1
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Davies KA, Czabotar PE, Murphy JM. Death at a funeral: Activation of the dead enzyme, MLKL, to kill cells by necroptosis. Curr Opin Struct Biol 2024; 88:102891. [PMID: 39059047 DOI: 10.1016/j.sbi.2024.102891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 06/25/2024] [Accepted: 07/05/2024] [Indexed: 07/28/2024]
Abstract
Necroptosis is a lytic form of programmed cell death implicated in inflammatory pathologies, leading to intense interest in the underlying mechanisms and therapeutic prospects. Here, we review our current structural understanding of how the terminal executioner of the pathway, the dead kinase, mixed lineage kinase domain-like (MLKL), is converted from a dormant to killer form by the upstream regulatory kinase, RIPK3. RIPK3-mediated phosphorylation of MLKL's pseudokinase domain toggles a molecular switch that induces dissociation from a cytoplasmic platform, assembly of MLKL oligomers, and trafficking to the plasma membrane, where activated MLKL accumulates and permeabilises the lipid bilayer to induce cell death. We highlight gaps in mechanistic knowledge of MLKL's activation, how mechanisms diverge between species, and the power of modelling in advancing structural insights.
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Affiliation(s)
- Katherine A Davies
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia.
| | - Peter E Czabotar
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia.
| | - James M Murphy
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia; Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia.
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2
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Xiao L, Pi X, Goss AC, El-Baba T, Ehrmann JF, Grinkevich E, Bazua-Valenti S, Padovano V, Alper SL, Carey D, Udeshi ND, Carr SA, Pablo JL, Robinson CV, Greka A, Wu H. Molecular basis of TMED9 oligomerization and entrapment of misfolded protein cargo in the early secretory pathway. SCIENCE ADVANCES 2024; 10:eadp2221. [PMID: 39303030 PMCID: PMC11414720 DOI: 10.1126/sciadv.adp2221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 08/14/2024] [Indexed: 09/22/2024]
Abstract
Intracellular accumulation of misfolded proteins causes serious human proteinopathies. The transmembrane emp24 domain 9 (TMED9) cargo receptor promotes a general mechanism of cytotoxicity by entrapping misfolded protein cargos in the early secretory pathway. However, the molecular basis for this TMED9-mediated cargo retention remains elusive. Here, we report cryo-electron microscopy structures of TMED9, which reveal its unexpected self-oligomerization into octamers, dodecamers, and, by extension, even higher-order oligomers. The TMED9 oligomerization is driven by an intrinsic symmetry mismatch between the trimeric coiled coil domain and the tetrameric transmembrane domain. Using frameshifted Mucin 1 as an example of aggregated disease-related protein cargo, we implicate a mode of direct interaction with the TMED9 luminal Golgi-dynamics domain. The structures suggest and we confirm that TMED9 oligomerization favors the recruitment of coat protein I (COPI), but not COPII coatomers, facilitating retrograde transport and explaining the observed cargo entrapment. Our work thus reveals a molecular basis for TMED9-mediated misfolded protein retention in the early secretory pathway.
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Affiliation(s)
- Le Xiao
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Xiong Pi
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Alissa C. Goss
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Tarick El-Baba
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford OX1 3QU, UK
| | - Julian F. Ehrmann
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Elizabeth Grinkevich
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Silvana Bazua-Valenti
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Seth L. Alper
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Division of Nephrology, Beth Israel Deaconess Medical Center and Department of Medicine, Harvard Medical School, Boston, MA 02215, USA
| | - Dominique Carey
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Steven A. Carr
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Juan Lorenzo Pablo
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Carol V. Robinson
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford OX1 3QU, UK
| | - Anna Greka
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Hao Wu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
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3
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Liu Y, Yang J, Ruan M, Zhang H, Wang J, Li Y. NMR-Based Characterization of the Interaction between Yeast Oxa1-CTD and Ribosomes. Int J Mol Sci 2023; 24:14657. [PMID: 37834108 PMCID: PMC10572626 DOI: 10.3390/ijms241914657] [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] [Received: 08/26/2023] [Revised: 09/25/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023] Open
Abstract
In mitochondria, the major subunits of oxidative phosphorylation complexes are translated by the mitochondrial ribosome (mito-ribosome). The correct insertion and assembly of these subunits into the inner mitochondrial membrane (IMM) are facilitated by mitochondrial oxidase assembly protein 1 (Oxa1) during the translation process. This co-translational insertion process involves an association between the mito-ribosome and the C-terminus of Oxa1 (Oxa1-CTD) Nuclear magnetic resonance (NMR) methods were mainly used to investigate the structural characterization of yeast Oxa1-CTD and its mode of interaction with the E. coli 70S ribosome. Oxa1-CTD forms a transient α-helical structure within the residues P342-Q385, which were reported to form an α-helix when combining with the ribosome. Two conserved contact sites that could interact with the ribosome were further identified. The first site was located on the very end of the N-terminus (V321-I327), and the second one encompassed a stretch of amino acid residues I348-Q370. Based on our discoveries and previous reports, a model has been proposed in which Oxa1-CTD interacts with ribosomes, accompanied by transient-to-stable transitions at the second contact site. These observations may enhance our understanding of the potential role of Oxa1-CTD in facilitating the assembly of oxidative phosphorylation complexes and provide insight into the structural characteristics of Oxa1-CTD.
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Affiliation(s)
- Yong Liu
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China; (Y.L.); (J.Y.); (M.R.); (H.Z.)
- Science Island Branch of Graduate School, University of Science and Technology of China, Hefei 230026, China
| | - Jing Yang
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China; (Y.L.); (J.Y.); (M.R.); (H.Z.)
| | - Maosen Ruan
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China; (Y.L.); (J.Y.); (M.R.); (H.Z.)
| | - Huiqin Zhang
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China; (Y.L.); (J.Y.); (M.R.); (H.Z.)
- Institutes of Physical Science and Information Technology, Anhui University, Hefei 230601, China
| | - Junfeng Wang
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China; (Y.L.); (J.Y.); (M.R.); (H.Z.)
- Science Island Branch of Graduate School, University of Science and Technology of China, Hefei 230026, China
- Institutes of Physical Science and Information Technology, Anhui University, Hefei 230601, China
| | - Yunyan Li
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China; (Y.L.); (J.Y.); (M.R.); (H.Z.)
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4
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Chen X, Portran D, Widmer LA, Stangier MM, Czub MP, Liakopoulos D, Stelling J, Steinmetz MO, Barral Y. The motor domain of the kinesin Kip2 promotes microtubule polymerization at microtubule tips. J Cell Biol 2023; 222:214052. [PMID: 37093124 PMCID: PMC10130750 DOI: 10.1083/jcb.202110126] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 01/01/2023] [Accepted: 03/22/2023] [Indexed: 04/25/2023] Open
Abstract
Kinesins are microtubule-dependent motor proteins, some of which moonlight as microtubule polymerases, such as the yeast protein Kip2. Here, we show that the CLIP-170 ortholog Bik1 stabilizes Kip2 at microtubule ends where the motor domain of Kip2 promotes microtubule polymerization. Live-cell imaging and mathematical estimation of Kip2 dynamics reveal that disrupting the Kip2-Bik1 interaction aborts Kip2 dwelling at microtubule ends and abrogates its microtubule polymerization activity. Structural modeling and biochemical experiments identify a patch of positively charged residues that enables the motor domain to bind free tubulin dimers alternatively to the microtubule shaft. Neutralizing this patch abolished the ability of Kip2 to promote microtubule growth both in vivo and in vitro without affecting its ability to walk along microtubules. Our studies suggest that Kip2 utilizes Bik1 as a cofactor to track microtubule tips, where its motor domain then recruits free tubulin and catalyzes microtubule assembly.
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Affiliation(s)
- Xiuzhen Chen
- Institute of Biochemistry, Eidgenössische Technische Hochschule Zürich , Zurich, Switzerland
| | - Didier Portran
- CRBM, Université de Montpellier , CNRS, Montpellier, France
| | - Lukas A Widmer
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule Zürich, and Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Marcel M Stangier
- Department of Biology and Chemistry, Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, Switzerland
| | - Mateusz P Czub
- Department of Biology and Chemistry, Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, Switzerland
| | - Dimitris Liakopoulos
- CRBM, Université de Montpellier , CNRS, Montpellier, France
- Laboratory of Biology, University of Ioannina, Faculty of Medicine, Ioannina, Greece
| | - Jörg Stelling
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule Zürich, and Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Michel O Steinmetz
- Department of Biology and Chemistry, Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, Switzerland
- University of Basel, Biozentrum , Basel, Switzerland
| | - Yves Barral
- Institute of Biochemistry, Eidgenössische Technische Hochschule Zürich , Zurich, Switzerland
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5
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Amin A, Wu R, Khan MA, Cheung MH, Liang Y, Liu C, Zhu G, Yu ZL, Liang C. An essential Noc3p dimerization cycle mediates ORC double-hexamer formation in replication licensing. Life Sci Alliance 2023; 6:e202201594. [PMID: 36599624 PMCID: PMC9813392 DOI: 10.26508/lsa.202201594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 12/17/2022] [Accepted: 12/19/2022] [Indexed: 01/05/2023] Open
Abstract
Replication licensing, a prerequisite of DNA replication, helps to ensure once-per-cell-cycle genome duplication. Some DNA replication-initiation proteins are sequentially loaded onto replication origins to form pre-replicative complexes (pre-RCs). ORC and Noc3p bind replication origins throughout the cell cycle, providing a platform for pre-RC assembly. We previously reported that cell cycle-dependent ORC dimerization is essential for the chromatin loading of the symmetric MCM double-hexamers. Here, we used Saccharomyces cerevisiae separation-of-function NOC3 mutants to confirm the separable roles of Noc3p in DNA replication and ribosome biogenesis. We also show that an essential and cell cycle-dependent Noc3p dimerization cycle regulates the ORC dimerization cycle. Noc3p dimerizes at the M-to-G1 transition and de-dimerizes in S-phase. The Noc3p dimerization cycle coupled with the ORC dimerization cycle enables replication licensing, protects nascent sister replication origins after replication initiation, and prevents re-replication. This study has revealed a new mechanism of replication licensing and elucidated the molecular mechanism of Noc3p as a mediator of ORC dimerization in pre-RC formation.
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Affiliation(s)
- Aftab Amin
- Division of Life Science, Center for Cancer Research, and State Key Lab of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - Rentian Wu
- Division of Life Science, Center for Cancer Research, and State Key Lab of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
| | - Muhammad Ajmal Khan
- Division of Life Science, Center for Cancer Research, and State Key Lab of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
| | - Man Hei Cheung
- Division of Life Science, Center for Cancer Research, and State Key Lab of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
| | - Yanting Liang
- Division of Life Science, Center for Cancer Research, and State Key Lab of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
| | - Changdong Liu
- Division of Life Science, Center for Cancer Research, and State Key Lab of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
| | - Guang Zhu
- Division of Life Science, Center for Cancer Research, and State Key Lab of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
| | - Zhi-Ling Yu
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - Chun Liang
- Division of Life Science, Center for Cancer Research, and State Key Lab of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
- EnKang Pharmaceuticals (Guangzhou), Ltd., Guangzhou, China
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6
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Fasola E, Alboreggia G, Pieraccini S, Oliva F, Agharbaoui FE, Bollati M, Bertoni G, Recchia S, Marelli M, Piarulli U, Pellegrino S, Gazzola S. Conformational switch and multiple supramolecular structures of a newly identified self-assembling protein-mimetic peptide from Pseudomonas aeruginosa YeaZ protein. Front Chem 2022; 10:1038796. [PMID: 36583150 PMCID: PMC9792601 DOI: 10.3389/fchem.2022.1038796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 11/29/2022] [Indexed: 12/15/2022] Open
Abstract
Protein-mimetic peptides (PMPs) are shorter sequences of self-assembling proteins, that represent remarkable building blocks for the generation of bioinspired functional supramolecular structures with multiple applications. The identification of novel aminoacidic sequences that permit the access to valuable biocompatible materials is an attractive area of research. In this work, in silico analysis of the Pseudomonas aeruginosa YeaZ protein (PaYeaZ) led to the identification of a tetradecapeptide that represents the shortest sequence responsible for the YeaZ-YeaZ dimer formation. Based on its sequence, an innovative 20-meric peptide, called PMP-2, was designed, synthesized, and characterized in terms of secondary structure and self-assembly properties. PMP-2 conserves a helical character and self-assembles into helical nanofibers in non-polar solvents (DMSO and trifluoroethanol), as well as in dilute (0.5 mM) aqueous solutions. In contrast, at higher concentrations (>2 mM) in water, a conformational transition from α-helix to β-sheet occurs, which is accompanied by the Protein-mimetic peptide aggregation into 2D-sheets and formation supramolecular gel in aqueous environment. Our findings reveal a newly identified Protein-mimetic peptide that could turn as a promising candidate for future material applications.
