1
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Ruan J, Yin Z, Yi P. Effects of fluorescent tags and activity status on the membrane localization of ROP GTPases. PLANT SIGNALING & BEHAVIOR 2024; 19:2306790. [PMID: 38270144 PMCID: PMC10813580 DOI: 10.1080/15592324.2024.2306790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 01/08/2024] [Indexed: 01/26/2024]
Abstract
Plant-specific Rho-type GTPases (ROPs) are master regulators of cell polarity and development. Over the past 30 years, their localization and dynamics have been largely examined with fluorescent proteins fused at the amino terminus without investigating their impact on protein function. The moss Physcomitrium patens genome encodes four rop genes. In this study, we introduce a fluorescent tag at the endogenous amino terminus of ROP4 in wild-type and rop1,2,3 triple mutant via homologous recombination and demonstrate that the fluorescent tag severely impairs ROP4 function and inhibits its localization on the plasma membrane. This phenotype is exacerbated in mutants lacking ROP-related GTPase-activating proteins. By comparing the localization of nonfunctional and functional ROP4 fusion reporters, we provide insight into the mechanism that governs the membrane association of ROPs.
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Affiliation(s)
- Jingtong Ruan
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Zihan Yin
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Peishan Yi
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, P. R. China
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2
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Nguyen PT, Harris BJ, Mateos DL, González AH, Murray AM, Yarov-Yarovoy V. Structural modeling of ion channels using AlphaFold2, RoseTTAFold2, and ESMFold. Channels (Austin) 2024; 18:2325032. [PMID: 38445990 PMCID: PMC10936637 DOI: 10.1080/19336950.2024.2325032] [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: 09/05/2023] [Accepted: 01/14/2024] [Indexed: 03/07/2024] Open
Abstract
Ion channels play key roles in human physiology and are important targets in drug discovery. The atomic-scale structures of ion channels provide invaluable insights into a fundamental understanding of the molecular mechanisms of channel gating and modulation. Recent breakthroughs in deep learning-based computational methods, such as AlphaFold, RoseTTAFold, and ESMFold have transformed research in protein structure prediction and design. We review the application of AlphaFold, RoseTTAFold, and ESMFold to structural modeling of ion channels using representative voltage-gated ion channels, including human voltage-gated sodium (NaV) channel - NaV1.8, human voltage-gated calcium (CaV) channel - CaV1.1, and human voltage-gated potassium (KV) channel - KV1.3. We compared AlphaFold, RoseTTAFold, and ESMFold structural models of NaV1.8, CaV1.1, and KV1.3 with corresponding cryo-EM structures to assess details of their similarities and differences. Our findings shed light on the strengths and limitations of the current state-of-the-art deep learning-based computational methods for modeling ion channel structures, offering valuable insights to guide their future applications for ion channel research.
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Affiliation(s)
- Phuong Tran Nguyen
- Department of Physiology and Membrane Biology, University of California School of Medicine, Davis, CA, USA
| | - Brandon John Harris
- Department of Physiology and Membrane Biology, University of California School of Medicine, Davis, CA, USA
- Biophysics Graduate Group, University of California School of Medicine, Davis, CA, USA
| | - Diego Lopez Mateos
- Department of Physiology and Membrane Biology, University of California School of Medicine, Davis, CA, USA
- Biophysics Graduate Group, University of California School of Medicine, Davis, CA, USA
| | - Adriana Hernández González
- Department of Physiology and Membrane Biology, University of California School of Medicine, Davis, CA, USA
- Biophysics Graduate Group, University of California School of Medicine, Davis, CA, USA
| | | | - Vladimir Yarov-Yarovoy
- Department of Physiology and Membrane Biology, University of California School of Medicine, Davis, CA, USA
- Department of Anesthesiology and Pain Medicine, University of California School of Medicine, Davis, CA, USA
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3
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Kim JD, Lee AR, Moon DH, Chung YU, Hong SY, Cho HJ, Kang TH, Jang YH, Sohn MH, Seong BL, Seo SU. Efficacy of genotype-matched vaccine against re-emerging genotype V Japanese encephalitis virus. Emerg Microbes Infect 2024; 13:2343910. [PMID: 38618740 PMCID: PMC11060017 DOI: 10.1080/22221751.2024.2343910] [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: 01/01/2024] [Accepted: 04/11/2024] [Indexed: 04/16/2024]
Abstract
Japanese encephalitis (JE), caused by the Japanese encephalitis virus (JEV), is a highly threatening disease with no specific treatment. Fortunately, the development of vaccines has enabled effective defense against JE. However, re-emerging genotype V (GV) JEV poses a challenge as current vaccines are genotype III (GIII)-based and provide suboptimal protection. Given the isolation of GV JEVs from Malaysia, China, and the Republic of Korea, there is a concern about the potential for a broader outbreak. Under the hypothesis that a GV-based vaccine is necessary for effective defense against GV JEV, we developed a pentameric recombinant antigen using cholera toxin B as a scaffold and mucosal adjuvant, which was conjugated with the E protein domain III of GV by genetic fusion. This GV-based vaccine antigen induced a more effective immune response in mice against GV JEV isolates compared to GIII-based antigen and efficiently protected animals from lethal challenges. Furthermore, a bivalent vaccine approach, inoculating simultaneously with GIII- and GV-based antigens, showed protective efficacy against both GIII and GV JEVs. This strategy presents a promising avenue for comprehensive protection in regions facing the threat of diverse JEV genotypes, including both prevalent GIII and GI as well as emerging GV strains.
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MESH Headings
- Encephalitis Virus, Japanese/genetics
- Encephalitis Virus, Japanese/immunology
- Encephalitis Virus, Japanese/classification
- Animals
- Genotype
- Encephalitis, Japanese/prevention & control
- Encephalitis, Japanese/immunology
- Encephalitis, Japanese/virology
- Japanese Encephalitis Vaccines/immunology
- Japanese Encephalitis Vaccines/administration & dosage
- Japanese Encephalitis Vaccines/genetics
- Mice
- Antibodies, Viral/immunology
- Antibodies, Viral/blood
- Humans
- Mice, Inbred BALB C
- Female
- Antigens, Viral/immunology
- Antigens, Viral/genetics
- Vaccine Efficacy
- Cholera Toxin/genetics
- Cholera Toxin/immunology
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Affiliation(s)
- Jae-Deog Kim
- Department of Biomedicine & Health Sciences, Graduate School, The Catholic University of Korea, Seoul, Republic of Korea
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Ah-Ra Lee
- Department of Biomedicine & Health Sciences, Graduate School, The Catholic University of Korea, Seoul, Republic of Korea
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Dah-Hyun Moon
- The Interdisciplinary Graduate Program in Integrative Biotechnology & Translational Medicine, Yonsei University, Incheon, Republic of Korea
| | - Young-Uk Chung
- Department of Biomedicine & Health Sciences, Graduate School, The Catholic University of Korea, Seoul, Republic of Korea
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Su-Yeon Hong
- Department of Biomedicine & Health Sciences, Graduate School, The Catholic University of Korea, Seoul, Republic of Korea
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Hyo Je Cho
- Department of Biochemistry, Chungbuk National University, Cheongju, Republic of Korea
| | - Tae Hyun Kang
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul, Republic of Korea
| | - Yo Han Jang
- Department of Vaccine Biotechnology, Andong National University, Andong, Republic of Korea
| | - Myung Hyun Sohn
- Department of Pediatrics, College of Medicine, Yonsei University, Seoul, Republic of Korea
| | - Baik-Lin Seong
- Department of Microbiology and Immunology, College of Medicine, Yonsei University, Seoul, Republic of Korea
- Vaccine Innovative Technology ALliance (VITAL)-Korea, Yonsei University, Seoul, Republic of Korea
| | - Sang-Uk Seo
- Department of Biomedicine & Health Sciences, Graduate School, The Catholic University of Korea, Seoul, Republic of Korea
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
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4
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Madsen AV, Mejias-Gomez O, Pedersen LE, Preben Morth J, Kristensen P, Jenkins TP, Goletz S. Structural trends in antibody-antigen binding interfaces: a computational analysis of 1833 experimentally determined 3D structures. Comput Struct Biotechnol J 2024; 23:199-211. [PMID: 38161735 PMCID: PMC10755492 DOI: 10.1016/j.csbj.2023.11.056] [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: 10/08/2023] [Revised: 11/27/2023] [Accepted: 11/28/2023] [Indexed: 01/03/2024] Open
Abstract
Antibodies are attractive therapeutic candidates due to their ability to bind cognate antigens with high affinity and specificity. Still, the underlying molecular rules governing the antibody-antigen interface remain poorly understood, making in silico antibody design inherently difficult and keeping the discovery and design of novel antibodies a costly and laborious process. This study investigates the characteristics of antibody-antigen binding interfaces through a computational analysis of more than 850,000 atom-atom contacts from the largest reported set of antibody-antigen complexes with 1833 nonredundant, experimentally determined structures. The analysis compares binding characteristics of conventional antibodies and single-domain antibodies (sdAbs) targeting both protein- and peptide antigens. We find clear patterns in the number antibody-antigen contacts and amino acid frequencies in the paratope. The direct comparison of sdAbs and conventional antibodies helps elucidate the mechanisms employed by sdAbs to compensate for their smaller size and the fact that they harbor only half the number of complementarity-determining regions compared to conventional antibodies. Furthermore, we pinpoint antibody interface hotspot residues that are often found at the binding interface and the amino acid frequencies at these positions. These findings have direct potential applications in antibody engineering and the design of improved antibody libraries.
