes, EMBL, 71 avenue des Martyrs, F-38042, Grenoble, France
| | - Lars Østergaard
- Crop Genetics Department, John Innes Centre, Norwich Research Park, Colney Lane, NR4 7UH, Norwich, UK.
| | - Darren J Hart
- Institut de Biologie Structurale, CEA, CNRS, Université Grenoble Alpes, 71 avenue des Martyrs, F-38042, Grenoble, France.
| |
Collapse
|
7
|
Tarbouriech N, Ducournau C, Hutin S, Mas PJ, Man P, Forest E, Hart DJ, Peyrefitte CN, Burmeister WP, Iseni F. The vaccinia virus DNA polymerase structure provides insights into the mode of processivity factor binding. Nat Commun 2017; 8:1455. [PMID: 29129932 PMCID: PMC5682278 DOI: 10.1038/s41467-017-01542-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 09/26/2017] [Indexed: 11/12/2022] Open
Abstract
Vaccinia virus (VACV), the prototype member of the Poxviridae, replicates in the cytoplasm of an infected cell. The catalytic subunit of the DNA polymerase E9 binds the heterodimeric processivity factor A20/D4 to form the functional polymerase holoenzyme. Here we present the crystal structure of full-length E9 at 2.7 Å resolution that permits identification of important poxvirus-specific structural insertions. One insertion in the palm domain interacts with C-terminal residues of A20 and thus serves as the processivity factor-binding site. This is in strong contrast to all other family B polymerases that bind their co-factors at the C terminus of the thumb domain. The VACV E9 structure also permits rationalization of polymerase inhibitor resistance mutations when compared with the closely related eukaryotic polymerase delta–DNA complex. The catalytic subunit E9 of the vaccinia virus DNA polymerase forms a functional polymerase holoenzyme by interacting with the heterodimeric processivity factor A20/D4. Here the authors present the structure of full-length E9 and show that an insertion within its palm domain binds A20, in a mode different from other family B polymerases.
Collapse
Affiliation(s)
- Nicolas Tarbouriech
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CNRS, CEA, 71 Avenue des Martyrs, 38042, Grenoble, France
| | - Corinne Ducournau
- Unité de Virologie, Institut de Recherche Biomédicale des Armées, BP 73, 91223, Brétigny-sur-Orge Cedex, France
| | - Stephanie Hutin
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CNRS, CEA, 71 Avenue des Martyrs, 38042, Grenoble, France
| | - Philippe J Mas
- Integrated Structural Biology Grenoble (ISBG) CNRS, CEA, Université Grenoble Alpes, EMBL, 71 Avenue des Martyrs, 38042, Grenoble, France
| | - Petr Man
- BioCeV-Institute of Microbiology, Czech Academy of Sciences, Prumyslova 595, 252 50, Vestec, Czech Republic.,Faculty of Science, Charles University, Hlavova 8, 128 43, Prague 2, Czech Republic
| | - Eric Forest
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CNRS, CEA, 71 Avenue des Martyrs, 38042, Grenoble, France
| | - Darren J Hart
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CNRS, CEA, 71 Avenue des Martyrs, 38042, Grenoble, France
| | - Christophe N Peyrefitte
- Unité de Virologie, Institut de Recherche Biomédicale des Armées, BP 73, 91223, Brétigny-sur-Orge Cedex, France.,Emerging Pathogens Laboratory, Fondation Mérieux, 21 Avenue Tony Garnier, 69007, Lyon, France
| | - Wim P Burmeister
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CNRS, CEA, 71 Avenue des Martyrs, 38042, Grenoble, France
| | - Frédéric Iseni
- Unité de Virologie, Institut de Recherche Biomédicale des Armées, BP 73, 91223, Brétigny-sur-Orge Cedex, France.
| |
Collapse
|
8
|
Bradshaw NJ. The interaction of schizophrenia-related proteins DISC1 and NDEL1, in light of the newly identified domain structure of DISC1. Commun Integr Biol 2017. [PMCID: PMC5595412 DOI: 10.1080/19420889.2017.1335375] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
DISC1 and NDEL1 are both key proteins in cortical neurodevelopment, which are each also implicated in the pathogenesis of mental illness. That the two proteins interact with each other in a functionally important manner is well established, but two distinct binding domains for NDEL1 on DISC1 have been proposed. A partial domain structure for DISC1 has recently been described, consisting of 4 structured regions referred to as “D,” “I,” “S” and “C” respectively, with one of the NDEL1 binding sites lying in the “C” region of DISC1. In light of this domain structure, it can be deduced that this site is the likely location at which NDEL1 binds, although the other proposed site (which lies in the DISC1 “I” and “S” regions) may indirectly impact on DISC1-NDEL1 interactions through determination of the oligomeric state of DISC1.
Collapse
Affiliation(s)
- Nicholas J. Bradshaw
- Department of Biotechnology, University of Rijeka, Rijeka, Croatia
- Department of Neuropathology, Heinrich Heine University, Düsseldorf, Germany
| |
Collapse
|