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Affiliation(s)
- Elettra Fasola
- Science and High Technology Department, University of Insubria, Como, Italy
| | - Giulia Alboreggia
- Science and High Technology Department, University of Insubria, Como, Italy
| | | | | | | | - Michela Bollati
- CNR and Department of Biosciences, Institute of Biophysics, University of Milan, Milan, Italy
| | | | - Sandro Recchia
- Science and High Technology Department, University of Insubria, Como, Italy
| | - Marcello Marelli
- CNR-SCITEC—Istituto di Scienze e Tecnologie Chimiche “Giulio Natta”, Milan, Italy
| | - Umberto Piarulli
- Science and High Technology Department, University of Insubria, Como, Italy,*Correspondence: Umberto Piarulli, ; Silvia Gazzola,
| | - Sara Pellegrino
- Pharmaceutical Science Department, University of Milan, Milan, Italy
| | - Silvia Gazzola
- Science and High Technology Department, University of Insubria, Como, Italy,*Correspondence: Umberto Piarulli, ; Silvia Gazzola,
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7
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Pollenz RS, Bland J, Pope WH. Bioinformatic characterization of endolysins and holin-like membrane proteins in the lysis cassette of phages that infect Gordonia rubripertincta. PLoS One 2022; 17:e0276603. [PMID: 36395171 PMCID: PMC9671378 DOI: 10.1371/journal.pone.0276603] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 10/11/2022] [Indexed: 11/19/2022] Open
Abstract
Holins are bacteriophage-encoded transmembrane proteins that function to control the timing of bacterial lysis event, assist with the destabilization of the membrane proton motive force and in some models, generate large "pores" in the cell membrane to allow the exit of the phage-encoded endolysin so they can access the peptidoglycan components of the cell wall. The lysis mechanism has been rigorously evaluated through biochemical and genetic studies in very few phages, and the results indicate that phages utilize endolysins, holins and accessory proteins to the outer membrane to achieve cell lysis through several distinct operational models. This observation suggests the possibility that phages may evolve novel variations of how the lysis proteins functionally interact in an effort to improve fitness or evade host defenses. To begin to address this hypothesis, the current study utilized a comprehensive bioinformatic approach to systematically identify the proteins encoded by the genes within the lysis cassettes in 16 genetically diverse phages that infect the Gram-positive Gordonia rubripertincta NRLL B-16540 strain. The results show that there is a high level of diversity of the various lysis genes and 16 different genome organizations of the putative lysis cassette, many which have never been described. Thirty-four different genes encoding holin-like proteins were identified as well as a potential holin-major capsid fusion protein. The holin-like proteins contained between 1-4 transmembrane helices, were not shared to a high degree amongst the different phages and are present in the lysis cassette in a wide range of combinations of up to 4 genes in which none are duplicated. Detailed evaluation of the transmembrane domains and predicted membrane topologies of the holin-like proteins show that many have novel structures that have not been previously characterized. These results provide compelling support that there are novel operational lysis models yet to be discovered.
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Affiliation(s)
- Richard S. Pollenz
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, Florida, United States of America
| | - Jackson Bland
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, Florida, United States of America
| | - Welkin H. Pope
- Science Department, Chatham University, Pittsburgh, Pennsylvania, United States of America
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8
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Qing R, Hao S, Smorodina E, Jin D, Zalevsky A, Zhang S. Protein Design: From the Aspect of Water Solubility and Stability. Chem Rev 2022; 122:14085-14179. [PMID: 35921495 PMCID: PMC9523718 DOI: 10.1021/acs.chemrev.1c00757] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Indexed: 12/13/2022]
Abstract
Water solubility and structural stability are key merits for proteins defined by the primary sequence and 3D-conformation. Their manipulation represents important aspects of the protein design field that relies on the accurate placement of amino acids and molecular interactions, guided by underlying physiochemical principles. Emulated designer proteins with well-defined properties both fuel the knowledge-base for more precise computational design models and are used in various biomedical and nanotechnological applications. The continuous developments in protein science, increasing computing power, new algorithms, and characterization techniques provide sophisticated toolkits for solubility design beyond guess work. In this review, we summarize recent advances in the protein design field with respect to water solubility and structural stability. After introducing fundamental design rules, we discuss the transmembrane protein solubilization and de novo transmembrane protein design. Traditional strategies to enhance protein solubility and structural stability are introduced. The designs of stable protein complexes and high-order assemblies are covered. Computational methodologies behind these endeavors, including structure prediction programs, machine learning algorithms, and specialty software dedicated to the evaluation of protein solubility and aggregation, are discussed. The findings and opportunities for Cryo-EM are presented. This review provides an overview of significant progress and prospects in accurate protein design for solubility and stability.
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Affiliation(s)
- Rui Qing
- State
Key Laboratory of Microbial Metabolism, School of Life Sciences and
Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Media
Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- The
David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Shilei Hao
- Media
Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Key
Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400030, China
| | - Eva Smorodina
- Department
of Immunology, University of Oslo and Oslo
University Hospital, Oslo 0424, Norway
| | - David Jin
- Avalon GloboCare
Corp., Freehold, New Jersey 07728, United States
| | - Arthur Zalevsky
- Laboratory
of Bioinformatics Approaches in Combinatorial Chemistry and Biology, Shemyakin−Ovchinnikov Institute of Bioorganic
Chemistry RAS, Moscow 117997, Russia
| | - Shuguang Zhang
- Media
Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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9
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Murph M, Singh S, Schvarzstein M. A combined in silico and in vivo approach to the structure-function annotation of SPD-2 provides mechanistic insight into its functional diversity. Cell Cycle 2022; 21:1958-1979. [PMID: 35678569 PMCID: PMC9415446 DOI: 10.1080/15384101.2022.2078458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 04/10/2022] [Accepted: 05/04/2022] [Indexed: 11/03/2022] Open
Abstract
Centrosomes are organelles that function as hubs of microtubule nucleation and organization, with key roles in organelle positioning, asymmetric cell division, ciliogenesis, and signaling. Aberrant centrosome number, structure or function is linked to neurodegenerative diseases, developmental abnormalities, ciliopathies, and tumor development. A major regulator of centrosome biogenesis and function in C. elegans is the conserved Spindle-defective protein 2 (SPD-2), a homolog of the human CEP-192 protein. CeSPD-2 is required for centrosome maturation, centriole duplication, spindle assembly and possibly cell polarity establishment. Despite its importance, the specific molecular mechanism of CeSPD-2 regulation and function is poorly understood. Here, we combined computational analysis with cell biology approaches to uncover possible structure-function relationships of CeSPD-2 that may shed mechanistic light on its function. Domain prediction analysis corroborated and refined previously identified coiled-coils and ASH (Aspm-SPD-2 Hydin) domains and identified new domains: a GEF domain, an Ig-like domain, and a PDZ-like domain. In addition to these predicted structural features, CeSPD-2 is also predicted to be intrinsically disordered. Surface electrostatic maps identified a large basic region unique to the ASH domain of CeSPD-2. This basic region overlaps with most of the residues predicted to be involved in protein-protein interactions. In vivo, ASH::GFP localized to centrosomes and centrosome-associated microtubules. Our analysis groups ASH domains, PapD, Usher chaperone domains, and Major Sperm Protein (MSP) domains into a single superfold within the larger Immunoglobulin superfamily. This study lays the groundwork for designing rational hypothesis-based experiments to uncover the mechanisms of CeSPD-2 function in vivo.Abbreviations: AIR, Aurora kinase; ASH, Aspm-SPD-2 Hydin; ASP, Abnormal Spindle Protein; ASPM, Abnormal Spindle-like Microcephaly-associated Protein; CC, coiled-coil; CDK, Cyclin-dependent Kinase; Ce, Caenorhabditis elegans; CEP, Centrosomal Protein; CPAP, centrosomal P4.1-associated protein; D, Drosophila; GAP, GTPase activating protein; GEF, GTPase guanine nucleotide exchange factor; Hs, Homo sapiens/Human; Ig, Immunoglobulin; MAP, Microtubule associated Protein; MSP, Major Sperm Protein; MDP, Major Sperm Domain-Containing Protein; OCRL-1, Golgi endocytic trafficking protein Inositol polyphosphate 5-phosphatase; PAR, abnormal embryonic PARtitioning of the cytosol; PCM, Pericentriolar material; PCMD, pericentriolar matrix deficient; PDZ, PSD95/Dlg-1/zo-1; PLK, Polo like kinase; RMSD, Root Mean Square Deviation; SAS, Spindle assembly abnormal proteins; SPD, Spindle-defective protein; TRAPP, TRAnsport Protein Particle; Xe, Xenopus; ZYG, zygote defective protein.
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Affiliation(s)
- Mikaela Murph
- Department of Biology, City University of New York, Brooklyn College, New York, NY, USA
| | - Shaneen Singh
- Department of Biology, City University of New York, Brooklyn College, New York, NY, USA
- Department of Biology, The Graduate Center at City University of New York, New York, NY, USA
- Department Biochemistry, The Graduate Center at City University of New York, New York, NY, USA
| | - Mara Schvarzstein
- Department of Biology, City University of New York, Brooklyn College, New York, NY, USA
- Department of Biology, The Graduate Center at City University of New York, New York, NY, USA
- Department Biochemistry, The Graduate Center at City University of New York, New York, NY, USA
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10
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Identification and characterization of coiled-coil motifs across Autographa californica multiple nucleopolyhedrovirus genome. Heliyon 2022; 8:e10588. [PMID: 36132175 PMCID: PMC9483598 DOI: 10.1016/j.heliyon.2022.e10588] [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: 01/25/2022] [Revised: 05/15/2022] [Accepted: 09/05/2022] [Indexed: 12/02/2022] Open
Abstract
Coiled coils (CCs) are protein structural motifs universally found in proteins and mediate a plethora of biological interactions, and thus their reliable annotation is crucial for studies of protein structure and function. Autographa californica multiple nucleopolyhedrovirus (AcMNPV) is a large double-stranded DNA (dsDNA) virus and encodes 154 proteins. In this study, genome-wide scans of previously uncharacterized CC motifs throughout AcMNPV was conducted using CC prediction software. In total, 24 CC motifs in 19 CC proteins with high confidence were identified. The characteristic of viral CC motifs were analyzed. The CC proteins could be divided into 12 viral structural proteins and 7 non-structural proteins, including viral membrane fusion proteins, enzymes, and transcription factors. Moreover, CC motifs are conserved in the baculoviral orthologs of 14 of the 19 proteins. It is noted that five CC proteins, including Ac51, Ac66, Exon0, Ac13, and GP16, were previously identified to function in the nuclear egress of nucleocapsids, and Ac66 contains multiple CC motifs, the longest of which comprises 252 amino acids, suggesting a role of CC motifs in this process. Taken together, the CC motifs identified in this study are valuable resource for studying protein function and protein interaction networks during virus replication.
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11
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Parihar PS, Singh A, Karade SS, Sahasrabuddhe AA, Pratap JV. Structural insights into kinetoplastid coronin oligomerization domain and F-actin interaction. Curr Res Struct Biol 2021; 3:268-276. [PMID: 34746809 PMCID: PMC8554105 DOI: 10.1016/j.crstbi.2021.10.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 09/18/2021] [Accepted: 10/11/2021] [Indexed: 12/25/2022] Open
Abstract
The two-domain actin associated protein coronin interacts with filamentous (F-) actin, facilitating diverse biological processes including cell proliferation, motility, phagocytosis, host-parasite interaction and cargo binding. The conserved N-terminal β-propeller domain is involved in protein: protein interactions, while the C-terminal coiled-coil domain mediates oligomerization, transducing conformational changes. The L. donovani coronin coiled-coil (LdCoroCC) domain exhibited a novel topology and oligomer association with an inherent asymmetry, caused primarily by three a residues of successive heptads. In the T.brucei homolog (TbrCoro), two of these 'a' residues are different (Val 493 & 507 replacing LdCoroCC Ile 486 and Met 500 respectively). The elucidated structure possesses a similar topology and assembly while comparative structural analysis shows that the T.brucei coronin coiled-coil domain (TbrCoroCC) too possesses the asymmetry though its magnitude is smaller. Analysis identifies that the asymmetric state is stabilized via cyclic salt bridges formed by Arg 497 and Glu 504. Co-localization studies (LdCoro, TbrCoro and corresponding mutant coiled coil constructs) with actin show that there are subtle differences in their binding patterns, with the double mutant V493I-V507M showing maximal effect. None of the constructs have an effect on F-actin length. Taken together with LdCoroCC, we therefore conclude that the inherent asymmetric structures are essential for kinetoplastids, and are of interest in understanding and exploiting actin dynamics.