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Affiliation(s)
- Andreas V. Madsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Oscar Mejias-Gomez
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Lasse E. Pedersen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - J. Preben Morth
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Peter Kristensen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Timothy P. Jenkins
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Steffen Goletz
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
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5
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Liang F, Sun M, Xie L, Zhao X, Liu D, Zhao K, Zhang G. Recent advances and challenges in protein complex model accuracy estimation. Comput Struct Biotechnol J 2024; 23:1824-1832. [PMID: 38707538 PMCID: PMC11066466 DOI: 10.1016/j.csbj.2024.04.049] [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: 01/27/2024] [Revised: 04/18/2024] [Accepted: 04/18/2024] [Indexed: 05/07/2024] Open
Abstract
Estimation of model accuracy plays a crucial role in protein structure prediction, aiming to evaluate the quality of predicted protein structure models accurately and objectively. This process is not only key to screening candidate models that are close to the real structure, but also provides guidance for further optimization of protein structures. With the significant advancements made by AlphaFold2 in monomer structure, the problem of single-domain protein structure prediction has been widely solved. Correspondingly, the importance of assessing the quality of single-domain protein models decreased, and the research focus has shifted to estimation of model accuracy of protein complexes. In this review, our goal is to provide a comprehensive overview of the reference and statistical metrics, as well as representative methods, and the current challenges within four distinct facets (Topology Global Score, Interface Total Score, Interface Residue-Wise Score, and Tertiary Residue-Wise Score) in the field of complex EMA.
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Affiliation(s)
| | | | - Lei Xie
- College of Information Engineering, Zhejiang University of Technology, Hangzhou 310023, China
| | - Xuanfeng Zhao
- College of Information Engineering, Zhejiang University of Technology, Hangzhou 310023, China
| | - Dong Liu
- College of Information Engineering, Zhejiang University of Technology, Hangzhou 310023, China
| | - Kailong Zhao
- College of Information Engineering, Zhejiang University of Technology, Hangzhou 310023, China
| | - Guijun Zhang
- College of Information Engineering, Zhejiang University of Technology, Hangzhou 310023, China
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6
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Wang X, Gao X, Fan X, Huai Z, Zhang G, Yao M, Wang T, Huang X, Lai L. WUREN: Whole-modal union representation for epitope prediction. Comput Struct Biotechnol J 2024; 23:2122-2131. [PMID: 38817963 PMCID: PMC11137340 DOI: 10.1016/j.csbj.2024.05.023] [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: 01/26/2024] [Revised: 05/14/2024] [Accepted: 05/14/2024] [Indexed: 06/01/2024] Open
Abstract
B-cell epitope identification plays a vital role in the development of vaccines, therapies, and diagnostic tools. Currently, molecular docking tools in B-cell epitope prediction are heavily influenced by empirical parameters and require significant computational resources, rendering a great challenge to meet large-scale prediction demands. When predicting epitopes from antigen-antibody complex, current artificial intelligence algorithms cannot accurately implement the prediction due to insufficient protein feature representations, indicating novel algorithm is desperately needed for efficient protein information extraction. In this paper, we introduce a multimodal model called WUREN (Whole-modal Union Representation for Epitope predictioN), which effectively combines sequence, graph, and structural features. It achieved AUC-PR scores of 0.213 and 0.193 on the solved structures and AlphaFold-generated structures, respectively, for the independent test proteins selected from DiscoTope3 benchmark. Our findings indicate that WUREN is an efficient feature extraction model for protein complexes, with the generalizable application potential in the development of protein-based drugs. Moreover, the streamlined framework of WUREN could be readily extended to model similar biomolecules, such as nucleic acids, carbohydrates, and lipids.
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Affiliation(s)
| | | | - Xuezhe Fan
- XtalPi Innovation Center, Beijing, China
| | - Zhe Huai
- XtalPi Innovation Center, Beijing, China
| | | | | | | | | | - Lipeng Lai
- XtalPi Innovation Center, Beijing, China
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7
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Li M, Qing R, Tao F, Xu P, Zhang S. Inhibitory effect of truncated isoforms on GPCR dimerization predicted by combinatorial computational strategy. Comput Struct Biotechnol J 2024; 23:278-286. [PMID: 38173876 PMCID: PMC10762321 DOI: 10.1016/j.csbj.2023.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/07/2023] [Accepted: 12/07/2023] [Indexed: 01/05/2024] Open
Abstract
G protein-coupled receptors (GPCRs) play a pivotal role in fundamental biological processes and disease development. GPCR isoforms, derived from alternative splicing, can exhibit distinct signaling patterns. Some highly-truncated isoforms can impact functional performance of full-length receptors, suggesting their intriguing regulatory roles. However, how these truncated isoforms interact with full-length counterparts remains largely unexplored. Here, we computationally investigated the interaction patterns of three human GPCRs from three different classes, ADORA1 (Class A), mGlu2 (Class C) and SMO (Class F) with their respective truncated isoforms because their homodimer structures have been experimentally determined, and they have truncated isoforms deposited and identified at protein level in Uniprot database. Combining the neural network-based AlphaFold2 and two physics-based protein-protein docking tools, we generated multiple complex structures and assessed the binding affinity in the context of atomistic molecular dynamics simulations. Our computational results suggested all the four studied truncated isoforms showed potent binding to their counterparts and overlapping interfaces with homodimers, indicating their strong potential to block homodimerization of their counterparts. Our study offers insights into functional significance of GPCR truncated isoforms and supports the ubiquity of their regulatory roles.
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Affiliation(s)
- Mengke Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Laboratory of Molecular Architecture, Media Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Rui Qing
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Fei Tao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shuguang Zhang
- Laboratory of Molecular Architecture, Media Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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8
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David C, Arango-Franco CA, Badonyi M, Fouchet J, Rice GI, Didry-Barca B, Maisonneuve L, Seabra L, Kechiche R, Masson C, Cobat A, Abel L, Talouarn E, Béziat V, Deswarte C, Livingstone K, Paul C, Malik G, Ross A, Adam J, Walsh J, Kumar S, Bonnet D, Bodemer C, Bader-Meunier B, Marsh JA, Casanova JL, Crow YJ, Manoury B, Frémond ML, Bohlen J, Lepelley A. Gain-of-function human UNC93B1 variants cause systemic lupus erythematosus and chilblain lupus. J Exp Med 2024; 221:e20232066. [PMID: 38869500 DOI: 10.1084/jem.20232066] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 03/29/2024] [Accepted: 05/15/2024] [Indexed: 06/14/2024] Open
Abstract
UNC93B1 is a transmembrane domain protein mediating the signaling of endosomal Toll-like receptors (TLRs). We report five families harboring rare missense substitutions (I317M, G325C, L330R, R466S, and R525P) in UNC93B1 causing systemic lupus erythematosus (SLE) or chilblain lupus (CBL) as either autosomal dominant or autosomal recessive traits. As for a D34A mutation causing murine lupus, we recorded a gain of TLR7 and, to a lesser extent, TLR8 activity with the I317M (in vitro) and G325C (in vitro and ex vivo) variants in the context of SLE. Contrastingly, in three families segregating CBL, the L330R, R466S, and R525P variants were isomorphic with respect to TLR7 activity in vitro and, for R525P, ex vivo. Rather, these variants demonstrated a gain of TLR8 activity. We observed enhanced interaction of the G325C, L330R, and R466S variants with TLR8, but not the R525P substitution, indicating different disease mechanisms. Overall, these observations suggest that UNC93B1 mutations cause monogenic SLE or CBL due to differentially enhanced TLR7 and TLR8 signaling.
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Affiliation(s)
- Clémence David
- Laboratory of Neurogenetics and Neuroinflammation, Imagine Institute, INSERM UMR1163, Paris, France
| | - Carlos A Arango-Franco
- Laboratory of Human Genetics of Infectious Diseases, INSERM UMR1163, Necker Hospital for Sick Children, Paris, France
- Department of Microbiology and Parasitology, Group of Primary Immunodeficiencies, School of Medicine, University of Antioquia, Medellín, Colombia
| | - Mihaly Badonyi
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh , Edinburgh, UK
| | - Julien Fouchet
- Faculté de Médecine Necker, Institut Necker Enfants Malades, INSERM U1151-CNRS UMR 8253, Université Paris Cité, Paris, France
| | - Gillian I Rice
- Faculty of Biology, Medicine and Health, Division of Evolution and Genomic Sciences, School of Biological Sciences, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Blaise Didry-Barca
- Laboratory of Neurogenetics and Neuroinflammation, Imagine Institute, INSERM UMR1163, Paris, France
| | - Lucie Maisonneuve
- Faculté de Médecine Necker, Institut Necker Enfants Malades, INSERM U1151-CNRS UMR 8253, Université Paris Cité, Paris, France
| | - Luis Seabra
- Laboratory of Neurogenetics and Neuroinflammation, Imagine Institute, INSERM UMR1163, Paris, France
| | - Robin Kechiche
- Laboratory of Neurogenetics and Neuroinflammation, Imagine Institute, INSERM UMR1163, Paris, France
- Department of Paediatric Hematology-Immunology and Rheumatology, Necker-Enfants Malades Hospital, Assistance publique-hôpitaux de Paris (AP-HP), Paris, France
| | - Cécile Masson
- Bioinformatics Core Facility, Université Paris Cité-Structure Fédérative de Recherche Necker, INSERM US24/CNRS UMS3633, Paris, France
| | - Aurélie Cobat
- Laboratory of Human Genetics of Infectious Diseases, INSERM UMR1163, Necker Hospital for Sick Children, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Imagine Institute, Université Paris Cité , Paris, France