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Affiliation(s)
- Pankaj Singh Parihar
- Division of Biochemistry and Structural Biology, CSIR - Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, 226031, Uttar Pradesh, India
| | - Aastha Singh
- Division of Biochemistry and Structural Biology, CSIR - Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, 226031, Uttar Pradesh, India
| | - Sharanbasappa Shrimant Karade
- Division of Biochemistry and Structural Biology, CSIR - Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, 226031, Uttar Pradesh, India
| | - Amogh Anant Sahasrabuddhe
- Division of Biochemistry and Structural Biology, CSIR - Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, 226031, Uttar Pradesh, India
| | - J Venkatesh Pratap
- Division of Biochemistry and Structural Biology, CSIR - Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, 226031, Uttar Pradesh, India
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12
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Riehl J, Rijal R, Nitz L, Clemen CS, Hofmann A, Eichinger L. Domain Organization of the UBX Domain Containing Protein 9 and Analysis of Its Interactions With the Homohexameric AAA + ATPase p97 (Valosin-Containing Protein). Front Cell Dev Biol 2021; 9:748860. [PMID: 34631722 PMCID: PMC8495200 DOI: 10.3389/fcell.2021.748860] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 08/31/2021] [Indexed: 11/13/2022] Open
Abstract
The abundant homohexameric AAA + ATPase p97 (also known as valosin-containing protein, VCP) is highly conserved from Dictyostelium discoideum to human and a pivotal factor of cellular protein homeostasis as it catalyzes the unfolding of proteins. Owing to its fundamental function in protein quality control pathways, it is regulated by more than 30 cofactors, including the UBXD protein family, whose members all carry an Ubiquitin Regulatory X (UBX) domain that enables binding to p97. One member of this latter protein family is the largely uncharacterized UBX domain containing protein 9 (UBXD9). Here, we analyzed protein-protein interactions of D. discoideum UBXD9 with p97 using a series of N- and C-terminal truncation constructs and probed the UBXD9 interactome in D. discoideum. Pull-down assays revealed that the UBX domain (amino acids 384-466) is necessary and sufficient for p97 interactions and that the N-terminal extension of the UBX domain, which folds into a β0-α- 1-α0 lariat structure, is required for the dissociation of p97 hexamers. Functionally, this finding is reflected by strongly reduced ATPase activity of p97 upon addition of full length UBXD9 or UBXD9261-573. Results from Blue Native PAGE as well as structural model prediction suggest that hexamers of UBXD9 or UBXD9261-573 interact with p97 hexamers and disrupt the p97 subunit interactions via insertion of a helical lariat structure, presumably by destabilizing the p97 D1:D1' intermolecular interface. We thus propose that UBXD9 regulates p97 activity in vivo by shifting the quaternary structure equilibrium from hexamers to monomers. Using three independent approaches, we further identified novel interaction partners of UBXD9, including glutamine synthetase type III as well as several actin-binding proteins. These findings suggest a role of UBXD9 in the organization of the actin cytoskeleton, and are in line with the hypothesized oligomerization-dependent mechanism of p97 regulation.
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Affiliation(s)
- Jana Riehl
- Medical Faculty, Center for Biochemistry, Institute of Biochemistry I, University of Cologne, Cologne, Germany
| | - Ramesh Rijal
- Department of Biology, College Station, Texas A&M University, Texas, TX, United States
| | - Leonie Nitz
- Medical Faculty, Center for Biochemistry, Institute of Biochemistry I, University of Cologne, Cologne, Germany
| | - Christoph S. Clemen
- Medical Faculty, Center for Biochemistry, Institute of Biochemistry I, University of Cologne, Cologne, Germany
- German Aerospace Center, Institute of Aerospace Medicine, Cologne, Germany
- Medical Faculty, Center for Physiology and Pathophysiology, Institute of Vegetative Physiology, University of Cologne, Cologne, Germany
| | - Andreas Hofmann
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, VIC, Australia
| | - Ludwig Eichinger
- Medical Faculty, Center for Biochemistry, Institute of Biochemistry I, University of Cologne, Cologne, Germany
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13
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Woods BL, Cannon KS, Vogt EJD, Crutchley JM, Gladfelter AS. Interplay of septin amphipathic helices in sensing membrane-curvature and filament bundling. Mol Biol Cell 2021; 32:br5. [PMID: 34319771 PMCID: PMC8684760 DOI: 10.1091/mbc.e20-05-0303] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The curvature of the membrane defines cell shape. Septins are GTP-binding proteins that assemble into heteromeric complexes and polymerize into filaments at areas of micron-scale membrane curvature. An amphipathic helix (AH) domain within the septin complex is necessary and sufficient for septins to preferentially assemble onto micron-scale curvature. Here we report that the nonessential fungal septin, Shs1, also has an AH domain capable of recognizing membrane curvature. In a septin mutant strain lacking a fully functional Cdc12 AH domain (cdc12-6), the C-terminal extension of Shs1, containing an AH domain, becomes essential. Additionally, we find that the Cdc12 AH domain is important for regulating septin filament bundling, suggesting septin AH domains have multiple, distinct functions and that bundling and membrane binding may be coordinately controlled.
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Affiliation(s)
- Benjamin L Woods
- Biology Department, University of North Carolina, Chapel Hill, NC 27599
| | - Kevin S Cannon
- Biology Department, University of North Carolina, Chapel Hill, NC 27599
| | - Ellysa J D Vogt
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599
| | - John M Crutchley
- Biology Department, University of North Carolina, Chapel Hill, NC 27599
| | - Amy S Gladfelter
- Biology Department, University of North Carolina, Chapel Hill, NC 27599.,Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599.,Marine Biological Laboratory, Woods Hole, MA 02543
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14
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Dact1 is expressed during chicken and mouse skeletal myogenesis and modulated in human muscle diseases. Comp Biochem Physiol B Biochem Mol Biol 2021; 256:110645. [PMID: 34252542 DOI: 10.1016/j.cbpb.2021.110645] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 06/02/2021] [Accepted: 07/06/2021] [Indexed: 12/23/2022]
Abstract
Vertebrate skeletal muscle development and repair relies on the precise control of Wnt signaling. Dact1 (Dapper/Frodo) is an important modulator of Wnt signaling, interacting with key components of the various Wnt transduction pathways. Here, we characterized Dact1 mRNA and protein expression in chicken and mouse fetal muscles in vivo and during the differentiation of chick primary and mouse C2C12 myoblasts in vitro. We also performed in silico analysis to investigate Dact1 gene expression in human myopathies, and evaluated the Dact1 protein structure to seek an explanation for the accumulation of Dact1 protein aggregates in the nuclei of myogenic cells. Our results show for the first time that in both chicken and mouse, Dact1 is expressed during myogenesis, with a strong upregulation as cells engage in terminal differentiation, cell cycle withdrawal and cell fusion. In humans, Dact1 expression was found to be altered in specific muscle pathologies, including muscular dystrophies. Our bioinformatic analyses of Dact1 proteins revealed long intrinsically disordered regions, which may underpin the ability of Dact1 to interact with its many partners in the various Wnt pathways. In addition, we found that Dact1 has strong propensity for liquid-liquid phase separation, a feature that explains its ability to form nuclear aggregates and points to a possible role as a molecular 'on'-'off' switch. Taken together, our data suggest Dact1 as a candidate, multi-faceted regulator of amniote myogenesis with a possible pathophysiological role in human muscular diseases.
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15
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Bepler T, Berger B. Learning the protein language: Evolution, structure, and function. Cell Syst 2021; 12:654-669.e3. [PMID: 34139171 PMCID: PMC8238390 DOI: 10.1016/j.cels.2021.05.017] [Citation(s) in RCA: 144] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 05/20/2021] [Accepted: 05/20/2021] [Indexed: 02/06/2023]
Abstract
Language models have recently emerged as a powerful machine-learning approach for distilling information from massive protein sequence databases. From readily available sequence data alone, these models discover evolutionary, structural, and functional organization across protein space. Using language models, we can encode amino-acid sequences into distributed vector representations that capture their structural and functional properties, as well as evaluate the evolutionary fitness of sequence variants. We discuss recent advances in protein language modeling and their applications to downstream protein property prediction problems. We then consider how these models can be enriched with prior biological knowledge and introduce an approach for encoding protein structural knowledge into the learned representations. The knowledge distilled by these models allows us to improve downstream function prediction through transfer learning. Deep protein language models are revolutionizing protein biology. They suggest new ways to approach protein and therapeutic design. However, further developments are needed to encode strong biological priors into protein language models and to increase their accessibility to the broader community.
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Affiliation(s)
- Tristan Bepler
- Simons Machine Learning Center, New York Structural Biology Center, New York, NY, USA; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA; Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Bonnie Berger
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA, USA.
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16
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Simm D, Hatje K, Waack S, Kollmar M. Critical assessment of coiled-coil predictions based on protein structure data. Sci Rep 2021; 11:12439. [PMID: 34127723 PMCID: PMC8203680 DOI: 10.1038/s41598-021-91886-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 05/28/2021] [Indexed: 02/05/2023] Open
Abstract
Coiled-coil regions were among the first protein motifs described structurally and theoretically. The simplicity of the motif promises that coiled-coil regions can be detected with reasonable accuracy and precision in any protein sequence. Here, we re-evaluated the most commonly used coiled-coil prediction tools with respect to the most comprehensive reference data set available, the entire Protein Data Bank, down to each amino acid and its secondary structure. Apart from the 30-fold difference in minimum and maximum number of coiled coils predicted the tools strongly vary in where they predict coiled-coil regions. Accordingly, there is a high number of false predictions and missed, true coiled-coil regions. The evaluation of the binary classification metrics in comparison with naïve coin-flip models and the calculation of the Matthews correlation coefficient, the most reliable performance metric for imbalanced data sets, suggests that the tested tools' performance is close to random. This implicates that the tools' predictions have only limited informative value. Coiled-coil predictions are often used to interpret biochemical data and are part of in-silico functional genome annotation. Our results indicate that these predictions should be treated very cautiously and need to be supported and validated by experimental evidence.
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Affiliation(s)
- Dominic Simm
- grid.418140.80000 0001 2104 4211Group Systems Biology of Motor Proteins, Department of NMR-Based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany ,grid.7450.60000 0001 2364 4210Theoretical Computer Science and Algorithmic Methods, Institute of Computer Science, Georg-August-University Göttingen, Göttingen, Germany
| | - Klas Hatje
- grid.418140.80000 0001 2104 4211Group Systems Biology of Motor Proteins, Department of NMR-Based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany ,grid.417570.00000 0004 0374 1269Present Address: Roche Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Stephan Waack
- grid.7450.60000 0001 2364 4210Theoretical Computer Science and Algorithmic Methods, Institute of Computer Science, Georg-August-University Göttingen, Göttingen, Germany
| | - Martin Kollmar
- grid.418140.80000 0001 2104 4211Group Systems Biology of Motor Proteins, Department of NMR-Based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany ,grid.7450.60000 0001 2364 4210Theoretical Computer Science and Algorithmic Methods, Institute of Computer Science, Georg-August-University Göttingen, Göttingen, Germany
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17
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Kumbhar R, Sanchez A, Perren J, Gong F, Corujo D, Medina F, Devanathan SK, Xhemalce B, Matouschek A, Buschbeck M, Buck-Koehntop BA, Miller KM. Poly(ADP-ribose) binding and macroH2A mediate recruitment and functions of KDM5A at DNA lesions. J Cell Biol 2021; 220:212163. [PMID: 34003252 PMCID: PMC8135068 DOI: 10.1083/jcb.202006149] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 03/15/2021] [Accepted: 04/12/2021] [Indexed: 12/13/2022] Open
Abstract
The histone demethylase KDM5A erases histone H3 lysine 4 methylation, which is involved in transcription and DNA damage responses (DDRs). While DDR functions of KDM5A have been identified, how KDM5A recognizes DNA lesion sites within chromatin is unknown. Here, we identify two factors that act upstream of KDM5A to promote its association with DNA damage sites. We have identified a noncanonical poly(ADP-ribose) (PAR)–binding region unique to KDM5A. Loss of the PAR-binding region or treatment with PAR polymerase (PARP) inhibitors (PARPi’s) blocks KDM5A–PAR interactions and DNA repair functions of KDM5A. The histone variant macroH2A1.2 is also specifically required for KDM5A recruitment and function at DNA damage sites, including homology-directed repair of DNA double-strand breaks and repression of transcription at DNA breaks. Overall, this work reveals the importance of PAR binding and macroH2A1.2 in KDM5A recognition of DNA lesion sites that drive transcriptional and repair activities at DNA breaks within chromatin that are essential for maintaining genome integrity.
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Affiliation(s)
- Ramhari Kumbhar
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX
| | - Anthony Sanchez
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX
| | - Jullian Perren
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX
| | - Fade Gong
- Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, TX
| | - David Corujo
- Cancer and Leukemia Epigenetics and Biology Program, Josep Carreras Leukaemia Cancer Institute, Barcelona, Spain
| | - Frank Medina
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX
| | - Sravan K Devanathan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX
| | - Blerta Xhemalce
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX.,Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX
| | - Andreas Matouschek
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX
| | - Marcus Buschbeck
- Cancer and Leukemia Epigenetics and Biology Program, Josep Carreras Leukaemia Cancer Institute, Barcelona, Spain.,Program for Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute, Badalona, Spain
| | | | - Kyle M Miller
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX.,Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX
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18
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Ma X, Chen T, Peng Z, Wang Z, Liu J, Yang T, Wu L, Liu G, Zhou M, Tong M, Guan Y, Zhang X, Lin Y, Tang X, Li L, Tang Z, Pan T, Zhang H. Histone chaperone CAF-1 promotes HIV-1 latency by leading the formation of phase-separated suppressive nuclear bodies. EMBO J 2021; 40:e106632. [PMID: 33739466 PMCID: PMC8126954 DOI: 10.15252/embj.2020106632] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 02/11/2021] [Accepted: 02/19/2021] [Indexed: 01/08/2023] Open
Abstract
HIV-1 latency is a major obstacle to achieving a functional cure for AIDS. Reactivation of HIV-1-infected cells followed by their elimination via immune surveillance is one proposed strategy for eradicating the viral reservoir. However, current latency-reversing agents (LRAs) show high toxicity and low efficiency, and new targets are needed to develop more promising LRAs. Here, we found that the histone chaperone CAF-1 (chromatin assembly factor 1) is enriched on the HIV-1 long terminal repeat (LTR) and forms nuclear bodies with liquid-liquid phase separation (LLPS) properties. CAF-1 recruits epigenetic modifiers and histone chaperones to the nuclear bodies to establish and maintain HIV-1 latency in different latency models and primary CD4+ T cells. Three disordered regions of the CHAF1A subunit are important for phase-separated CAF-1 nuclear body formation and play a key role in maintaining HIV-1 latency. Disruption of phase-separated CAF-1 bodies could be a potential strategy to reactivate latent HIV-1.
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Affiliation(s)
- Xiancai Ma
- Institute of Human VirologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
- Key Laboratory of Tropical Disease Control of Ministry of EducationZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Tao Chen
- Institute of Human VirologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
- Key Laboratory of Tropical Disease Control of Ministry of EducationZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Zhilin Peng
- Institute of Human VirologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
- Key Laboratory of Tropical Disease Control of Ministry of EducationZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Ziwen Wang
- Institute of Human VirologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
- Key Laboratory of Tropical Disease Control of Ministry of EducationZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Jun Liu
- Institute of Human VirologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
- Key Laboratory of Tropical Disease Control of Ministry of EducationZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Tao Yang
- Institute of Human VirologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
- Key Laboratory of Tropical Disease Control of Ministry of EducationZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Liyang Wu
- Institute of Human VirologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
- Key Laboratory of Tropical Disease Control of Ministry of EducationZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Guangyan Liu
- College of Basic Medical SciencesShenyang Medical CollegeShenyangLiaoningChina
| | - Mo Zhou
- Institute of Human VirologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
- Key Laboratory of Tropical Disease Control of Ministry of EducationZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Muye Tong
- Institute of Human VirologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
- Key Laboratory of Tropical Disease Control of Ministry of EducationZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Yuanjun Guan
- Core Laboratory Platform for Medical ScienceZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Xu Zhang
- Institute of Human VirologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
- Key Laboratory of Tropical Disease Control of Ministry of EducationZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Yingtong Lin
- Institute of Human VirologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
- Key Laboratory of Tropical Disease Control of Ministry of EducationZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Xiaoping Tang
- Department of Infectious DiseasesGuangzhou 8th People’s HospitalGuangzhouGuangdongChina
| | - Linghua Li
- Department of Infectious DiseasesGuangzhou 8th People’s HospitalGuangzhouGuangdongChina
| | - Zhonghui Tang
- Department of BioinformaticsZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Ting Pan
- Institute of Human VirologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
- Center for Infection and Immunity StudySchool of MedicineSun Yat‐sen UniversityShenzhenGuangdongChina
| | - Hui Zhang
- Institute of Human VirologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
- Key Laboratory of Tropical Disease Control of Ministry of EducationZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
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19
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Cappele J, Mohamad Ali A, Leblond-Bourget N, Mathiot S, Dhalleine T, Payot S, Savko M, Didierjean C, Favier F, Douzi B. Structural and Biochemical Analysis of OrfG: The VirB8-like Component of the Conjugative Type IV Secretion System of ICE St3 From Streptococcus thermophilus. Front Mol Biosci 2021; 8:642606. [PMID: 33816557 PMCID: PMC8012802 DOI: 10.3389/fmolb.2021.642606] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 02/01/2021] [Indexed: 12/02/2022] Open
Abstract
Conjugative transfer is a major threat to global health since it contributes to the spread of antibiotic resistance genes and virulence factors among commensal and pathogenic bacteria. To allow their transfer, mobile genetic elements including Integrative and Conjugative Elements (ICEs) use a specialized conjugative apparatus related to Type IV secretion systems (Conj-T4SS). Therefore, Conj-T4SSs are excellent targets for strategies that aim to limit the spread of antibiotic resistance. In this study, we combined structural, biochemical and biophysical approaches to study OrfG, a protein that belongs to Conj-T4SS of ICESt3 from Streptococcus thermophilus. Structural analysis of OrfG by X-ray crystallography revealed that OrfG central domain is similar to VirB8-like proteins but displays a different quaternary structure in the crystal. To understand, at a structural level, the common and the diverse features between VirB8-like proteins from both Gram-negative and -positive bacteria, we used an in silico structural alignment method that allowed us to identify different structural classes of VirB8-like proteins. Biochemical and biophysical characterizations of purified OrfG soluble domain and its central and C-terminal subdomains indicated that they are mainly monomeric in solution but able to form an unprecedented 6-mer oligomers. Our study provides new insights into the structural analysis of VirB8-like proteins and discusses the interplay between tertiary and quaternary structures of these proteins as an essential component of the conjugative transfer.
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Affiliation(s)
| | | | | | | | | | - Sophie Payot
- Université de Lorraine, INRAE, DynAMic, Nancy, France
| | - Martin Savko
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint Aubin BP 48, Gif-sur-Yvette, France
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20
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Kefala A, Amprazi M, Mylonas E, Kotsifaki D, Providaki M, Pozidis C, Fotiadou M, Kokkinidis M. Probing Protein Folding with Sequence-Reversed α-Helical Bundles. Int J Mol Sci 2021; 22:ijms22041955. [PMID: 33669383 PMCID: PMC7920257 DOI: 10.3390/ijms22041955] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/11/2021] [Accepted: 02/11/2021] [Indexed: 12/22/2022] Open
Abstract
Recurrent protein folding motifs include various types of helical bundles formed by α-helices that supercoil around each other. While specific patterns of amino acid residues (heptad repeats) characterize the highly versatile folding motif of four-α-helical bundles, the significance of the polypeptide chain directionality is not sufficiently understood, although it determines sequence patterns, helical dipoles, and other parameters for the folding and oligomerization processes of bundles. To investigate directionality aspects in sequence-structure relationships, we reversed the amino acid sequences of two well-characterized, highly regular four-α-helical bundle proteins and studied the folding, oligomerization, and structural properties of the retro-proteins, using Circular Dichroism Spectroscopy (CD), Size Exclusion Chromatography combined with Multi-Angle Laser Light Scattering (SEC-MALS), and Small Angle X-ray Scattering (SAXS). The comparison of the parent proteins with their retro-counterparts reveals that while the α-helical character of the parents is affected to varying degrees by sequence reversal, the folding states, oligomerization propensities, structural stabilities, and shapes of the new molecules strongly depend on the characteristics of the heptad repeat patterns. The highest similarities between parent and retro-proteins are associated with the presence of uninterrupted heptad patterns in helical bundles sequences.
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Affiliation(s)
- Aikaterini Kefala
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology–Hellas (IMBB-FORTH), 70013 Heraklion, Greece; (A.K.); (M.A.); (E.M.); (D.K.); (M.P.); (C.P.)
- Department of Biology, University of Crete, 70013 Heraklion, Greece;
| | - Maria Amprazi
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology–Hellas (IMBB-FORTH), 70013 Heraklion, Greece; (A.K.); (M.A.); (E.M.); (D.K.); (M.P.); (C.P.)
- Department of Biology, University of Crete, 70013 Heraklion, Greece;
| | - Efstratios Mylonas
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology–Hellas (IMBB-FORTH), 70013 Heraklion, Greece; (A.K.); (M.A.); (E.M.); (D.K.); (M.P.); (C.P.)
| | - Dina Kotsifaki
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology–Hellas (IMBB-FORTH), 70013 Heraklion, Greece; (A.K.); (M.A.); (E.M.); (D.K.); (M.P.); (C.P.)
| | - Mary Providaki
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology–Hellas (IMBB-FORTH), 70013 Heraklion, Greece; (A.K.); (M.A.); (E.M.); (D.K.); (M.P.); (C.P.)
| | - Charalambos Pozidis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology–Hellas (IMBB-FORTH), 70013 Heraklion, Greece; (A.K.); (M.A.); (E.M.); (D.K.); (M.P.); (C.P.)
| | - Melina Fotiadou
- Department of Biology, University of Crete, 70013 Heraklion, Greece;
| | - Michael Kokkinidis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology–Hellas (IMBB-FORTH), 70013 Heraklion, Greece; (A.K.); (M.A.); (E.M.); (D.K.); (M.P.); (C.P.)
- Department of Biology, University of Crete, 70013 Heraklion, Greece;
- Correspondence: ; Tel.: +30-2810-394350
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21
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Popelka H, Reinhart EF, Metur SP, Leary KA, Ragusa MJ, Klionsky DJ. Membrane Binding and Homodimerization of Atg16 Via Two Distinct Protein Regions is Essential for Autophagy in Yeast. J Mol Biol 2021; 433:166809. [PMID: 33484718 DOI: 10.1016/j.jmb.2021.166809] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/27/2020] [Accepted: 01/03/2021] [Indexed: 12/29/2022]
Abstract
Macroautophagy is a bulk degradation mechanism in eukaryotic cells. Efficiency of an essential step of this process in yeast, Atg8 lipidation, relies on the presence of Atg16, a subunit of the Atg12-Atg5-Atg16 complex acting as the E3-like enzyme in the ubiquitination-like reaction. A current view on the functional structure of Atg16 in the yeast S. cerevisiae comes from the two crystal structures that reveal the Atg5-interacting α-helix linked via a flexible linker to another α-helix of Atg16, which then assembles into a homodimer. This view does not explain the results of previous in vitro studies revealing Atg16-dependent deformations of membranes and liposome-binding of the Atg12-Atg5 conjugate upon addition of Atg16. Here we show that Atg16 acts as both a homodimerizing and peripheral membrane-binding polypeptide. These two characteristics are imposed by the two distinct regions that are disordered in the nascent protein. Atg16 binds to membranes in vivo via the amphipathic α-helix (amino acid residues 113-131) that has a coiled-coil-like propensity and a strong hydrophobic face for insertion into the membrane. The other protein region (residues 64-99) possesses a coiled-coil propensity, but not amphipathicity, and is dispensable for membrane anchoring of Atg16. This region acts as a Leu-zipper essential for formation of the Atg16 homodimer. Mutagenic disruption in either of these two distinct domains renders Atg16 proteins that, in contrast to wild type, completely fail to rescue the autophagy-defective phenotype of atg16Δ cells. Together, the results of this study yield a model for the molecular mechanism of Atg16 function in macroautophagy.
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Affiliation(s)
- Hana Popelka
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, United States.
| | - Erin F Reinhart
- Department of Chemistry, Dartmouth College, Hanover, NH 03755, United States
| | - Shree Padma Metur
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, United States; Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, United States
| | - Kelsie A Leary
- Department of Chemistry, Dartmouth College, Hanover, NH 03755, United States
| | - Michael J Ragusa
- Department of Chemistry, Dartmouth College, Hanover, NH 03755, United States
| | - Daniel J Klionsky
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, United States; Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, United States
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22
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Lewicka E, Mitura M, Steczkiewicz K, Kieracinska J, Skrzynska K, Adamczyk M, Jagura-Burdzy G. Unique Properties of the Alpha-Helical DNA-Binding Protein KfrA Encoded by the IncU Incompatibility Group Plasmid RA3 and Its Host-Dependent Role in Plasmid Maintenance. Appl Environ Microbiol 2021; 87:e01771-20. [PMID: 33097508 PMCID: PMC7783346 DOI: 10.1128/aem.01771-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 10/18/2020] [Indexed: 01/15/2023] Open
Abstract
KfrA, encoded on the broad-host-range RA3 plasmid, is an alpha-helical DNA-binding protein that acts as a transcriptional autoregulator. The KfrARA3 operator site overlaps the kfrA promoter and is composed of five 9-bp direct repeats (DRs). Here, the biological properties of KfrA were studied using both in vivo and in vitro approaches. Localization of the DNA-binding helix-turn-helix motif (HTH) was mapped to the N29-R52 region by protein structure modeling and confirmed by alanine scanning. KfrA repressor ability depended on the number and orientation of DRs in the operator, as well as the ability of the protein to oligomerize. The long alpha-helical tail from residues 54 to 355 was shown to be involved in self-interactions, whereas the region from residue 54 to 177 was involved in heterodimerization with KfrC, another RA3-encoded alpha-helical protein. KfrA also interacted with the segrosome proteins IncC (ParA) and KorB (ParB), representatives of the class Ia active partition systems. Deletion of the kfr genes from the RA3 stability module decreased the plasmid retention in diverse hosts in a species-dependent manner. The specific interactions of KfrA with DNA are essential not only for the transcriptional regulatory function but also for the accessory role of KfrA in stable plasmid maintenance.IMPORTANCE Alpha-helical coiled-coil KfrA-type proteins are encoded by various broad-host-range low-copy-number conjugative plasmids. The DNA-binding protein KfrA encoded on the RA3 plasmid, a member of the IncU incompatibility group, oligomerizes, forms a complex with another plasmid-encoded, alpha-helical protein, KfrC, and interacts with the segrosome proteins IncC and KorB. The unique mode of KfrA dimer binding to the repetitive operator is required for a KfrA role in the stable maintenance of RA3 plasmid in distinct hosts.