| | - Laurent Abel
- Laboratory of Human Genetics of Infectious Diseases, INSERM UMR1163, Necker Hospital for Sick Children, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Imagine Institute, Université Paris Cité , Paris, France
| | - Estelle Talouarn
- Laboratory of Human Genetics of Infectious Diseases, INSERM UMR1163, Necker Hospital for Sick Children, Paris, France
- Imagine Institute, Université Paris Cité , Paris, France
| | - Vivien Béziat
- Laboratory of Human Genetics of Infectious Diseases, INSERM UMR1163, Necker Hospital for Sick Children, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Imagine Institute, Université Paris Cité , Paris, France
| | - Caroline Deswarte
- Laboratory of Human Genetics of Infectious Diseases, INSERM UMR1163, Necker Hospital for Sick Children, Paris, France
- Imagine Institute, Université Paris Cité , Paris, France
| | - Katie Livingstone
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh , Edinburgh, UK
| | - Carle Paul
- Université Toulouse Paul Sabatier , Toulouse, France
| | - Gulshan Malik
- Paediatric Rheumatology, Royal Aberdeen Children's Hospital, Aberdeen, UK
| | - Alison Ross
- Paediatric Rheumatology, Royal Aberdeen Children's Hospital, Aberdeen, UK
| | - Jane Adam
- Paediatric Rheumatology, Royal Aberdeen Children's Hospital, Aberdeen, UK
| | - Jo Walsh
- Department of Paediatric Rheumatology, Royal Hospital for Children, Glasgow, UK
| | - Sathish Kumar
- Department of Pediatrics, Pediatric Rheumatology, Christian Medical College, Vellore, India
| | - Damien Bonnet
- Medical and Surgical Unit of Congenital and Paediatric Cardiology, Reference Centre for Complex Congenital Heart Defects-M3C, University Hospital Necker-Enfants Malades, Paris, France
- Université Paris Cité , Paris, France
| | - Christine Bodemer
- Department of Dermatology, Hospital Necker-Enfants Malades, AP-HP. Université Paris Cité, Paris, France
| | - Brigitte Bader-Meunier
- Department of Paediatric Hematology-Immunology and Rheumatology, Necker-Enfants Malades Hospital, Assistance publique-hôpitaux de Paris (AP-HP), Paris, France
- Centre for Inflammatory Rheumatism, AutoImmune Diseases and Systemic Interferonopathies in Children (RAISE) , Paris, France
| | - Joseph A Marsh
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh , Edinburgh, UK
| | - Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, INSERM UMR1163, Necker Hospital for Sick Children, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Imagine Institute, Université Paris Cité , Paris, France
- Howard Hughes Medical Institute , New York, NY, USA
- Department of Pediatrics, Necker Hospital for Sick Children, Paris, France
| | - Yanick J Crow
- Laboratory of Neurogenetics and Neuroinflammation, Imagine Institute, INSERM UMR1163, Paris, France
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh , Edinburgh, UK
- Université Paris Cité , Paris, France
| | - Bénédicte Manoury
- Faculté de Médecine Necker, Institut Necker Enfants Malades, INSERM U1151-CNRS UMR 8253, Université Paris Cité, Paris, France
| | - Marie-Louise Frémond
- Laboratory of Neurogenetics and Neuroinflammation, Imagine Institute, INSERM UMR1163, Paris, France
- Department of Paediatric Hematology-Immunology and Rheumatology, Necker-Enfants Malades Hospital, Assistance publique-hôpitaux de Paris (AP-HP), Paris, France
- Centre for Inflammatory Rheumatism, AutoImmune Diseases and Systemic Interferonopathies in Children (RAISE) , Paris, France
| | - Jonathan Bohlen
- Laboratory of Human Genetics of Infectious Diseases, INSERM UMR1163, Necker Hospital for Sick Children, Paris, France
- Imagine Institute, Université Paris Cité , Paris, France
| | - Alice Lepelley
- Laboratory of Neurogenetics and Neuroinflammation, Imagine Institute, INSERM UMR1163, Paris, France
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9
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Veronese M, Kallabis S, Kaczmarek AT, Das A, Robers L, Schumacher S, Lofrano A, Brodesser S, Müller S, Hofmann K, Krüger M, Rugarli EI. ERLIN1/2 scaffolds bridge TMUB1 and RNF170 and restrict cholesterol esterification to regulate the secretory pathway. Life Sci Alliance 2024; 7:e202402620. [PMID: 38782601 PMCID: PMC11116810 DOI: 10.26508/lsa.202402620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 05/06/2024] [Accepted: 05/07/2024] [Indexed: 05/25/2024] Open
Abstract
Complexes of ERLIN1 and ERLIN2 (ER lipid raft-associated 1 and 2) form large ring-like cup-shaped structures on the endoplasmic reticulum (ER) membrane and serve as platforms to bind cholesterol and E3 ubiquitin ligases, potentially defining functional nanodomains. Here, we show that ERLIN scaffolds mediate the interaction between the full-length isoform of TMUB1 (transmembrane and ubiquitin-like domain-containing 1) and RNF170 (RING finger protein 170). We identify a luminal N-terminal conserved region in TMUB1 and RNF170, which is required for this interaction. Three-dimensional modelling shows that this conserved motif binds the stomatin/prohibitin/flotillin/HflKC domain of two adjacent ERLIN subunits at different interfaces. Protein variants that preclude these interactions have been previously linked to hereditary spastic paraplegia. Using omics-based approaches in combination with phenotypic characterization of HeLa cells lacking both ERLINs, we demonstrate a role of ERLIN scaffolds in limiting cholesterol esterification, thereby favouring cholesterol transport from the ER to the Golgi apparatus and regulating Golgi morphology and the secretory pathway.
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Affiliation(s)
- Matteo Veronese
- https://ror.org/00rcxh774 Institute for Genetics, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
| | - Sebastian Kallabis
- https://ror.org/00rcxh774 Institute for Genetics, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
| | - Alexander Tobias Kaczmarek
- https://ror.org/00rcxh774 Institute for Genetics, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
| | - Anushka Das
- https://ror.org/00rcxh774 Institute for Genetics, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
| | - Lennart Robers
- https://ror.org/00rcxh774 Institute for Genetics, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
| | - Simon Schumacher
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
- Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Alessia Lofrano
- https://ror.org/00rcxh774 Institute for Genetics, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
| | - Susanne Brodesser
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
- Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Stefan Müller
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
| | - Kay Hofmann
- https://ror.org/00rcxh774 Institute for Genetics, University of Cologne, Cologne, Germany
| | - Marcus Krüger
- https://ror.org/00rcxh774 Institute for Genetics, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
- https://ror.org/00rcxh774 Center for Molecular Medicine (CMMC), University of Cologne, Cologne, Germany
| | - Elena I Rugarli
- https://ror.org/00rcxh774 Institute for Genetics, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
- https://ror.org/00rcxh774 Center for Molecular Medicine (CMMC), University of Cologne, Cologne, Germany
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10
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Gemmer M, Chaillet ML, Förster F. Exploring the molecular composition of the multipass translocon in its native membrane environment. Life Sci Alliance 2024; 7:e202302496. [PMID: 38866426 PMCID: PMC11169918 DOI: 10.26508/lsa.202302496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 05/22/2024] [Accepted: 05/23/2024] [Indexed: 06/14/2024] Open
Abstract
Multispanning membrane proteins are inserted into the endoplasmic reticulum membrane by the ribosome-bound multipass translocon (MPT) machinery. Based on cryo-electron tomography and extensive subtomogram analysis, we reveal the composition and arrangement of ribosome-bound MPT components in their native membrane environment. The intramembrane chaperone complex PAT and the translocon-associated protein (TRAP) complex associate substoichiometrically with the MPT in a translation-dependent manner. Although PAT is preferentially part of MPTs bound to translating ribosomes, the abundance of TRAP is highest in MPTs associated with non-translating ribosomes. The subtomogram average of the TRAP-containing MPT reveals intermolecular contacts between the luminal domains of TRAP and an unknown subunit of the back-of-Sec61 complex. AlphaFold modeling suggests this protein is nodal modulator, bridging the luminal domains of nicalin and TRAPα. Collectively, our results visualize the variability of MPT factors in the native membrane environment dependent on the translational activity of the bound ribosome.
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Affiliation(s)
- Max Gemmer
- https://ror.org/04pp8hn57 Structural Biochemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - Marten L Chaillet
- https://ror.org/04pp8hn57 Structural Biochemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - Friedrich Förster
- https://ror.org/04pp8hn57 Structural Biochemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
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11
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Houston J, Vissotsky C, Deep A, Hakozaki H, Crews E, Oegema K, Corbett KD, Lara-Gonzalez P, Kim T, Desai A. Phospho-KNL-1 recognition by a TPR domain targets the BUB-1-BUB-3 complex to C. elegans kinetochores. J Cell Biol 2024; 223:e202402036. [PMID: 38578284 PMCID: PMC10996584 DOI: 10.1083/jcb.202402036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 03/21/2024] [Accepted: 03/25/2024] [Indexed: 04/06/2024] Open
Abstract
During mitosis, the Bub1-Bub3 complex concentrates at kinetochores, the microtubule-coupling interfaces on chromosomes, where it contributes to spindle checkpoint activation, kinetochore-spindle microtubule interactions, and protection of centromeric cohesion. Bub1 has a conserved N-terminal tetratricopeptide repeat (TPR) domain followed by a binding motif for its conserved interactor Bub3. The current model for Bub1-Bub3 localization to kinetochores is that Bub3, along with its bound motif from Bub1, recognizes phosphorylated "MELT" motifs in the kinetochore scaffold protein Knl1. Motivated by the greater phenotypic severity of BUB-1 versus BUB-3 loss in C. elegans, we show that the BUB-1 TPR domain directly recognizes a distinct class of phosphorylated motifs in KNL-1 and that this interaction is essential for BUB-1-BUB-3 localization and function. BUB-3 recognition of phospho-MELT motifs additively contributes to drive super-stoichiometric accumulation of BUB-1-BUB-3 on its KNL-1 scaffold during mitotic entry. Bub1's TPR domain interacts with Knl1 in other species, suggesting that collaboration of TPR-dependent and Bub3-dependent interfaces in Bub1-Bub3 localization and functions may be conserved.