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Affiliation(s)
- Ewa Lewicka
- Institute of Biochemistry and Biophysics, Department of Microbial Biochemistry, PAS, Warsaw, Poland
| | - Monika Mitura
- Institute of Biochemistry and Biophysics, Department of Microbial Biochemistry, PAS, Warsaw, Poland
| | - Kamil Steczkiewicz
- Institute of Biochemistry and Biophysics, Department of Bioinformatics, PAS, Warsaw, Poland
| | - Justyna Kieracinska
- Institute of Biochemistry and Biophysics, Department of Microbial Biochemistry, PAS, Warsaw, Poland
- Warsaw University of Technology, Faculty of Chemistry, Chair of Drug and Cosmetics Biotechnology, Warsaw, Poland
| | - Kamila Skrzynska
- Warsaw University of Technology, Faculty of Chemistry, Chair of Drug and Cosmetics Biotechnology, Warsaw, Poland
| | - Malgorzata Adamczyk
- Warsaw University of Technology, Faculty of Chemistry, Chair of Drug and Cosmetics Biotechnology, Warsaw, Poland
| | - Grazyna Jagura-Burdzy
- Institute of Biochemistry and Biophysics, Department of Microbial Biochemistry, PAS, Warsaw, Poland
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23
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Hellmund KS, Lospichl B, Böttcher C, Ludwig K, Keiderling U, Noirez L, Weiß A, Mikolajczak DJ, Gradzielski M, Koksch B. Functionalized peptide hydrogels as tunable extracellular matrix mimics for biological applications. Pept Sci (Hoboken) 2020. [DOI: 10.1002/pep2.24201] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Katharina S. Hellmund
- Department of Biology, Chemistry, Pharmacy Institute of Chemistry and Biochemistry–Organic Chemistry, Freie Universität Berlin Berlin Germany
| | - Benjamin Lospichl
- Stranski‐Laboratory of Physical and Theoretical Chemistry Institute of Chemistry, Technische Universität Berlin Berlin Germany
| | - Christoph Böttcher
- Center of Electron Microscopy at Freie Universität Berlin Institute of Chemistry and Biochemistry and CoreFacility BioSupraMol Freie Universität Berlin Berlin Germany
| | - Kai Ludwig
- Center of Electron Microscopy at Freie Universität Berlin Institute of Chemistry and Biochemistry and CoreFacility BioSupraMol Freie Universität Berlin Berlin Germany
| | - Uwe Keiderling
- Department Experiment Control and Data Acquisition Helmholtz‐Zentrum Berlin für Materialien und Energie Berlin Germany
| | - Laurence Noirez
- Laboratoire Léon Brillouin (CEA‐CNRS) Université Paris‐Saclay Gif‐sur‐Yvette Cédex France
| | - Annika Weiß
- Department of Biology, Chemistry, Pharmacy Institute of Chemistry and Biochemistry–Organic Chemistry, Freie Universität Berlin Berlin Germany
| | - Dorian J. Mikolajczak
- Department of Biology, Chemistry, Pharmacy Institute of Chemistry and Biochemistry–Organic Chemistry, Freie Universität Berlin Berlin Germany
| | - Michael Gradzielski
- Stranski‐Laboratory of Physical and Theoretical Chemistry Institute of Chemistry, Technische Universität Berlin Berlin Germany
| | - Beate Koksch
- Department of Biology, Chemistry, Pharmacy Institute of Chemistry and Biochemistry–Organic Chemistry, Freie Universität Berlin Berlin Germany
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24
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Shakya AK, Pratap JV. The coiled-coil domain of glycosomal membrane-associated Leishmania donovani PEX14: cloning, overexpression, purification and preliminary crystallographic analysis. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2020; 76:464-468. [PMID: 33006573 DOI: 10.1107/s2053230x20011127] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 08/12/2020] [Indexed: 12/29/2022]
Abstract
The glycosomal membrane-associated Leishmania donovani protein PEX14, which plays a crucial role in protein import from the cytosol to the glycosomal matrix, consists of three domains: an N-terminal domain where the signalling molecule binds, a transmembrane domain and an 84-residue coiled-coil domain (CC) that is responsible for oligomerization. CCs are versatile domains that participate in a variety of functions including supramolecular assembly, cellular signalling and transport. Recombinant PEX14 CC was cloned, overexpressed, affinity-purified with in-column thrombin cleavage and further purified by size-exclusion chromatography. Crystals that diffracted to 1.98 Å resolution were obtained from a condition consisting of 1.4 M sodium citrate tribasic dihydrate, 0.1 M HEPES buffer pH 7.5. The crystals belonged to the monoclinic space group C2, with unit-cell parameters a = 143.98, b = 32.62, c = 95.62 Å, β = 94.68°. Structure determination and characterization are in progress.
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Affiliation(s)
- Anil Kumar Shakya
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, BS-10/1, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, Uttar Pradesh 226031, India
| | - J Venkatesh Pratap
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, BS-10/1, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, Uttar Pradesh 226031, India
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25
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Spitzenkörper assembly mechanisms reveal conserved features of fungal and metazoan polarity scaffolds. Nat Commun 2020; 11:2830. [PMID: 32503980 PMCID: PMC7275032 DOI: 10.1038/s41467-020-16712-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 05/14/2020] [Indexed: 02/08/2023] Open
Abstract
The Spitzenkörper (SPK) constitutes a collection of secretory vesicles and polarity-related proteins intimately associated with polarized growth of fungal hyphae. Many SPK-localized proteins are known, but their assembly and dynamics remain poorly understood. Here, we identify protein-protein interaction cascades leading to assembly of two SPK scaffolds and recruitment of diverse effectors in Neurospora crassa. Both scaffolds are transported to the SPK by the myosin V motor (MYO-5), with the coiled-coil protein SPZ-1 acting as cargo adaptor. Neither scaffold appears to be required for accumulation of SPK secretory vesicles. One scaffold consists of Leashin-2 (LAH-2), which is required for SPK localization of the signalling kinase COT-1 and the glycolysis enzyme GPI-1. The other scaffold comprises a complex of Janus-1 (JNS-1) and the polarisome protein SPA-2. Via its Spa homology domain (SHD), SPA-2 recruits a calponin domain-containing F-actin effector (CCP-1). The SHD NMR structure reveals a conserved surface groove required for effector binding. Similarities between SPA-2/JNS-1 and the metazoan GIT/PIX complex identify foundational features of the cell polarity apparatus that predate the fungal-metazoan divergence. The Spitzenkörper (SPK) is a polarized accumulation of proteins and secretory vesicles associated with tip growth of fungal hyphae. Here, Zheng et al. study SPK assembly and dynamics, identify SPK protein scaffolds and associated proteins, and reveal similarities with other scaffolds from metazoans.
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26
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Milner DS, Ray LJ, Saxon EB, Lambert C, Till R, Fenton AK, Sockett RE. DivIVA Controls Progeny Morphology and Diverse ParA Proteins Regulate Cell Division or Gliding Motility in Bdellovibrio bacteriovorus. Front Microbiol 2020; 11:542. [PMID: 32373080 PMCID: PMC7186360 DOI: 10.3389/fmicb.2020.00542] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 03/12/2020] [Indexed: 01/12/2023] Open
Abstract
The predatory bacterium B. bacteriovorus grows and divides inside the periplasm of Gram-negative bacteria, forming a structure known as a bdelloplast. Cell division of predators inside the dead prey cell is not by binary fission but instead by synchronous division of a single elongated filamentous cell into odd or even numbers of progeny cells. Bdellovibrio replication and cell division processes are dependent on the finite level of nutrients available from inside the prey bacterium. The filamentous growth and division process of the predator maximizes the number of progeny produced by the finite nutrients in a way that binary fission could not. To learn more about such an unusual growth profile, we studied the role of DivIVA in the growing Bdellovibrio cell. This protein is well known for its link to polar cell growth and spore formation in Gram-positive bacteria, but little is known about its function in a predatory growth context. We show that DivIVA is expressed in the growing B. bacteriovorus cell and controls cell morphology during filamentous cell division, but not the number of progeny produced. Bacterial Two Hybrid (BTH) analysis shows DivIVA may interact with proteins that respond to metabolic indicators of amino-acid biosynthesis or changes in redox state. Such changes may be relevant signals to the predator, indicating the consumption of prey nutrients within the sealed bdelloplast environment. ParA, a chromosome segregation protein, also contributes to bacterial septation in many species. The B. bacteriovorus genome contains three ParA homologs; we identify a canonical ParAB pair required for predatory cell division and show a BTH interaction between a gene product encoded from the same operon as DivIVA with the canonical ParA. The remaining ParA proteins are both expressed in Bdellovibrio but are not required for predator cell division. Instead, one of these ParA proteins coordinates gliding motility, changing the frequency at which the cells reverse direction. Our work will prime further studies into how one bacterium can co-ordinate its cell division with the destruction of another bacterium that it dwells within.
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Affiliation(s)
- David S Milner
- Laboratory C15, Division of Infections, Immunity and Microbes, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Luke J Ray
- Laboratory C15, Division of Infections, Immunity and Microbes, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Emma B Saxon
- Laboratory C15, Division of Infections, Immunity and Microbes, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Carey Lambert
- Laboratory C15, Division of Infections, Immunity and Microbes, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Rob Till
- Laboratory C15, Division of Infections, Immunity and Microbes, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Andrew K Fenton
- Laboratory C15, Division of Infections, Immunity and Microbes, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Renee Elizabeth Sockett
- Laboratory C15, Division of Infections, Immunity and Microbes, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
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27
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Fiedler T, Fabrice TN, Studer V, Vinet A, Faltova L, Kammerer RA, Steinmetz MO, Sharpe T, Pieters J. Homodimerization of coronin A through the C-terminal coiled-coil domain is essential for multicellular differentiation of Dictyostelium discoideum. FEBS Lett 2020; 594:2116-2127. [PMID: 32298460 DOI: 10.1002/1873-3468.13787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 03/25/2020] [Accepted: 03/26/2020] [Indexed: 11/09/2022]
Abstract
Coronin proteins are widely expressed among eukaryotic organisms. Most coronins consist of a WD-repeat domain followed by a C-terminal coiled coil. Dictyostelium discoideum expresses a single short coronin coronin A, which has been implicated in both actin modulation and multicellular differentiation. Whether coronin A's coiled coil is important for functionality, as well as the oligomeric state of coronin A is not known. Here, we show that the coiled-coil domain in Dictyostelium coronin A functions in homodimerization, is dispensable for coronin A stability and localization but essential for multicellular differentiation. These results allow a better understanding of the role for the coiled-coil domain of coronin A in oligomerization and demonstrate that its presence is essential for multicellular differentiation.
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Affiliation(s)
| | | | - Vera Studer
- Biozentrum, University of Basel, Switzerland
| | | | - Lenka Faltova
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen, Switzerland
| | - Richard A Kammerer
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen, Switzerland
| | - Michel O Steinmetz
- Biozentrum, University of Basel, Switzerland
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen, Switzerland
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28
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Intrinsically disordered proteins of viruses: Involvement in the mechanism of cell regulation and pathogenesis. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 174:1-78. [PMID: 32828463 PMCID: PMC7129803 DOI: 10.1016/bs.pmbts.2020.03.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Intrinsically disordered proteins (IDPs) possess the property of inherent flexibility and can be distinguished from other proteins in terms of lack of any fixed structure. Such dynamic behavior of IDPs earned the name "Dancing Proteins." The exploration of these dancing proteins in viruses has just started and crucial details such as correlation of rapid evolution, high rate of mutation and accumulation of disordered contents in viral proteome at least understood partially. In order to gain a complete understanding of this correlation, there is a need to decipher the complexity of viral mediated cell hijacking and pathogenesis in the host organism. Further there is necessity to identify the specific patterns within viral and host IDPs such as aggregation; Molecular recognition features (MoRFs) and their association to virulence, host range and rate of evolution of viruses in order to tackle the viral-mediated diseases. The current book chapter summarizes the aforementioned details and suggests the novel opportunities for further research of IDPs senses in viruses.
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29
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Rachev E, Schuster-Gossler K, Fuhl F, Ott T, Tveriakhina L, Beckers A, Hegermann J, Boldt K, Mai M, Kremmer E, Ueffing M, Blum M, Gossler A. CFAP43 modulates ciliary beating in mouse and Xenopus. Dev Biol 2020; 459:109-125. [DOI: 10.1016/j.ydbio.2019.12.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 12/14/2019] [Accepted: 12/18/2019] [Indexed: 11/26/2022]
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30
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Cuvertino S, Hartill V, Colyer A, Garner T, Nair N, Al-Gazali L, Canham N, Faundes V, Flinter F, Hertecant J, Holder-Espinasse M, Jackson B, Lynch SA, Nadat F, Narasimhan VM, Peckham M, Sellers R, Seri M, Montanari F, Southgate L, Squeo GM, Trembath R, van Heel D, Venuto S, Weisberg D, Stals K, Ellard S, Barton A, Kimber SJ, Sheridan E, Merla G, Stevens A, Johnson CA, Banka S. A restricted spectrum of missense KMT2D variants cause a multiple malformations disorder distinct from Kabuki syndrome. Genet Med 2020; 22:867-877. [PMID: 31949313 PMCID: PMC7200597 DOI: 10.1038/s41436-019-0743-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 12/24/2019] [Indexed: 12/19/2022] Open
Abstract
Purpose To investigate if specific exon 38 or 39 KMT2D missense variants (MVs) cause a condition distinct from
Kabuki syndrome type 1 (KS1). Methods Multiple individuals, with MVs in exons 38 or 39 of KMT2D that encode a highly conserved region of 54
amino acids flanked by Val3527 and Lys3583, were identified and phenotyped.
Functional tests were performed to study their pathogenicity and understand the
disease mechanism. Results The consistent clinical features of the affected individuals, from
seven unrelated families, included choanal atresia, athelia or hypoplastic
nipples, branchial sinus abnormalities, neck pits, lacrimal duct anomalies,
hearing loss, external ear malformations, and thyroid abnormalities. None of the
individuals had intellectual disability. The frequency of clinical features,
objective software-based facial analysis metrics, and genome-wide peripheral
blood DNA methylation patterns in these patients were significantly different
from that of KS1. Circular dichroism spectroscopy indicated that these MVs
perturb KMT2D secondary structure through an increased disordered to ɑ-helical
transition. Conclusion KMT2D MVs located in a specific
region spanning exons 38 and 39 and affecting highly conserved residues cause a
novel multiple malformations syndrome distinct from KS1. Unlike KMT2D haploinsufficiency in KS1, these MVs likely
result in disease through a dominant negative mechanism.
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Affiliation(s)
- Sara Cuvertino
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, UK.,Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, UK
| | - Verity Hartill
- Leeds Institute of Medical Research, Faculty of Medicine and Health, The University of Leeds, Leeds, UK.,Department of Clinical Genetics, Chapel Allerton Hospital, Leeds Teaching Hospitals Trust, Leeds, UK
| | - Alice Colyer
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, The University of Leeds, Leeds, UK
| | - Terence Garner
- Division of Developmental Biology & Medicine, School of Biological Sciences, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, UK
| | - Nisha Nair
- Centre of Genetics & Genomics Versus Arthritis, Manchester Academic Health Sciences Centre, The University of Manchester, Manchester, UK
| | - Lihadh Al-Gazali
- Department of Paediatrics, College of Medicine & Health Sciences, United Arab University, Al-Ain, UAE
| | - Natalie Canham
- Liverpool Centre for Genomic Medicine, Liverpool Women's NHS Foundation Trust, Liverpool, UK.,North West Thames Regional Genetics Service, Northwick Park Hospital, Harrow, UK
| | - Victor Faundes
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, UK.,Laboratorio de Genética y Enfermedades Metabólicas, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile
| | - Frances Flinter
- Department of Clinical Genetics, Guy's & St Thomas NHS Foundation Trust, London, UK
| | | | | | - Brian Jackson
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, The University of Leeds, Leeds, UK
| | - Sally Ann Lynch
- Temple street Children's University Hospital, Dublin, Ireland
| | - Fatima Nadat
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, The University of Leeds, Leeds, UK
| | | | - Michelle Peckham
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, The University of Leeds, Leeds, UK
| | - Robert Sellers
- Division of Developmental Biology & Medicine, School of Biological Sciences, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, UK
| | - Marco Seri
- Medical Genetics Unit, St. Orsola-Malpighi, University of Bologna, Bologna, Italy
| | - Francesca Montanari
- Medical Genetics Unit, St. Orsola-Malpighi, University of Bologna, Bologna, Italy
| | - Laura Southgate
- Molecular and Clinical Sciences Research Institute, St George's University of London, London, UK.,Department of Medical & Molecular Genetics, King's College London, London, UK
| | - Gabriella Maria Squeo
- Division of Medical Genetics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Foggia, Italy
| | - Richard Trembath
- Department of Medical & Molecular Genetics, King's College London, London, UK
| | | | - Santina Venuto
- Division of Medical Genetics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Foggia, Italy
| | - Daniel Weisberg
- Clinical Psychology Department, Royal Manchester Children's Hospital, Manchester University Foundation NHS Trust, Health Innovation Manchester, Manchester, UK
| | - Karen Stals
- Molecular Genetics Department, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Sian Ellard
- Molecular Genetics Department, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK.,Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | | | - Anne Barton
- Centre of Genetics & Genomics Versus Arthritis, Manchester Academic Health Sciences Centre, The University of Manchester, Manchester, UK
| | - Susan J Kimber
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, UK
| | - Eamonn Sheridan
- Leeds Institute of Medical Research, Faculty of Medicine and Health, The University of Leeds, Leeds, UK.,Department of Clinical Genetics, Chapel Allerton Hospital, Leeds Teaching Hospitals Trust, Leeds, UK
| | - Giuseppe Merla
- Division of Medical Genetics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Foggia, Italy
| | - Adam Stevens
- Division of Developmental Biology & Medicine, School of Biological Sciences, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, UK
| | - Colin A Johnson
- Leeds Institute of Medical Research, Faculty of Medicine and Health, The University of Leeds, Leeds, UK
| | - Siddharth Banka
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, UK. .,Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University Foundation NHS Trust, Health Innovation Manchester, Manchester, UK.
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31
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Liu H, Cao M, Wang Y, Lv B, Li C. Bioengineering oligomerization and monomerization of enzymes: learning from natural evolution to matching the demands for industrial applications. Crit Rev Biotechnol 2020; 40:231-246. [PMID: 31914816 DOI: 10.1080/07388551.2019.1711014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
It is generally accepted that oligomeric enzymes evolve from their monomeric ancestors, and the evolution process generates superior structural benefits for functional advantages. Furthermore, adjusting the transition between different oligomeric states is an important mechanism for natural enzymes to regulate their catalytic functions for adapting environmental fluctuations in nature, which inspires researchers to mimic such a strategy to develop artificially oligomerized enzymes through protein engineering for improved performance under specific conditions. On the other hand, transforming oligomeric enzymes into their monomers is needed in fundamental research for deciphering catalytic mechanisms as well as exploring their catalytic capacities for better industrial applications. In this article, strategies for developing artificially oligomerized and monomerized enzymes are reviewed and highlighted by their applications. Furthermore, advances in the computational prediction of oligomeric structures are introduced, which would accelerate the systematic design of oligomeric and monomeric enzymes. Finally, the current challenges and future directions in this field are discussed.
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Affiliation(s)
- Hu Liu
- Institute for Synthetic Biosystem, Department of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Mingming Cao
- Institute for Synthetic Biosystem, Department of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Ying Wang
- Institute for Synthetic Biosystem, Department of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Bo Lv
- Institute for Synthetic Biosystem, Department of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Chun Li
- Institute for Synthetic Biosystem, Department of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
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32
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Conti D, Gul P, Islam A, Martín-Durán JM, Pickersgill RW, Draviam VM. Kinetochores attached to microtubule-ends are stabilised by Astrin bound PP1 to ensure proper chromosome segregation. eLife 2019; 8:49325. [PMID: 31808746 PMCID: PMC6930079 DOI: 10.7554/elife.49325] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 12/01/2019] [Indexed: 12/12/2022] Open
Abstract
Microtubules segregate chromosomes by attaching to macromolecular kinetochores. Only microtubule-end attached kinetochores can be pulled apart; how these end-on attachments are selectively recognised and stabilised is not known. Using the kinetochore and microtubule-associated protein, Astrin, as a molecular probe, we show that end-on attachments are rapidly stabilised by spatially-restricted delivery of PP1 near the C-terminus of Ndc80, a core kinetochore-microtubule linker. PP1 is delivered by the evolutionarily conserved tail of Astrin and this promotes Astrin’s own enrichment creating a highly-responsive positive feedback, independent of biorientation. Abrogating Astrin:PP1-delivery disrupts attachment stability, which is not rescued by inhibiting Aurora-B, an attachment destabiliser, but is reversed by artificially tethering PP1 near the C-terminus of Ndc80. Constitutive Astrin:PP1-delivery disrupts chromosome congression and segregation, revealing a dynamic mechanism for stabilising attachments. Thus, Astrin-PP1 mediates a dynamic ‘lock’ that selectively and rapidly stabilises end-on attachments, independent of biorientation, and ensures proper chromosome segregation.
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Affiliation(s)
- Duccio Conti
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom.,Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Parveen Gul
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Asifa Islam
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - José M Martín-Durán
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Richard W Pickersgill
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Viji M Draviam
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom.,Department of Genetics, University of Cambridge, Cambridge, United Kingdom
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33
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Choukate K, Gupta A, Basu B, Virk K, Ganguli M, Chaudhuri B. Higher order assembling of the mycobacterial polar growth factor DivIVA/Wag31. J Struct Biol 2019; 209:107429. [PMID: 31778770 DOI: 10.1016/j.jsb.2019.107429] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 10/04/2019] [Accepted: 11/21/2019] [Indexed: 12/26/2022]
Abstract
DivIVA or Wag31, which is an essential pole organizing protein in mycobacteria, can self-assemble at the negatively curved side of the membrane at the growing pole to form a higher order structural scaffold for maintaining cellular morphology and localizing various target proteins for cell-wall biogenesis. The structural organization of polar scaffold formed by polymerization of coiled-coil rich Wag31, which is implicated in the anti-tubercular activities of amino-pyrimidine sulfonamides, remains to be determined. A single-site phosphorylation in Wag31 regulates peptidoglycan biosynthesis in mycobacteria. We report biophysical characterizations of filaments formed by mycobacterial Wag31 using circular dichroism, atomic force microscopy and small angle solution X-ray scattering. Atomic force microscopic images of the wild-type, a phospho-mimetic (T73E) and a phospho-ablative (T73A) form of Wag31 show mostly linear filament formation with occasional curving, kinking and apparent branching. Solution X-ray scattering data indicates that the phospho-mimetic forms of the Wag31 polymers are on average more compact than their phospho-ablative counterparts, which is likely due to the extent of bending/branching. Observed structural features in this first view of Wag31 filaments suggest a basis for higher order Wag31 scaffold formation at the pole.
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Affiliation(s)
- Komal Choukate
- CSIR Institute of Microbial Technology, Chandigarh, India
| | - Aanchal Gupta
- CSIR Institute of Genomics and Integrative Biology, New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi 110001, India
| | - Brohmomoy Basu
- CSIR Institute of Microbial Technology, Chandigarh, India
| | - Karman Virk
- CSIR Institute of Microbial Technology, Chandigarh, India
| | - Munia Ganguli
- CSIR Institute of Genomics and Integrative Biology, New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi 110001, India
| | - Barnali Chaudhuri
- CSIR Institute of Microbial Technology, Chandigarh, India; Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi 110001, India.
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34
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Wolf D, Hofbrucker-MacKenzie SA, Izadi M, Seemann E, Steiniger F, Schwintzer L, Koch D, Kessels MM, Qualmann B. Ankyrin repeat-containing N-Ank proteins shape cellular membranes. Nat Cell Biol 2019; 21:1191-1205. [PMID: 31548610 DOI: 10.1038/s41556-019-0381-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 07/25/2019] [Indexed: 01/02/2023]
Abstract
Cells of multicellular organisms need to adopt specific morphologies. However, the molecular mechanisms bringing about membrane topology changes are far from understood-mainly because knowledge of membrane-shaping proteins that can promote local membrane curvatures is still limited. Our analyses unveiled that several members of a large, previously unrecognised protein family, which we termed N-Ank proteins, use a combination of their ankyrin repeat array and an amino (N)-terminal amphipathic helix to bind and shape membranes. Consistently, functional analyses revealed that the N-Ank protein ankycorbin (NORPEG/RAI14), which was exemplarily characterised further, plays an important, ankyrin repeat-based and N-terminal amphipathic helix-dependent role in early morphogenesis of neurons. This function furthermore required coiled coil-mediated self-assembly and manifested as ankycorbin nanodomains marked by protrusive membrane topologies. In summary, here, we unveil a class of powerful membrane shapers and thereby assign mechanistic and cell biological functions to the N-Ank protein superfamily.
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Affiliation(s)
- David Wolf
- Institute of Biochemistry I, Jena University Hospital, Friedrich Schiller University Jena, Jena, Germany
| | | | - Maryam Izadi
- Institute of Biochemistry I, Jena University Hospital, Friedrich Schiller University Jena, Jena, Germany
| | - Eric Seemann
- Institute of Biochemistry I, Jena University Hospital, Friedrich Schiller University Jena, Jena, Germany
| | - Frank Steiniger
- Electron Microscopy Centre, Jena University Hospital, Friedrich Schiller University Jena, Jena, Germany
| | - Lukas Schwintzer
- Institute of Biochemistry I, Jena University Hospital, Friedrich Schiller University Jena, Jena, Germany
| | - Dennis Koch
- Institute of Biochemistry I, Jena University Hospital, Friedrich Schiller University Jena, Jena, Germany
| | - Michael Manfred Kessels
- Institute of Biochemistry I, Jena University Hospital, Friedrich Schiller University Jena, Jena, Germany.
| | - Britta Qualmann
- Institute of Biochemistry I, Jena University Hospital, Friedrich Schiller University Jena, Jena, Germany.
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35
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Vogan AA, Ament-Velásquez SL, Granger-Farbos A, Svedberg J, Bastiaans E, Debets AJ, Coustou V, Yvanne H, Clavé C, Saupe SJ, Johannesson H. Combinations of Spok genes create multiple meiotic drivers in Podospora. eLife 2019; 8:46454. [PMID: 31347500 PMCID: PMC6660238 DOI: 10.7554/elife.46454] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 06/09/2019] [Indexed: 11/13/2022] Open
Abstract
Meiotic drive is the preferential transmission of a particular allele during sexual reproduction. The phenomenon is observed as spore killing in multiple fungi. In natural populations of Podospora anserina, seven spore killer types (Psks) have been identified through classical genetic analyses. Here we show that the Spok gene family underlies the Psks. The combination of Spok genes at different chromosomal locations defines the spore killer types and creates a killing hierarchy within a population. We identify two novel Spok homologs located within a large (74–167 kbp) region (the Spok block) that resides in different chromosomal locations in different strains. We confirm that the SPOK protein performs both killing and resistance functions and show that these activities are dependent on distinct domains, a predicted nuclease and kinase domain. Genomic and phylogenetic analyses across ascomycetes suggest that the Spok genes disperse through cross-species transfer, and evolve by duplication and diversification within lineages. In many organisms, most cells carry two versions of a given gene, one coming from the mother and the other from the father. An exception is sexual cells such as eggs, sperm, pollen or spores, which should only contain one variant of a gene. During their formation, these cells usually have an equal chance of inheriting one of the two gene versions. However, a certain class of gene variants called meiotic drivers can cheat this process and end up in more than half of the sexual cells; often, the cells that contain the drivers can kill sibling cells that do not carry these variants. This results in the selfish genetic elements spreading through populations at a higher rate, sometimes with severe consequences such as shifting the ratio of males to females. Meiotic drivers have been discovered in a wide range of organisms, from corn to mice to fruit flies and bread mold. They also exist in the fungus Podospora anserina, where they are called ‘spore killers’. Fungi are often used to study complex genetic processes, yet the identity and mode of action of spore killers in P. anserina were still unknown. Vogan, Ament-Velásquez et al. used a combination of genetic methods to identify three genes from the Spok family which are responsible for certain spores being able to kill their siblings. Two of these were previously unknown, and they could be found in different locations throughout the genome as part of a larger genetic region. Depending on the combination of Spok genes it carries, a spore can kill or be protected against other spores that contain different permutations of the genes. Copies of these genes were also shown to be present in other fungi, including species that are a threat to crops. Scientists have already started to create synthetic meiotic drivers to manipulate how certain traits are inherited within a population. This could be useful to control or eradicate pests and insects that transmit dangerous diseases. The results by Vogan, Ament-Velásquez et al. shine a light on the complex ways that natural meiotic drivers work, including how they can be shared between species; this knowledge could inform how to safely deploy synthetic drivers in the wild.