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Affiliation(s)
- Jack Houston
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, USA
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | | | - Amar Deep
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Hiroyuki Hakozaki
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
| | - Enice Crews
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Karen Oegema
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, USA
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Kevin D. Corbett
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
- Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Pablo Lara-Gonzalez
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
| | - Taekyung Kim
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
- Department of Biology Education, Pusan National University, Busan, Republic of Korea
| | - Arshad Desai
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, USA
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
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12
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Zhao X, Quintremil S, Rodriguez Castro ED, Cui H, Moraga D, Wang T, Vallee RB, Solmaz SR. Molecular mechanism for recognition of the cargo adapter Rab6 GTP by the dynein adapter BicD2. Life Sci Alliance 2024; 7:e202302430. [PMID: 38719748 PMCID: PMC11077774 DOI: 10.26508/lsa.202302430] [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: 10/11/2023] [Revised: 04/24/2024] [Accepted: 04/25/2024] [Indexed: 05/12/2024] Open
Abstract
Rab6 is a key modulator of protein secretion. The dynein adapter Bicaudal D2 (BicD2) recruits the motors cytoplasmic dynein and kinesin-1 to Rab6GTP-positive vesicles for transport; however, it is unknown how BicD2 recognizes Rab6. Here, we establish a structural model for recognition of Rab6GTP by BicD2, using structure prediction and mutagenesis. The binding site of BicD2 spans two regions of Rab6 that undergo structural changes upon the transition from the GDP- to GTP-bound state, and several hydrophobic interface residues are rearranged, explaining the increased affinity of the active GTP-bound state. Mutations of Rab6GTP that abolish binding to BicD2 also result in reduced co-migration of Rab6GTP/BicD2 in cells, validating our model. These mutations also severely diminished the motility of Rab6-positive vesicles in cells, highlighting the importance of the Rab6GTP/BicD2 interaction for overall motility of the multi-motor complex that contains both kinesin-1 and dynein. Our results provide insights into trafficking of secretory and Golgi-derived vesicles and will help devise therapies for diseases caused by BicD2 mutations, which selectively affect the affinity to Rab6 and other cargoes.
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Affiliation(s)
- Xiaoxin Zhao
- https://ror.org/008rmbt77 Department of Chemistry, Binghamton University, Binghamton, NY, USA
| | - Sebastian Quintremil
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
| | | | - Heying Cui
- https://ror.org/008rmbt77 Department of Chemistry, Binghamton University, Binghamton, NY, USA
| | - David Moraga
- https://ror.org/008rmbt77 Department of Chemistry, Binghamton University, Binghamton, NY, USA
| | - Tingyao Wang
- https://ror.org/008rmbt77 Department of Chemistry, Binghamton University, Binghamton, NY, USA
| | - Richard B Vallee
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Sozanne R Solmaz
- https://ror.org/008rmbt77 Department of Chemistry, Binghamton University, Binghamton, NY, USA
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13
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Simpson MS, De Luca H, Cauthorn S, Luong P, Udeshi ND, Svinkina T, Schmieder SS, Carr SA, Grey MJ, Lencer WI. IRE1α recognizes a structural motif in cholera toxin to activate an unfolded protein response. J Cell Biol 2024; 223:e202402062. [PMID: 38578285 PMCID: PMC10996581 DOI: 10.1083/jcb.202402062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 03/18/2024] [Accepted: 03/20/2024] [Indexed: 04/06/2024] Open
Abstract
IRE1α is an endoplasmic reticulum (ER) sensor that recognizes misfolded proteins to induce the unfolded protein response (UPR). We studied cholera toxin (CTx), which invades the ER and activates IRE1α in host cells, to understand how unfolded proteins are recognized. Proximity labeling colocalized the enzymatic and metastable A1 segment of CTx (CTxA1) with IRE1α in live cells, where we also found that CTx-induced IRE1α activation enhanced toxicity. In vitro, CTxA1 bound the IRE1α lumenal domain (IRE1αLD), but global unfolding was not required. Rather, the IRE1αLD recognized a seven-residue motif within an edge β-strand of CTxA1 that must locally unfold for binding. Binding mapped to a pocket on IRE1αLD normally occupied by a segment of the IRE1α C-terminal flexible loop implicated in IRE1α oligomerization. Mutation of the CTxA1 recognition motif blocked CTx-induced IRE1α activation in live cells, thus linking the binding event with IRE1α signal transduction and induction of the UPR.
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Affiliation(s)
- Mariska S. Simpson
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children’s Hospital, Boston MA, USA
- Graduate School of Life Sciences, Utrecht University, Utrecht, Netherlands
| | - Heidi De Luca
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children’s Hospital, Boston MA, USA
| | - Sarah Cauthorn
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children’s Hospital, Boston MA, USA
- Division of Gastroenterology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Phi Luong
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children’s Hospital, Boston MA, USA
| | | | | | - Stefanie S. Schmieder
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children’s Hospital, Boston MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | | | - Michael J. Grey
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children’s Hospital, Boston MA, USA
- Division of Gastroenterology, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Harvard Digestive Disease Center, Boston, MA, USA
| | - Wayne I. Lencer
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children’s Hospital, Boston MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Harvard Digestive Disease Center, Boston, MA, USA
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14
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Medhanavyn D, Muranaka T, Yasumoto S. Characterization of unique EDTA-insensitive methylthioalkylmalate synthase from Eutrema japonicum and its potential application in synthetic biology. J Biosci Bioeng 2024; 138:13-20. [PMID: 38614832 DOI: 10.1016/j.jbiosc.2024.02.009] [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: 12/13/2023] [Revised: 02/25/2024] [Accepted: 02/25/2024] [Indexed: 04/15/2024]
Abstract
6-(Methylsulfinyl)hexyl isothiocyanate (6-MSITC), a derivative of glucosinolate with a six-carbon chain, is a compound found in wasabi and has diverse health-promoting properties. The biosynthesis of glucosinolates from methionine depends on a crucial step catalyzed methylthioalkylmalate synthases (MAMs), which are responsible for the generation of glucosinolates with varying chain lengths. In this study, our primary focus was the characterization of two methylthioalkyl malate synthases, MAM1-1 and MAM1-2, derived from Eutrema japonicum, commonly referred to as Japanese wasabi. Eutremajaponicum MAMs (EjMAMs) were expressed in an Escherichiacoli expression system, subsequently purified, and in vitro enzymatic activity was assayed. We explored the kinetic properties, optimal pH conditions, and cofactor preferences of EjMAMs and compared them with those of previously documented MAMs. Surprisingly, EjMAM1-2, categorized as a metallolyase family enzyme, displayed 20% of its maximum activity even in the absence of divalent metal cofactors or under high concentrations of EDTA. Additionally, we utilized AlphaFold2 to generate structural homology models of EjMAMs, and used in silico analysis and mutagenesis studies to investigate the key residues participating in catalytic activity. Moreover, we examined in vivo biosynthesis in E. coli containing Arabidopsis thaliana branched-chain amino acid transferase 3 (AtBCAT3) along with AtMAMs or EjMAMs and demonstrated that EjMAM1-2 exhibited the highest conversion rate among those MAMs, converting l-methionine to 2-(2-methylthio) ethyl malate (2-(2-MT)EM). EjMAM1-2 shows a unique property in vitro and highest activity on converting l-methionine to 2-(2-MT)EM in vivo which displays high potential for isothiocyanate biosynthesis in E. coli platform.
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Affiliation(s)
- Dheeradhach Medhanavyn
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Toshiya Muranaka
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Industrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka, Japan
| | - Shuhei Yasumoto
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Industrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka, Japan.
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15
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McCloskey E, Kashipathy M, Cooper A, Gao P, Johnson DK, Battaile KP, Lovell S, Davido DJ. HSV-1 ICP0 dimer domain adopts a novel β-barrel fold. Proteins 2024; 92:830-841. [PMID: 38372168 PMCID: PMC11147711 DOI: 10.1002/prot.26673] [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: 10/16/2023] [Revised: 01/05/2024] [Accepted: 01/19/2024] [Indexed: 02/20/2024]
Abstract
Infected cell protein 0 (ICP0) is an immediate-early regulatory protein of herpes simplex virus 1 (HSV-1) that possesses E3 ubiquitin ligase activity. ICP0 transactivates viral genes, in part, through its C-terminal dimer domain (residues 555-767). Deletion of this dimer domain results in reduced viral gene expression, lytic infection, and reactivation from latency. Since ICP0's dimer domain is associated with its transactivation activity and efficient viral replication, we wanted to determine the structure of this specific domain. The C-terminus of ICP0 was purified from bacteria and analyzed by X-ray crystallography to solve its structure. Each subunit or monomer in the ICP0 dimer is composed of nine β-strands and two α-helices. Interestingly, two adjacent β-strands from one monomer "reach" into the adjacent subunit during dimer formation, generating two β-barrel-like structures. Additionally, crystallographic analyses indicate a tetramer structure is formed from two β-strands of each dimer, creating a "stacking" of the β-barrels. The structural protein database searches indicate the fold or structure adopted by the ICP0 dimer is novel. The dimer is held together by an extensive network of hydrogen bonds. Computational analyses reveal that ICP0 can either form a dimer or bind to SUMO1 via its C-terminal SUMO-interacting motifs but not both. Understanding the structure of the dimer domain will provide insights into the activities of ICP0 and, ultimately, the HSV-1 life cycle.
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Affiliation(s)
- Erick McCloskey
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA
| | - Maithri Kashipathy
- Protein Structure and X-Ray Crystallography Laboratory, University of Kansas, Lawrence, Kansas, USA
| | - Anne Cooper
- Protein Production Group, University of Kansas, Lawrence, Kansas, USA
| | - Philip Gao
- Protein Production Group, University of Kansas, Lawrence, Kansas, USA
| | - David K Johnson
- Chemical Computational Biology Core, University of Kansas, Lawrence, Kansas, USA
| | | | - Scott Lovell
- Protein Structure and X-Ray Crystallography Laboratory, University of Kansas, Lawrence, Kansas, USA
| | - David J Davido
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA
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16
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Nishihara A, Tsukatani Y, Azai C, Nobu MK. Illuminating the coevolution of photosynthesis and Bacteria. Proc Natl Acad Sci U S A 2024; 121:e2322120121. [PMID: 38875151 DOI: 10.1073/pnas.2322120121] [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: 12/18/2023] [Accepted: 05/06/2024] [Indexed: 06/16/2024] Open
Abstract
Life harnessing light energy transformed the relationship between biology and Earth-bringing a massive flux of organic carbon and oxidants to Earth's surface that gave way to today's organotrophy- and respiration-dominated biosphere. However, our understanding of how life drove this transition has largely relied on the geological record; much remains unresolved due to the complexity and paucity of the genetic record tied to photosynthesis. Here, through holistic phylogenetic comparison of the bacterial domain and all photosynthetic machinery (totally spanning >10,000 genomes), we identify evolutionary congruence between three independent biological systems-bacteria, (bacterio)chlorophyll-mediated light metabolism (chlorophototrophy), and carbon fixation-and uncover their intertwined history. Our analyses uniformly mapped progenitors of extant light-metabolizing machinery (reaction centers, [bacterio]chlorophyll synthases, and magnesium-chelatases) and enzymes facilitating the Calvin-Benson-Bassham cycle (form I RuBisCO and phosphoribulokinase) to the same ancient Terrabacteria organism near the base of the bacterial domain. These phylogenies consistently showed that extant phototrophs ultimately derived light metabolism from this bacterium, the last phototroph common ancestor (LPCA). LPCA was a non-oxygen-generating (anoxygenic) phototroph that already possessed carbon fixation and two reaction centers, a type I analogous to extant forms and a primitive type II. Analyses also indicate chlorophototrophy originated before LPCA. We further reconstructed evolution of chlorophototrophs/chlorophototrophy post-LPCA, including vertical inheritance in Terrabacteria, the rise of oxygen-generating chlorophototrophy in one descendant branch near the Great Oxidation Event, and subsequent emergence of Cyanobacteria. These collectively unveil a detailed view of the coevolution of light metabolism and Bacteria having clear congruence with the geological record.