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Affiliation(s)
- Aaron A Vogan
- Organismal biology, Uppsala University, Uppsala, Sweden
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36
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Fernández-Correa I, Truchado DA, Gomez-Lucia E, Doménech A, Pérez-Tris J, Schmidt-Chanasit J, Cadar D, Benítez L. A novel group of avian astroviruses from Neotropical passerine birds broaden the diversity and host range of Astroviridae. Sci Rep 2019; 9:9513. [PMID: 31266971 PMCID: PMC6606752 DOI: 10.1038/s41598-019-45889-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 06/10/2019] [Indexed: 01/04/2023] Open
Abstract
Metagenomics is helping to expand the known diversity of viruses, especially of those with poorly studied hosts in remote areas. The Neotropical region harbors a considerable diversity of avian species that may play a role as both host and short-distance vectors of unknown viruses. Viral metagenomics of cloacal swabs from 50 Neotropical birds collected in French Guiana revealed the presence of four complete astrovirus genomes. They constitute an early diverging novel monophyletic clade within the Avastrovirus phylogeny, representing a putative new astrovirus species (provisionally designated as Avastrovirus 5) according to the International Committee on Taxonomy of Viruses (ICTV) classification criteria. Their genomic organization shares some characteristics with Avastrovirus but also with Mamastrovirus. The pan-astrovirus RT-PCR analysis of the cloacal samples of 406 wild Neotropical birds showed a community-level prevalence of 4.9% (5.1% in passerines, the highest described so far in this order of birds). By screening birds of a remote region, we expanded the known host range of astroviruses to the avian families Cardinalidae, Conopophagidae, Furnariidae, Thamnophilidae, Turdidae and Tyrannidae. Our results provide important first insights into the unexplored viral communities, the ecology, epidemiology and features of host-pathogen interactions that shape the evolution of avastroviruses in a remote Neotropical rainforest.
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Affiliation(s)
- Izaskun Fernández-Correa
- Department of Genetics, Physiology and Microbiology, Faculty of Biology, Complutense University of Madrid, José Antonio Novais, 12, 28040, Madrid, Spain
| | - Daniel A Truchado
- Department of Genetics, Physiology and Microbiology, Faculty of Biology, Complutense University of Madrid, José Antonio Novais, 12, 28040, Madrid, Spain.,Department of Biodiversity, Ecology and Evolution, Faculty of Biology, Complutense University of Madrid, José Antonio Novais, 12, 28040, Madrid, Spain
| | - Esperanza Gomez-Lucia
- Department of Animal Health, Faculty of Veterinary Medicine, Complutense University of Madrid, Avda. Puerta de Hierro s/n, 28040, Madrid, Spain
| | - Ana Doménech
- Department of Animal Health, Faculty of Veterinary Medicine, Complutense University of Madrid, Avda. Puerta de Hierro s/n, 28040, Madrid, Spain
| | - Javier Pérez-Tris
- Department of Biodiversity, Ecology and Evolution, Faculty of Biology, Complutense University of Madrid, José Antonio Novais, 12, 28040, Madrid, Spain
| | - Jonas Schmidt-Chanasit
- Bernhard-Nocht-Institut fur Tropenmedizin, WHO Collaborating Centre for Arbovirus and Haemorrhagic Fever Reference and Research, National Reference Centre for Tropical Infectious Diseases, Bernhard-Nocht-Strasse 74, 20359, Hamburg, Germany.,University of Hamburg, Faculty of Mathematics, Informatics and Natural Sciences, Hamburg, Germany
| | - Daniel Cadar
- Bernhard-Nocht-Institut fur Tropenmedizin, WHO Collaborating Centre for Arbovirus and Haemorrhagic Fever Reference and Research, National Reference Centre for Tropical Infectious Diseases, Bernhard-Nocht-Strasse 74, 20359, Hamburg, Germany
| | - Laura Benítez
- Department of Genetics, Physiology and Microbiology, Faculty of Biology, Complutense University of Madrid, José Antonio Novais, 12, 28040, Madrid, Spain.
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37
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Torres-Sánchez A, Vanegas JM, Purohit PK, Arroyo M. Combined molecular/continuum modeling reveals the role of friction during fast unfolding of coiled-coil proteins. SOFT MATTER 2019; 15:4961-4975. [PMID: 31172154 DOI: 10.1039/c9sm00117d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Coiled-coils are filamentous proteins that form the basic building block of important force-bearing cellular elements, such as intermediate filaments and myosin motors. In addition to their biological importance, coiled-coil proteins are increasingly used in new biomaterials including fibers, nanotubes, or hydrogels. Coiled-coils undergo a structural transition from an α-helical coil to an unfolded state upon extension, which allows them to sustain large strains and is critical for their biological function. By performing equilibrium and out-of-equilibrium all-atom molecular dynamics (MD) simulations of coiled-coils in explicit solvent, we show that two-state models based on Kramers' or Bell's theories fail to predict the rate of unfolding at high pulling rates. We further show that an atomistically informed continuum rod model accounting for phase transformations and for the hydrodynamic interactions with the solvent can reconcile two-state models with our MD results. Our results show that frictional forces, usually neglected in theories of fibrous protein unfolding, reduce the thermodynamic force acting on the interface, and thus control the dynamics of unfolding at different pulling rates. Our results may help interpret MD simulations at high pulling rates, and could be pertinent to cytoskeletal networks or protein-based artificial materials subjected to shocks or blasts.
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38
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Lai X, Daher H, Galien A, Hugouvieux V, Zubieta C. Structural Basis for Plant MADS Transcription Factor Oligomerization. Comput Struct Biotechnol J 2019; 17:946-953. [PMID: 31360333 PMCID: PMC6639411 DOI: 10.1016/j.csbj.2019.06.014] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 06/06/2019] [Accepted: 06/11/2019] [Indexed: 10/26/2022] Open
Abstract
MADS transcription factors (TFs) are DNA binding proteins found in almost all eukaryotes that play essential roles in diverse biological processes. While present in animals and fungi as a small TF family, the family has dramatically expanded in plants over the course of evolution, with the model flowering plant, Arabidopsis thaliana, possessing over 100 type I and type II MADS TFs. All MADS TFs contain a core and highly conserved DNA binding domain called the MADS or M domain. Plant MADS TFs have diversified this domain with plant-specific auxiliary domains. Plant type I MADS TFs have a highly diverse and largely unstructured Carboxy-terminal (C domain), whereas type II MADS have added oligomerization domains, called Intervening (I domain) and Keratin-like (K domain), in addition to the C domain. In this mini review, we describe the overall structure of the type II "MIKC" type MADS TFs in plants, with a focus on the K domain, a critical oligomerization module. We summarize the determining factors for oligomerization and provide mechanistic insights on how secondary structural elements are required for oligomerization capability and specificity. Using MADS TFs that are involved in flower organ specification as an example, we provide case studies and homology modeling of MADS TFs complex formation. Finally, we highlight outstanding questions in the field.
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Affiliation(s)
- Xuelei Lai
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, Univ. Grenoble Alpes, CEA, INRA, IRIG, Grenoble, France
| | - Hussein Daher
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, Univ. Grenoble Alpes, CEA, INRA, IRIG, Grenoble, France
| | - Antonin Galien
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, Univ. Grenoble Alpes, CEA, INRA, IRIG, Grenoble, France
| | - Veronique Hugouvieux
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, Univ. Grenoble Alpes, CEA, INRA, IRIG, Grenoble, France
| | - Chloe Zubieta
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, Univ. Grenoble Alpes, CEA, INRA, IRIG, Grenoble, France
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39
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Zeng F, Liu F, Yuan L, Zhou S, Shen J, Li N, Ren H, Zeng H. A Pore-Forming Tripeptide as an Extraordinarily Active Anion Channel. Org Lett 2019; 21:4826-4830. [DOI: 10.1021/acs.orglett.9b01723] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Fei Zeng
- College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou, Hunan, China 425100
| | - Fang Liu
- College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou, Hunan, China 425100
| | - Lin Yuan
- College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou, Hunan, China 425100
| | - Shaoyuan Zhou
- College of Chemical Engineering, Sichuan University, Chengdu, China 610065
| | - Jie Shen
- NanoBio Lab, 31 Biopolis Way, The Nanos, Singapore 138669
| | - Ning Li
- NanoBio Lab, 31 Biopolis Way, The Nanos, Singapore 138669
| | - Haisheng Ren
- College of Chemical Engineering, Sichuan University, Chengdu, China 610065
| | - Huaqiang Zeng
- NanoBio Lab, 31 Biopolis Way, The Nanos, Singapore 138669
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40
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Hellmund KS, Koksch B. Self-Assembling Peptides as Extracellular Matrix Mimics to Influence Stem Cell's Fate. Front Chem 2019; 7:172. [PMID: 31001512 PMCID: PMC6455064 DOI: 10.3389/fchem.2019.00172] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 03/05/2019] [Indexed: 12/13/2022] Open
Abstract
Interest in biologically active materials that can be used as cell culture substrates for medicinal applications has increased dramatically over the last decade. The design and development of biomaterials mimicking the natural environment of different cell types, the so-called extracellular matrix (ECM), is the focus of research in this field. The ECM exists as an ensemble of several adhesion proteins with different functionalities that can be presented to the embedded cells. These functionalities regulate numerous cellular processes. Therefore, different approaches and strategies using peptide- and protein-based biopolymers have been investigated to support the proliferation, differentiation, and self-renewal of stem cells, in the context of regenerative medicine. This minireview summarizes recent developments in this area, with a focus on peptide-based biomaterials used as stem cell culture substrates.
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Affiliation(s)
| | - Beate Koksch
- Department of Biology, Chemistry, and Pharmacy, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
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41
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Sanghavi HM, Mallajosyula SS, Majumdar S. Classification of the human THAP protein family identifies an evolutionarily conserved coiled coil region. BMC STRUCTURAL BIOLOGY 2019; 19:4. [PMID: 30836974 PMCID: PMC6402169 DOI: 10.1186/s12900-019-0102-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 01/29/2019] [Indexed: 12/22/2022]
Abstract
Background The THAP (Thanatos Associated Proteins) protein family in humans is implicated in various important cellular processes like epigenetic regulation, maintenance of pluripotency, transposition and disorders like cancers and hemophilia. The human THAP protein family which consists of twelve members of different lengths has a well characterized amino terminal, zinc-coordinating, DNA-binding domain called the THAP domain. However, the carboxy terminus of most THAP proteins is yet to be structurally characterized. A coiled coil region is known to help in protein oligomerization in THAP1 and THAP11. It is not known if other human THAP proteins oligomerize. We have used bioinformatic tools to explore the possibility of dimerization of THAP proteins via a coiled coil region. Results Classification of human THAP protein into three size based groups led to the identification of an evolutionarily conserved alpha helical region, downstream of the amino terminal THAP domain. Secondary structure predictions, alpha helical wheel plots and protein models demonstrated the strong possibility of coiled coil formation in this conserved, leucine rich region of all THAP proteins except THAP10. Conclusions The identification of a predicted oligomerization region in the human THAP protein family opens new directions to investigate the members of this protein family. Electronic supplementary material The online version of this article (10.1186/s12900-019-0102-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hiral M Sanghavi
- Discipline of Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, India
| | - Sairam S Mallajosyula
- Discipline of Chemistry, Indian Institute of Technology Gandhinagar, Gandhinagar, India
| | - Sharmistha Majumdar
- Discipline of Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, India.
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42
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Chaudhary R, Gupta A, Kota S, Misra HS. N-terminal domain of DivIVA contributes to its dimerization and interaction with genome segregation proteins in a radioresistant bacterium Deinococcus radiodurans. Int J Biol Macromol 2019; 128:12-21. [PMID: 30682467 DOI: 10.1016/j.ijbiomac.2019.01.085] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 01/13/2019] [Accepted: 01/19/2019] [Indexed: 01/27/2023]
Abstract
Unlike in rod-shaped bacteria, cell polarity is not well defined in cocci and possibly gets marked during molecular events around cytokinesis. DivIVA is a member of Min system that is involved in spatial regulation of septum formation in bacteria. Recently, we showed that DivIVA of Deinococcus radiodurans (drDivIVA) interacts with proteins involved in cell division and genome segregation (segrosome). To map drDivIVA domain (s) that interact with these proteins, the N-terminal (DivIVA-N), C-terminal (DivIVA-C) and a middle (DivIVA-M) region/section of drDivIVA were generated. Circular Dichroism (CD) studies suggested that all three variants of drDivIVA fold properly, but they appeared different under transmission electron microscopy (TEM). Full length drDivIVA showed bundles under TEM whereas variants did not. Both full length drDivIVA and N-terminal domain showed repeats of heptad motifs, a characteristic of alpha-helical coiled-coil proteins. DivIVA-N showed dimerization and interaction with segrosome while DivIVA-M interacted with MinC, a cell division regulatory protein. Further, the C-terminal region seems to be crucial for the structural and functional integrity of drDivIVA. These results suggested that drDivIVA dimerizes through its N-terminal domain while both segrosome and MinC interact through different regions of this protein.