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Affiliation(s)
- Arisa Nishihara
- Department of Life Science and Biotechnology, The National Institute of Advanced Industrial Science and Technology, Ibaraki 305-0817, Japan
| | - Yusuke Tsukatani
- Biogeochemistry Research Center, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Kanagawa 237-0061, Japan
- Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Kanagawa 237-0061, Japan
| | - Chihiro Azai
- College of Life Sciences, Ritsumeikan University, Shiga 525-8577, Japan
- Department of Biological Sciences, Faculty of Science and Engineering, Chuo University, Tokyo 112-8551, Japan
| | - Masaru K Nobu
- Department of Life Science and Biotechnology, The National Institute of Advanced Industrial Science and Technology, Ibaraki 305-0817, Japan
- Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Kanagawa 237-0061, Japan
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17
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Olivieri FA, Marti MA, Wetzler DE. Phosphorylation Mechanism Switching in Histidine Kinases Is a Tool for Fast Protein Evolution: Insights From AlphaFold Models. Proteins 2024. [PMID: 38884545 DOI: 10.1002/prot.26708] [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: 12/28/2023] [Revised: 04/08/2024] [Accepted: 05/25/2024] [Indexed: 06/18/2024]
Abstract
Histidine kinases (HKs) are a central part of bacterial environmental-sensing two-component systems. They provide their hosts with the ability to respond to a wide range of physical and chemical signals. HKs are multidomain proteins consisting of at least a sensor domain, dimerization and phosphorylation domain (DHp), and a catalytic domain. They work as homodimers and the existence of two different autophosphorylation mechanisms (cis and trans) has been proposed as relevant for pathway specificity. Although several HKs have been intensively studied, a precise sequence-to-structure explanation of why and how either cis or trans phosphorylation occurs is still unavailable nor is there any evolutionary analysis on the subject. In this work, we show that AlphaFold can accurately determine whether an HK dimerizes in a cis or trans structure. By modeling multiple HKs we show that both cis- and trans-acting HKs are common in nature and the switch between mechanisms has happened multiple times in the evolutionary history of the family. We then use AlphaFold modeling to explore the molecular determinants of the phosphorylation mechanism. We conclude that it is the difference in lengths of the helices surrounding the DHp loop that determines the mechanism. We also show that very small changes in these helices can cause a mechanism switch. Despite this, previous evidence shows that for a particular HK the phosphorylation mechanism is conserved. This suggests that the phosphorylation mechanism participates in system specificity and mechanism switching provides these systems with a way to diverge.
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Affiliation(s)
- Federico A Olivieri
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEN-UBA), Ciudad de Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Concejo Nacional de Investigaciones Cinetíficas y Técnicas (CONICET), Ciudad de Buenos Aires, Argentina
| | - Marcelo A Marti
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEN-UBA), Ciudad de Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Concejo Nacional de Investigaciones Cinetíficas y Técnicas (CONICET), Ciudad de Buenos Aires, Argentina
| | - Diana E Wetzler
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEN-UBA), Ciudad de Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Concejo Nacional de Investigaciones Cinetíficas y Técnicas (CONICET), Ciudad de Buenos Aires, Argentina
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18
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Fox DR, Samuels I, Binks S, Grinter R. The structure of a haemoglobin-nanobody complex reveals human β-subunit-specific interactions. FEBS Lett 2024. [PMID: 38880764 DOI: 10.1002/1873-3468.14958] [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: 03/11/2024] [Revised: 05/10/2024] [Accepted: 05/15/2024] [Indexed: 06/18/2024]
Abstract
Haemoglobin (Hb) is a vital oxygen carrier in vertebrates. Low blood Hb levels may indicate anaemia or genetic disorders, while its presence in the lower digestive system suggests colon cancer. Detecting and quantifying human Hb is essential for medical diagnostics. A nanobody-based sandwich-ELISA test was recently developed utilising llama-derived nanobodies NbE11 and NbB9. These nanobodies specifically bind to human Hb without cross-reacting with Hb from other vertebrates. Here, we determine the crystal structure of NbE11 in complex with human Hb. NbE11 binds Hb with high affinity, predominantly binding the β-Hb subunit. Structural differences between human Hb and other vertebrates at the NbE11 binding interface likely explain the assay's lack of cross-reactivity, providing insights for developing Hb binding diagnostics.
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Affiliation(s)
- Daniel R Fox
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Australia
- Centre for Electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Parkville, Australia
| | - Imogen Samuels
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Australia
| | - Sebastian Binks
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Rhys Grinter
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Australia
- Centre for Electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Parkville, Australia
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Australia
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19
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Dersch L, Stahlhut A, Eichberg J, Paas A, Hardes K, Vilcinskas A, Lüddecke T. Engineering a wolf spider A-family toxin towards increased antimicrobial activity but low toxicity. Toxicon 2024:107810. [PMID: 38880255 DOI: 10.1016/j.toxicon.2024.107810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 06/13/2024] [Accepted: 06/14/2024] [Indexed: 06/18/2024]
Abstract
Spider-derived peptides with insecticidal, antimicrobial and/or cytolytic activities, also known as spider venom antimicrobial peptides (AMPs), can be found in the venoms of RTA-clade spiders. They show translational potential as therapeutic leads. A set of 52 AMPs has been described in the Chinese wolf spider (Lycosa shansia), and many have been shown to exhibit antibacterial effects. Here we explored the potential to enhance their antimicrobial activity using bioengineering. We generated a panel of artificial derivatives of an A-family peptide and screened their activity against selected microbial pathogens, vertebrate cells and insects. In several cases, we increased the antimicrobial activity of the derivatives while retaining the low cytotoxicity of the parental molecule. Furthermore, we injected the peptides into adult Drosophila suzukii and found no evidence of insecticidal effects, confirming the low levels of toxicity. Our data therefore suggest that spider venom linear peptides naturally defend the venom gland against microbial colonization and can be modified into more potent antimicrobial agents that could help to battle infectious diseases in the future.
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Affiliation(s)
- Ludwig Dersch
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Ohlebergsweg 12, 35392 Giessen, Germany; LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325 Frankfurt, Germany
| | - Antonia Stahlhut
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Ohlebergsweg 12, 35392 Giessen, Germany
| | - Johanna Eichberg
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Ohlebergsweg 12, 35392 Giessen, Germany; BMBF Junior Research Group in Infection Research "ASCRIBE", Ohlebergsweg 12, 35392 Giessen, Germany
| | - Anne Paas
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Ohlebergsweg 12, 35392 Giessen, Germany; LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325 Frankfurt, Germany
| | - Kornelia Hardes
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Ohlebergsweg 12, 35392 Giessen, Germany; LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325 Frankfurt, Germany; BMBF Junior Research Group in Infection Research "ASCRIBE", Ohlebergsweg 12, 35392 Giessen, Germany
| | - Andreas Vilcinskas
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Ohlebergsweg 12, 35392 Giessen, Germany; LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325 Frankfurt, Germany; Institute for Insect Biotechnology, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Tim Lüddecke
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Ohlebergsweg 12, 35392 Giessen, Germany; LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325 Frankfurt, Germany
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20
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Dilip H, Thiruvenkatam V, Kirubakaran S. Studies on Methylpyrazole-Substituted Benzimidazoles to Target Helicobacter pylori Infection through HpIMPDH Inhibition. ACS Infect Dis 2024; 10:2262-2275. [PMID: 38787329 DOI: 10.1021/acsinfecdis.4c00228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
The prevalence of Helicobacter pylori infection has been increasing rapidly due to the genetic heterogeneity and antibacterial resistance shown by the bacteria, affecting over 50% of the world population and over 80% of the Indian population, in particular. In this regard, novel drug targets are currently being explored, one of which is the crucial metabolic enzyme inosine-5'-monophosphate dehydrogenase (IMPDH) involved in the de novo nucleotide biosynthesis pathway, in order to combat the infection and devise efficient therapeutic strategies. The present study reports the development of methylpyrazole-substituted benzimidazoles as small molecule inhibitors of H. pylori IMPDH with a nanomolar range of enzyme inhibition. A set of 19 small molecules have been designed, synthesized, and further evaluated for their inhibitory potential against H. pylori IMPDH using in silico, in vitro, biochemical, and biophysical techniques. Compound 7j was found to inhibit H. pylori IMPDH with an IC50 value of 0.095 ± 0.023 μM, which is close to 1.5-fold increase in the inhibitory activity, in comparison to the previously reported benzimidazole-based hit C91. Moreover, kinetic characterization has provided significant insights into the uncompetitive inhibition shown by these small molecules on H. pylori IMPDH, thus providing details about the enzyme inhibition mechanism. In conclusion, methylpyrazole-based small molecules indicate a promising path to develop cheap and bioavailable drugs to efficiently treat H. pylori infection in the coming years, in comparison to the currently available therapy.
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Affiliation(s)
- Haritha Dilip
- Department of Chemistry, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, Gujarat 382055, India
| | - Vijay Thiruvenkatam
- Department of Biological Sciences and Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, Gujarat 382055, India
| | - Sivapriya Kirubakaran
- Department of Chemistry, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, Gujarat 382055, India
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21
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Tzfadia O, Gijsbers A, Vujkovic A, Snobre J, Vargas R, Dewaele K, Meehan CJ, Farhat M, Hakke S, Peters PJ, de Jong BC, Siroy A, Ravelli RBG. Single nucleotide variation catalog from clinical isolates mapped on tertiary and quaternary structures of ESX-1-related proteins reveals critical regions as putative Mtb therapeutic targets. Microbiol Spectr 2024:e0381623. [PMID: 38874407 DOI: 10.1128/spectrum.03816-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 05/02/2024] [Indexed: 06/15/2024] Open
Abstract
Proteins encoded by the ESX-1 genes of interest are essential for full virulence in all Mycobacterium tuberculosis complex (Mtbc) lineages, the pathogens causing the highest mortality worldwide. Identifying critical regions in these ESX-1-related proteins could provide preventive or therapeutic targets for Mtb infection, the game changer needed for tuberculosis control. We analyzed a compendium of whole genome sequences of clinical Mtb isolates from all lineages from >32,000 patients and identified single nucleotide polymorphisms. When mutations corresponding to all non-synonymous single nucleotide polymorphisms were mapped on structural models of the ESX-1 proteins, fully conserved regions emerged. Some could be assigned to known quaternary structures, whereas others could be predicted to be involved in yet-to-be-discovered interactions. Some mutants had clonally expanded (found in >1% of the isolates); these mutants were mostly located at the surface of globular domains, remote from known intra- and inter-molecular protein-protein interactions. Fully conserved intrinsically disordered regions of proteins were found, suggesting that these regions are crucial for the pathogenicity of the Mtbc. Altogether, our findings highlight fully conserved regions of proteins as attractive vaccine antigens and drug targets to control Mtb virulence. Extending this approach to the whole Mtb genome as well as other microorganisms will enhance vaccine development for various pathogens. IMPORTANCE We mapped all non-synonymous single nucleotide polymorphisms onto each of the experimental and predicted ESX-1 proteins' structural models and inspected their placement. Varying sizes of conserved regions were found. Next, we analyzed predicted intrinsically disordered regions within our set of proteins, finding two putative long stretches that are fully conserved, and discussed their potential essential role in immunological recognition. Combined, our findings highlight new targets for interfering with Mycobacterium tuberculosis complex virulence.
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Affiliation(s)
- Oren Tzfadia
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Abril Gijsbers
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Alexandra Vujkovic
- Clinical Virology Unit, Institute of Tropical Medicine, Antwerp, Belgium
- ADReM Data Lab, University of Antwerp, Antwerp, Belgium
| | - Jihad Snobre
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Roger Vargas
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Klaas Dewaele
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Conor J Meehan
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Biosciences, Nottingham Trent University, Nottingham, United Kingdom
| | - Maha Farhat
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Sneha Hakke
- Division of Nanoscopy, Maastricht Multimodal Imaging Institute (M4i), Maastricht University, Maastricht, the Netherlands
| | - Peter J Peters
- Division of Nanoscopy, Maastricht Multimodal Imaging Institute (M4i), Maastricht University, Maastricht, the Netherlands
| | - Bouke C de Jong
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Axel Siroy
- Unité de soutien à l'Institut Européen de Chimie et Biologie (IECB), CNRS, INSERM, IECB, US1, Université de Bordeaux, Pessac, France
| | - Raimond B G Ravelli
- Division of Nanoscopy, Maastricht Multimodal Imaging Institute (M4i), Maastricht University, Maastricht, the Netherlands
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22
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Zhao A, Xian L, Franco Ortega S, Yu G, Macho AP. A bacterial effector manipulates plant metabolism, cell death, and immune responses via independent mechanisms. THE NEW PHYTOLOGIST 2024. [PMID: 38877712 DOI: 10.1111/nph.19899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 05/19/2024] [Indexed: 06/16/2024]
Abstract
Bacterial pathogens inject effector proteins inside plant cells to manipulate cellular functions and achieve a successful infection. The soil-borne pathogen Ralstonia solanacearum (Smith), the causal agent of bacterial wilt disease, secretes > 70 different effectors inside plant cells, although only a handful of them have been thoroughly characterized. One of these effectors, named RipI, is required for full R. solanacearum pathogenicity. RipI associates with plant glutamate decarboxylases (GADs) to promote the accumulation of gamma-aminobutyric acid (GABA), which serves as bacterial nutrient. In this work, we found that RipI can also suppress plant immune responses to bacterial elicitors, which seems to be unrelated to the ability of RipI to induce GABA accumulation and plant cell death. A detailed characterization of the RipI features that contribute to its virulence activities identified two residues at the C-terminal domain that mediate RipI interaction with plant GADs and the subsequent promotion of GABA accumulation. These residues are also required for the appropriate homeostasis of RipI in plant cells and the induction of cell death, although they are partially dispensable for the suppression of plant immune responses. Altogether, we decipher and uncouple the virulence activities of an important bacterial effector at the biochemical level.
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Affiliation(s)
- Achen Zhao
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Liu Xian
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Sara Franco Ortega
- Department of Biology, Centre for Novel Agricultural Products (CNAP), University of York, York, YO10 5DD, UK
| | - Gang Yu
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Alberto P Macho
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
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23
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Peng Z, Lu P, Yang J. AI accurately predicting the structure of biomolecular interactions. Cell Res 2024:10.1038/s41422-024-00991-8. [PMID: 38877084 DOI: 10.1038/s41422-024-00991-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2024] Open
Affiliation(s)
- Zhenling Peng
- MOE Frontiers Science Center for Nonlinear Expectations, Research Center for Mathematics and Interdisciplinary Sciences, Shandong University, Qingdao, Shandong, China
| | - Peilong Lu
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China.
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences and Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China.
| | - Jianyi Yang
- MOE Frontiers Science Center for Nonlinear Expectations, Research Center for Mathematics and Interdisciplinary Sciences, Shandong University, Qingdao, Shandong, China.
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24
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Wang F, He Q, Yao NY, O'Donnell ME, Li H. The human ATAD5 has evolved unique structural elements to function exclusively as a PCNA unloader. Nat Struct Mol Biol 2024:10.1038/s41594-024-01332-4. [PMID: 38871854 DOI: 10.1038/s41594-024-01332-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 05/13/2024] [Indexed: 06/15/2024]
Abstract
Humans have three different proliferating cell nuclear antigen (PCNA) clamp-loading complexes: RFC and CTF18-RFC load PCNA onto DNA, but ATAD5-RFC can only unload PCNA from DNA. The underlying structural basis of ATAD5-RFC unloading is unknown. We show here that ATAD5 has two unique locking loops that appear to tie the complex into a rigid structure, and together with a domain that plugs the DNA-binding chamber, prevent conformation changes required for DNA binding, likely explaining why ATAD5-RFC is exclusively a PCNA unloader. These features are conserved in the yeast PCNA unloader Elg1-RFC. We observe intermediates in which PCNA bound to ATAD5-RFC exists as a closed planar ring, a cracked spiral or a gapped spiral. Surprisingly, ATAD5-RFC can open a PCNA gap between PCNA protomers 2 and 3, different from the PCNA protomers 1 and 3 gap observed in all previously characterized clamp loaders.
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Affiliation(s)
- Feng Wang
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA
| | - Qing He
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA
| | - Nina Y Yao
- DNA Replication Laboratory and Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
| | - Michael E O'Donnell
- DNA Replication Laboratory and Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA.
| | - Huilin Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA.
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25
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Awate OA, Ng D, Stoudenmire JL, Moraes TF, Cornelissen CN. Investigating the importance of selected surface-exposed loops in HpuB for hemoglobin binding and utilization by Neisseria gonorrhoeae. Infect Immun 2024:e0021124. [PMID: 38864605 DOI: 10.1128/iai.00211-24] [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: 05/10/2024] [Accepted: 05/16/2024] [Indexed: 06/13/2024] Open
Abstract
Neisseria gonorrhoeae is the etiological agent of the sexually transmitted infection gonorrhea. The pathogen is a global health challenge since no protective immunity results from infection, and far fewer treatment options are available with increasing antimicrobial resistance. With no efficacious vaccines, researchers are exploring new targets for vaccine development and innovative therapeutics. The outer membrane TonB-dependent transporters (TdTs) produced by N. gonorrhoeae are considered promising vaccine antigens as they are highly conserved and play crucial roles in overcoming nutritional immunity. One of these TdTs is part of the hemoglobin transport system comprised of HpuA and HpuB. This system allows N. gonorrhoeae to acquire iron from hemoglobin (hHb). In the current study, mutations in the hpuB gene were generated to better understand the structure-function relationships in HpuB. This study is one of the first to demonstrate that N. gonorrhoeae can bind to and utilize hemoglobin produced by animals other than humans. This study also determined that when HpuA is absent, mutations targeting extracellular loop 7 of HpuB led to defective hHb binding and utilization. However, when the lipoprotein HpuA is present, these loop 7 mutants recovered their ability to bind hHb, although the growth phenotype remained significantly impaired. Interestingly, loop 7 contains putative heme-binding motifs and a hypothetical α-helical region, both of which may be important for the use of hHb. Taken together, these results highlight the importance of loop 7 in the functionality of HpuB in binding hHb and extracting and internalizing iron.