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Affiliation(s)
- Reema Chaudhary
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai 400085, India; Life Sciences, Homi Bhabha National Institute, Mumbai 400094, India
| | - Alka Gupta
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - Swathi Kota
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai 400085, India; Life Sciences, Homi Bhabha National Institute, Mumbai 400094, India
| | - H S Misra
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai 400085, India; Life Sciences, Homi Bhabha National Institute, Mumbai 400094, India.
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43
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West AMV, Rosenberg SC, Ur SN, Lehmer MK, Ye Q, Hagemann G, Caballero I, Usón I, MacQueen AJ, Herzog F, Corbett KD. A conserved filamentous assembly underlies the structure of the meiotic chromosome axis. eLife 2019; 8:e40372. [PMID: 30657449 PMCID: PMC6349405 DOI: 10.7554/elife.40372] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 01/18/2019] [Indexed: 11/30/2022] Open
Abstract
The meiotic chromosome axis plays key roles in meiotic chromosome organization and recombination, yet the underlying protein components of this structure are highly diverged. Here, we show that 'axis core proteins' from budding yeast (Red1), mammals (SYCP2/SYCP3), and plants (ASY3/ASY4) are evolutionarily related and play equivalent roles in chromosome axis assembly. We first identify 'closure motifs' in each complex that recruit meiotic HORMADs, the master regulators of meiotic recombination. We next find that axis core proteins form homotetrameric (Red1) or heterotetrameric (SYCP2:SYCP3 and ASY3:ASY4) coiled-coil assemblies that further oligomerize into micron-length filaments. Thus, the meiotic chromosome axis core in fungi, mammals, and plants shares a common molecular architecture, and likely also plays conserved roles in meiotic chromosome axis assembly and recombination control.
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Affiliation(s)
- Alan MV West
- Biomedical Sciences Graduate ProgramUniversity of California, San DiegoLa JollaUnited States
- Department of Cellular and Molecular MedicineUniversity of California, San DiegoLa JollaUnited States
| | - Scott C Rosenberg
- Department of ChemistryUniversity of California, San DiegoLa JollaUnited States
| | - Sarah N Ur
- Biomedical Sciences Graduate ProgramUniversity of California, San DiegoLa JollaUnited States
| | - Madison K Lehmer
- Department of Cellular and Molecular MedicineUniversity of California, San DiegoLa JollaUnited States
| | - Qiaozhen Ye
- Department of Cellular and Molecular MedicineUniversity of California, San DiegoLa JollaUnited States
| | - Götz Hagemann
- Gene Center and Department of BiochemistryLudwig-Maximilians-Universität MünchenMunichGermany
| | - Iracema Caballero
- Crystallographic MethodsInstitute of Molecular Biology of Barcelona (IBMB-CSIC)BarcelonaSpain
| | - Isabel Usón
- Crystallographic MethodsInstitute of Molecular Biology of Barcelona (IBMB-CSIC)BarcelonaSpain
- Institució Catalana de Recerca i Estudis Avançats (ICREA)BarcelonaSpain
| | - Amy J MacQueen
- Department of Molecular Biology and BiochemistryWesleyan UniversityMiddletownUnited States
| | - Franz Herzog
- Gene Center and Department of BiochemistryLudwig-Maximilians-Universität MünchenMunichGermany
| | - Kevin D Corbett
- Department of Cellular and Molecular MedicineUniversity of California, San DiegoLa JollaUnited States
- Department of ChemistryUniversity of California, San DiegoLa JollaUnited States
- Ludwig Institute for Cancer ResearchLa JollaUnited States
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44
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Araújo ACD, Fonseca FCDA, Cotta MG, Alves GSC, Miller RNG. Plant NLR receptor proteins and their potential in the development of durable genetic resistance to biotic stresses. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.biori.2020.01.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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45
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Oldfield CJ, Chen K, Kurgan L. Computational Prediction of Secondary and Supersecondary Structures from Protein Sequences. Methods Mol Biol 2019; 1958:73-100. [PMID: 30945214 DOI: 10.1007/978-1-4939-9161-7_4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Many new methods for the sequence-based prediction of the secondary and supersecondary structures have been developed over the last several years. These and older sequence-based predictors are widely applied for the characterization and prediction of protein structure and function. These efforts have produced countless accurate predictors, many of which rely on state-of-the-art machine learning models and evolutionary information generated from multiple sequence alignments. We describe and motivate both types of predictions. We introduce concepts related to the annotation and computational prediction of the three-state and eight-state secondary structure as well as several types of supersecondary structures, such as β hairpins, coiled coils, and α-turn-α motifs. We review 34 predictors focusing on recent tools and provide detailed information for a selected set of 14 secondary structure and 3 supersecondary structure predictors. We conclude with several practical notes for the end users of these predictive methods.
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Affiliation(s)
- Christopher J Oldfield
- Department of Computer Science, College of Engineering, Virginia Commonwealth University, Richmond, VA, USA
| | - Ke Chen
- School of Computer Science and Software Engineering, Tianjin Polytechnic University, Tianjin, People's Republic of China
| | - Lukasz Kurgan
- Department of Computer Science, College of Engineering, Virginia Commonwealth University, Richmond, VA, USA.
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46
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MacCarthy E, Perry D, Kc DB. Advances in Protein Super-Secondary Structure Prediction and Application to Protein Structure Prediction. Methods Mol Biol 2019; 1958:15-45. [PMID: 30945212 DOI: 10.1007/978-1-4939-9161-7_2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Due to the advancement in various sequencing technologies, the gap between the number of protein sequences and the number of experimental protein structures is ever increasing. Community-wide initiatives like CASP have resulted in considerable efforts in the development of computational methods to accurately model protein structures from sequences. Sequence-based prediction of super-secondary structure has direct application in protein structure prediction, and there have been significant efforts in the prediction of super-secondary structure in the last decade. In this chapter, we first introduce the protein structure prediction problem and highlight some of the important progress in the field of protein structure prediction. Next, we discuss recent methods for the prediction of super-secondary structures. Finally, we discuss applications of super-secondary structure prediction in structure prediction/analysis of proteins. We also discuss prediction of protein structures that are composed of simple super-secondary structure repeats and protein structures that are composed of complex super-secondary structure repeats. Finally, we also discuss the recent trends in the field.
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Affiliation(s)
- Elijah MacCarthy
- Department of Computational Science and Engineering, North Carolina A&T State University, Greensboro, NC, USA
| | - Derrick Perry
- Department of Computational Science and Engineering, North Carolina A&T State University, Greensboro, NC, USA
| | - Dukka B Kc
- Department of Computational Science and Engineering, North Carolina A&T State University, Greensboro, NC, USA.
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47
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Yuan L, Shen J, Ye R, Chen F, Zeng H. Structurally simple trimesic amides as highly selective anion channels. Chem Commun (Camb) 2019; 55:4797-4800. [PMID: 30945706 DOI: 10.1039/c9cc00248k] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Trimesic amide molecules, which contain simple alkyl chains in their periphery, exhibit interesting anion-transport functions. The most active and highly selective channel TA12 efficiently transports ClO4- anions across membranes, with other anions conducted in the order of I- > NO3- > Br- > Cl-.
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Affiliation(s)
- Lin Yuan
- College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou, Hunan 425100, China
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48
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Wille M, Netter HJ, Littlejohn M, Yuen L, Shi M, Eden JS, Klaassen M, Holmes EC, Hurt AC. A Divergent Hepatitis D-Like Agent in Birds. Viruses 2018; 10:E720. [PMID: 30562970 PMCID: PMC6315422 DOI: 10.3390/v10120720] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 11/28/2018] [Accepted: 12/09/2018] [Indexed: 12/18/2022] Open
Abstract
Hepatitis delta virus (HDV) is currently only found in humans and is a satellite virus that depends on hepatitis B virus (HBV) envelope proteins for assembly, release, and entry. Using meta-transcriptomics, we identified the genome of a novel HDV-like agent in ducks. Sequence analysis revealed secondary structures that were shared with HDV, including self-complementarity and ribozyme features. The predicted viral protein shares 32% amino acid similarity to the small delta antigen of HDV and comprises a divergent phylogenetic lineage. The discovery of an avian HDV-like agent has important implications for the understanding of the origins of HDV and sub-viral agents.
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Affiliation(s)
- Michelle Wille
- WHO Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia.
| | - Hans J Netter
- Molecular Research and Development, Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia.
| | - Margaret Littlejohn
- Molecular Research and Development, Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia.
| | - Lilly Yuen
- Molecular Research and Development, Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia.
| | - Mang Shi
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia.
| | - John-Sebastian Eden
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia.
| | - Marcel Klaassen
- Centre for Integrative Ecology, Deakin University, Geelong, VIC 3220, Australia.
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia.
| | - Aeron C Hurt
- WHO Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia.
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49
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Bergues-Pupo AE, Blank KG, Lipowsky R, Vila Verde A. Trimeric coiled coils expand the range of strength, toughness and dynamics of coiled coil motifs under shear. Phys Chem Chem Phys 2018; 20:29105-29115. [PMID: 30426982 DOI: 10.1039/c8cp04896g] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Coiled coils are widespread protein motifs in nature, and promising building blocks for bio-inspired nanomaterials and nanoscale force sensors. Detailed structural insight into their mechanical response is required to understand their role in tissues and to design building blocks for applications. We use all-atom molecular dynamics simulations to elucidate the mechanical response of two types of coiled coils under shear: dimers and trimers. The amino acid sequences of both systems are similar, thus enabling universal (vs. system-specific) features to be identified. The trimer is mechanically more stable - it is both stronger and tougher - than the dimer, withstanding higher forces (127 pN vs. 49 pN at v = 10-3 nm ns-1) and dissipating up to five times more energy before rupture. The deformation mechanism of the trimer at all pull speeds is dominated by progressive helix unfolding. In contrast, at the lowest pull speeds, dimers deform by unfolding/refolding-assisted sliding. The additional helix in the trimer thus both determines the stability of the structure and affects the deformation mechanism, preventing helix sliding. The mechanical response of the coiled coils is not only sensitive to the oligomerization state but also to helix stability: preventing helix unfolding doubles the mechanical strength of the trimer, but decreases its toughness to half. Our results show that coiled coil trimers expand the range of coiled coil responses to an applied shear force. Altering the stability of individual helices against deformation emerges as one possible route towards fine-tuning this response, enabling the use of these motifs as nanomechanical building blocks.
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Affiliation(s)
- Ana E Bergues-Pupo
- Max Planck Institute of Colloids and Interfaces, Department of Theory & Bio-Systems, 14424 Potsdam, Germany.
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50
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Nakayama N, Takaoka S, Ota M, Takagaki K, Sano KI. Effect of the Aspect Ratio of Coiled-Coil Protein Carriers on Cellular Uptake. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:14286-14293. [PMID: 30384613 DOI: 10.1021/acs.langmuir.8b02616] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We showed previously that a rigid and fibrous-structured cationic coiled-coil artificial protein had cell-penetrating activity that was significantly greater when compared with a less-structured cell-penetrating peptide. Nanomaterials with anisotropic structures often show aspect-ratio-dependent unique physicochemical properties, as well as cell-penetrating activities. In this report, we have designed and demonstrated the cell-penetrating activity of a shorter cationic coiled-coil protein. An aspect ratio at 4.5:1 was found to be critical for ensuring that the cationic coiled-coil protein showed strong cell-penetrating activity. At an aspect ratio of 3.5:1, the cationic coiled-coil protein showed cell-penetrating activity that was similar to a less-structured short cationic cell-penetrating peptide. Interestingly, at an aspect ratio of 4:1, the cationic coiled-coil protein exhibited intermediate cell-penetrating activity. These findings should aid in the principle design of intracellular drug delivery carriers including coiled-coil artificial proteins, their derivatives, and α-helical cell-penetrating peptides as well as provide a framework for developing synthetic nanomaterials, such as metal nanorods and synthetic polymers.
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Affiliation(s)
- Norihisa Nakayama
- Graduate School of Environmental Symbiotic System Major , Nippon Institute of Technology , Miyashiro , Saitama 345-8501 , Japan
| | - Sho Takaoka
- BioMimetics Sympathies Inc. , Aomi, Koto-Ku, Tokyo 135-0064 , Japan
| | - Megumi Ota
- BioMimetics Sympathies Inc. , Aomi, Koto-Ku, Tokyo 135-0064 , Japan
| | - Kentaro Takagaki
- BioMimetics Sympathies Inc. , Aomi, Koto-Ku, Tokyo 135-0064 , Japan
| | - Ken-Ichi Sano
- Graduate School of Environmental Symbiotic System Major , Nippon Institute of Technology , Miyashiro , Saitama 345-8501 , Japan
- Department of Applied Chemistry, Faculty of Fundamental Engineering , Nippon Institute of Technology , Miyashiro , Saitama 345-8501 , Japan
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