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Affiliation(s)
- Olivia A Awate
- Institute for Biomedical Sciences, Georgia State University, Atlanta, Georgia, USA
| | - Dixon Ng
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Julie L Stoudenmire
- Institute for Biomedical Sciences, Georgia State University, Atlanta, Georgia, USA
| | - Trevor F Moraes
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
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26
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Sagmeister T, Gubensäk N, Buhlheller C, Grininger C, Eder M, Ðordić A, Millán C, Medina A, Murcia PAS, Berni F, Hynönen U, Vejzović D, Damisch E, Kulminskaya N, Petrowitsch L, Oberer M, Palva A, Malanović N, Codée J, Keller W, Usón I, Pavkov-Keller T. The molecular architecture of Lactobacillus S-layer: Assembly and attachment to teichoic acids. Proc Natl Acad Sci U S A 2024; 121:e2401686121. [PMID: 38838019 DOI: 10.1073/pnas.2401686121] [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: 01/26/2024] [Accepted: 04/26/2024] [Indexed: 06/07/2024] Open
Abstract
S-layers are crystalline arrays found on bacterial and archaeal cells. Lactobacillus is a diverse family of bacteria known especially for potential gut health benefits. This study focuses on the S-layer proteins from Lactobacillus acidophilus and Lactobacillus amylovorus common in the mammalian gut. Atomic resolution structures of Lactobacillus S-layer proteins SlpA and SlpX exhibit domain swapping, and the obtained assembly model of the main S-layer protein SlpA aligns well with prior electron microscopy and mutagenesis data. The S-layer's pore size suggests a protective role, with charged areas aiding adhesion. A highly similar domain organization and interaction network are observed across the Lactobacillus genus. Interaction studies revealed conserved binding areas specific for attachment to teichoic acids. The structure of the SlpA S-layer and the suggested incorporation of SlpX as well as its interaction with teichoic acids lay the foundation for deciphering its role in immune responses and for developing effective treatments for a variety of infectious and bacteria-mediated inflammation processes, opening opportunities for targeted engineering of the S-layer or lactobacilli bacteria in general.
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Affiliation(s)
- Theo Sagmeister
- Institute of Molecular Biosciences, University of Graz, Graz, Austria 8010
| | - Nina Gubensäk
- Institute of Molecular Biosciences, University of Graz, Graz, Austria 8010
| | | | | | - Markus Eder
- Institute of Molecular Biosciences, University of Graz, Graz, Austria 8010
| | - Anđela Ðordić
- Institute of Molecular Biosciences, University of Graz, Graz, Austria 8010
| | - Claudia Millán
- Structural Biology Unit, Institute of Molecular Biology of Barcelona, Spanish National Research Council, Barcelona 08028, Spain
| | - Ana Medina
- Structural Biology Unit, Institute of Molecular Biology of Barcelona, Spanish National Research Council, Barcelona 08028, Spain
| | - Pedro Alejandro Sánchez Murcia
- Laboratory of Computer-Aided Molecular Design, Division of Medicinal Chemistry, Otto-Loewi Research Center, Medical University of Graz, Graz, Austria 8010
| | - Francesca Berni
- Department of Bio-Organic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden 2333, The Netherlands
| | - Ulla Hynönen
- Department of Basic Veterinary Sciences, Division of Microbiology and Epidemiology, University of Helsinki, Helsinki 00100, Finland
| | - Djenana Vejzović
- Institute of Molecular Biosciences, University of Graz, Graz, Austria 8010
| | - Elisabeth Damisch
- Institute of Molecular Biosciences, University of Graz, Graz, Austria 8010
| | | | - Lukas Petrowitsch
- Institute of Molecular Biosciences, University of Graz, Graz, Austria 8010
| | - Monika Oberer
- Institute of Molecular Biosciences, University of Graz, Graz, Austria 8010
- Field of Excellence BioHealth, University of Graz, Graz 8010, Austria
- BioTechMed-Graz, University of Graz, Graz 8010, Austria
| | - Airi Palva
- Department of Basic Veterinary Sciences, Division of Microbiology and Epidemiology, University of Helsinki, Helsinki 00100, Finland
| | - Nermina Malanović
- Institute of Molecular Biosciences, University of Graz, Graz, Austria 8010
- Field of Excellence BioHealth, University of Graz, Graz 8010, Austria
- BioTechMed-Graz, University of Graz, Graz 8010, Austria
| | - Jeroen Codée
- Department of Bio-Organic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden 2333, The Netherlands
| | - Walter Keller
- Institute of Molecular Biosciences, University of Graz, Graz, Austria 8010
- Field of Excellence BioHealth, University of Graz, Graz 8010, Austria
- BioTechMed-Graz, University of Graz, Graz 8010, Austria
| | - Isabel Usón
- Structural Biology Unit, Institute of Molecular Biology of Barcelona, Spanish National Research Council, Barcelona 08028, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona 08003, Spain
| | - Tea Pavkov-Keller
- Institute of Molecular Biosciences, University of Graz, Graz, Austria 8010
- Field of Excellence BioHealth, University of Graz, Graz 8010, Austria
- BioTechMed-Graz, University of Graz, Graz 8010, Austria
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27
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Wang J, Wang X, Chu Y, Li C, Li X, Meng X, Fang Y, No KT, Mao J, Zeng X. Exploring the Conformational Ensembles of Protein-Protein Complex with Transformer-Based Generative Model. J Chem Theory Comput 2024; 20:4469-4480. [PMID: 38816696 DOI: 10.1021/acs.jctc.4c00255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
Protein-protein interactions are the basis of many protein functions, and understanding the contact and conformational changes of protein-protein interactions is crucial for linking the protein structure to biological function. Although difficult to detect experimentally, molecular dynamics (MD) simulations are widely used to study the conformational ensembles and dynamics of protein-protein complexes, but there are significant limitations in sampling efficiency and computational costs. In this study, a generative neural network was trained on protein-protein complex conformations obtained from molecular simulations to directly generate novel conformations with physical realism. We demonstrated the use of a deep learning model based on the transformer architecture to explore the conformational ensembles of protein-protein complexes through MD simulations. The results showed that the learned latent space can be used to generate unsampled conformations of protein-protein complexes for obtaining new conformations complementing pre-existing ones, which can be used as an exploratory tool for the analysis and enhancement of molecular simulations of protein-protein complexes.
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Affiliation(s)
- Jianmin Wang
- The Interdisciplinary Graduate Program in Integrative Biotechnology, Yonsei University, Incheon 21983, Korea
| | - Xun Wang
- School of Computer Science and Technology, China University of Petroleum, Qingdao, Shandong 266580, P. R. China
- High Performance Computer Research Center, University of Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Yanyi Chu
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Chunyan Li
- School of Informatics, Yunnan Normal University, Kunming, Yunnan 650500, P. R. China
| | - Xue Li
- School of Computer Science and Technology, China University of Petroleum, Qingdao, Shandong 266580, P. R. China
| | - Xiangyu Meng
- School of Computer Science and Technology, China University of Petroleum, Qingdao, Shandong 266580, P. R. China
| | - Yitian Fang
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, P. R. China
| | - Kyoung Tai No
- The Interdisciplinary Graduate Program in Integrative Biotechnology, Yonsei University, Incheon 21983, Korea
| | - Jiashun Mao
- School of Medical Information and Engineering, Southwest Medical University, Luzhou, Sichuan 646000, P. R. China
| | - Xiangxiang Zeng
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, Hunan 410082, P. R. China
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28
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Agapov A, Panteleev V, Kropocheva E, Kanevskaya A, Esyunina D, Kulbachinskiy A. Prokaryotic Argonaute nuclease cooperates with co-encoded RNase to acquire guide RNAs and target invader DNA. Nucleic Acids Res 2024; 52:5895-5911. [PMID: 38716875 PMCID: PMC11162769 DOI: 10.1093/nar/gkae345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 04/08/2024] [Accepted: 04/18/2024] [Indexed: 06/11/2024] Open
Abstract
Argonautes are an evolutionary conserved family of programmable nucleases that identify target nucleic acids using small guide oligonucleotides. In contrast to eukaryotic Argonautes (eAgos) that act on RNA, most studied prokaryotic Argonautes (pAgos) recognize DNA targets. Similarly to eAgos, pAgos can protect prokaryotic cells from invaders, but the biogenesis of guide oligonucleotides that confer them specificity to their targets remains poorly understood. Here, we have identified a new group of RNA-guided pAgo nucleases and demonstrated that a representative pAgo from this group, AmAgo from the mesophilic bacterium Alteromonas macleodii, binds guide RNAs of varying lengths for specific DNA targeting. Unlike most pAgos and eAgos, AmAgo is strictly specific to hydroxylated RNA guides containing a 5'-adenosine. AmAgo and related pAgos are co-encoded with a conserved RNA endonuclease from the HEPN superfamily (Ago-associated protein, Agap-HEPN). In vitro, Agap cleaves RNA between guanine and adenine nucleotides producing hydroxylated 5'-A guide oligonucleotides bound by AmAgo. In vivo, Agap cooperates with AmAgo in acquiring guide RNAs and counteracting bacteriophage infection. The AmAgo-Agap pair represents the first example of a pAgo system that autonomously produces RNA guides for DNA targeting and antiviral defense, which holds promise for programmable DNA targeting in biotechnology.
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Affiliation(s)
- Aleksei Agapov
- Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Vladimir Panteleev
- Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russia
| | | | - Anna Kanevskaya
- Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russia
| | - Daria Esyunina
- Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
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29
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Liu S, Yang Q, Zhang L, Luo S. Accurate Protein p Ka Prediction with Physical Organic Chemistry Guided 3D Protein Representation. J Chem Inf Model 2024; 64:4410-4418. [PMID: 38780156 DOI: 10.1021/acs.jcim.4c00354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Protein pKa is a fundamental physicochemical parameter that dictates protein structure and function. However, accurately determining protein site-pKa values remains a substantial challenge, both experimentally and theoretically. In this study, we introduce a physical organic approach, leveraging a protein structural and physical-organic-parameter-based representation (P-SPOC), to develop a rapid and intuitive model for protein pKa prediction. Our P-SPOC model achieves state-of-the-art predictive accuracy, with a mean absolute error (MAE) of 0.33 pKa units. Furthermore, we have incorporated advanced protein structure prediction models, like AlphaFold2, to approximate structures for proteins lacking three-dimensional representations, which enhances the applicability of our model in the context of structure-undetermined protein research. To promote broader accessibility within the research community, an online prediction interface was also established at isyn.luoszgroup.com.
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Affiliation(s)
- Siyuan Liu
- Center of Basic Molecular Science, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Qi Yang
- Center of Basic Molecular Science, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Long Zhang
- Center of Basic Molecular Science, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Sanzhong Luo
- Center of Basic Molecular Science, Department of Chemistry, Tsinghua University, Beijing 100084, China
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Langer LM, Kurscheidt K, Basquin J, Bonneau F, Iermak I, Basquin C, Conti E. UPF1 helicase orchestrates mutually exclusive interactions with the SMG6 endonuclease and UPF2. Nucleic Acids Res 2024; 52:6036-6048. [PMID: 38709891 PMCID: PMC11162806 DOI: 10.1093/nar/gkae323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Revised: 04/06/2024] [Accepted: 04/25/2024] [Indexed: 05/08/2024] Open
Abstract
Nonsense-mediated mRNA decay (NMD) is a conserved co-translational mRNA surveillance and turnover pathway across eukaryotes. NMD has a central role in degrading defective mRNAs and also regulates the stability of a significant portion of the transcriptome. The pathway is organized around UPF1, an RNA helicase that can interact with several NMD-specific factors. In human cells, degradation of the targeted mRNAs begins with a cleavage event that requires the recruitment of the SMG6 endonuclease to UPF1. Previous studies have identified functional links between SMG6 and UPF1, but the underlying molecular mechanisms have remained elusive. Here, we used mass spectrometry, structural biology and biochemical approaches to identify and characterize a conserved short linear motif in SMG6 that interacts with the cysteine/histidine-rich (CH) domain of UPF1. Unexpectedly, we found that the UPF1-SMG6 interaction is precluded when the UPF1 CH domain is engaged with another NMD factor, UPF2. Based on cryo-EM data, we propose that the formation of distinct SMG6-containing and UPF2-containing NMD complexes may be dictated by different conformational states connected to the RNA-binding status of UPF1. Our findings rationalize a key event in metazoan NMD and advance our understanding of mechanisms regulating activity and guiding substrate recognition by the SMG6 endonuclease.
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Affiliation(s)
- Lukas M Langer
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Martinsried/Munich D-82152, Germany
| | - Katharina Kurscheidt
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Martinsried/Munich D-82152, Germany
| | - Jérôme Basquin
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Martinsried/Munich D-82152, Germany
| | - Fabien Bonneau
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Martinsried/Munich D-82152, Germany
| | - Iuliia Iermak
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Martinsried/Munich D-82152, Germany
| | - Claire Basquin
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Martinsried/Munich D-82152, Germany
| | - Elena Conti
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Martinsried/Munich D-82152, Germany
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31
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Urvas L, Chiesa L, Bret G, Jacquemard C, Kellenberger E. Benchmarking AlphaFold-Generated Structures of Chemokine-Chemokine Receptor Complexes. J Chem Inf Model 2024; 64:4587-4600. [PMID: 38809680 DOI: 10.1021/acs.jcim.3c01835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
AlphaFold and AlphaFold-Multimer have become two essential tools for the modeling of unknown structures of proteins and protein complexes. In this work, we extensively benchmarked the quality of chemokine-chemokine receptor structures generated by AlphaFold-Multimer against experimentally determined structures. Our analysis considered both the global quality of the model, as well as key structural features for chemokine recognition. To study the effects of template and multiple sequence alignment parameters on the results, a new prediction pipeline called LIT-AlphaFold (https://github.com/LIT-CCM-lab/LIT-AlphaFold) was developed, allowing extensive input customization. AlphaFold-Multimer correctly predicted differences in chemokine binding orientation and accurately reproduced the unique binding orientation of the CXCL12-ACKR3 complex. Further, the predictions of the full receptor N-terminus provided insights into a putative chemokine recognition site 0.5. The accuracy of chemokine N-terminus binding mode prediction varied between complexes, but the confidence score permitted the distinguishing of residues that were very likely well positioned. Finally, we generated a high-confidence model of the unsolved CXCL12-CXCR4 complex, which agreed with experimental mutagenesis and cross-linking data.
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Affiliation(s)
- Lauri Urvas
- Laboratoire d'Innovation Thérapeutique, UMR 7200 CNRS, Université de Strasbourg, 67400 Illkirch, France
| | - Luca Chiesa
- Laboratoire d'Innovation Thérapeutique, UMR 7200 CNRS, Université de Strasbourg, 67400 Illkirch, France
| | - Guillaume Bret
- Laboratoire d'Innovation Thérapeutique, UMR 7200 CNRS, Université de Strasbourg, 67400 Illkirch, France
| | - Célien Jacquemard
- Laboratoire d'Innovation Thérapeutique, UMR 7200 CNRS, Université de Strasbourg, 67400 Illkirch, France
| | - Esther Kellenberger
- Laboratoire d'Innovation Thérapeutique, UMR 7200 CNRS, Université de Strasbourg, 67400 Illkirch, France
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32
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Rezi CK, Aslanyan MG, Diwan GD, Cheng T, Chamlali M, Junger K, Anvarian Z, Lorentzen E, Pauly KB, Afshar-Bahadori Y, Fernandes EF, Qian F, Tosi S, Christensen ST, Pedersen SF, Strømgaard K, Russell RB, Miner JH, Mahjoub MR, Boldt K, Roepman R, Pedersen LB. DLG1 functions upstream of SDCCAG3 and IFT20 to control ciliary targeting of polycystin-2. EMBO Rep 2024:10.1038/s44319-024-00170-1. [PMID: 38849673 DOI: 10.1038/s44319-024-00170-1] [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: 12/11/2023] [Revised: 05/08/2024] [Accepted: 05/29/2024] [Indexed: 06/09/2024] Open
Abstract
Polarized vesicular trafficking directs specific receptors and ion channels to cilia, but the underlying mechanisms are poorly understood. Here we describe a role for DLG1, a core component of the Scribble polarity complex, in regulating ciliary protein trafficking in kidney epithelial cells. Conditional knockout of Dlg1 in mouse kidney causes ciliary elongation and cystogenesis, and cell-based proximity labeling proteomics and fluorescence microscopy show alterations in the ciliary proteome upon loss of DLG1. Specifically, the retromer-associated protein SDCCAG3, IFT20, and polycystin-2 (PC2) are reduced in the cilia of DLG1-deficient cells compared to control cells. This phenotype is recapitulated in vivo and rescuable by re-expression of wild-type DLG1, but not a Congenital Anomalies of the Kidney and Urinary Tract (CAKUT)-associated DLG1 variant, p.T489R. Finally, biochemical approaches and Alpha Fold modelling suggest that SDCCAG3 and IFT20 form a complex that associates, at least indirectly, with DLG1. Our work identifies a key role for DLG1 in regulating ciliary protein composition and suggests that ciliary dysfunction of the p.T489R DLG1 variant may contribute to CAKUT.
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Affiliation(s)
- Csenge K Rezi
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Mariam G Aslanyan
- Department of Human Genetics, Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Gaurav D Diwan
- BioQuant, Heidelberg University, Heidelberg, Germany
- Biochemistry Center (BZH), Heidelberg University, Heidelberg, Germany
| | - Tao Cheng
- Department of Medicine (Nephrology Division) and Department of Cell Biology and Physiology, Washington University, St Louis, MO, USA
| | - Mohamed Chamlali
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Katrin Junger
- Institute for Ophthalmic Research, Eberhard Karl University of Tübingen, Tübingen, Germany
| | - Zeinab Anvarian
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Esben Lorentzen
- Department of Molecular Biology and Genetics - Protein Science, Aarhus University, Aarhus, Denmark
| | - Kleo B Pauly
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Eduardo Fa Fernandes
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Feng Qian
- Division of Nephrology, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Sébastien Tosi
- Danish BioImaging Infrastructure Image Analysis Core Facility (DBI-INFRA IACF), University of Copenhagen, Copenhagen, Denmark
| | | | - Stine F Pedersen
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kristian Strømgaard
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Robert B Russell
- BioQuant, Heidelberg University, Heidelberg, Germany
- Biochemistry Center (BZH), Heidelberg University, Heidelberg, Germany
| | - Jeffrey H Miner
- Department of Medicine (Nephrology Division) and Department of Cell Biology and Physiology, Washington University, St Louis, MO, USA
| | - Moe R Mahjoub
- Department of Medicine (Nephrology Division) and Department of Cell Biology and Physiology, Washington University, St Louis, MO, USA
| | - Karsten Boldt
- Institute for Ophthalmic Research, Eberhard Karl University of Tübingen, Tübingen, Germany
| | - Ronald Roepman
- Department of Human Genetics, Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Lotte B Pedersen
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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33
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Geiger CJ, Wong GCL, O'Toole GA. A bacterial sense of touch: T4P retraction motor as a means of surface sensing by Pseudomonas aeruginosa PA14. J Bacteriol 2024:e0044223. [PMID: 38832786 DOI: 10.1128/jb.00442-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2024] Open
Abstract
Most microbial cells found in nature exist in matrix-covered, surface-attached communities known as biofilms. This mode of growth is initiated by the ability of the microbe to sense a surface on which to grow. The opportunistic pathogen Pseudomonas aeruginosa (Pa) PA14 utilizes a single polar flagellum and type 4 pili (T4P) to sense surfaces. For Pa, T4P-dependent "twitching" motility is characterized by effectively pulling the cell across a surface through a complex process of cooperative binding, pulling, and unbinding. T4P retraction is powered by hexameric ATPases. Pa cells that have engaged a surface increase production of the second messenger cyclic AMP (cAMP) over multiple generations via the Pil-Chp system. This rise in cAMP allows cells and their progeny to become better adapted for surface attachment and activates virulence pathways through the cAMP-binding transcription factor Vfr. While many studies have focused on mechanisms of T4P twitching and regulation of T4P production and function by the Pil-Chp system, the mechanism by which Pa senses and relays a surface-engagement signal to the cell is still an open question. Here we review the current state of the surface sensing literature for Pa, with a focus on T4P, and propose an integrated model of surface sensing whereby the retraction motor PilT senses and relays the signal to the Pil-Chp system via PilJ to drive cAMP production and adaptation to a surface lifestyle.
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Affiliation(s)
- C J Geiger
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - G C L Wong
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, California, USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California, USA
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California, USA
| | - G A O'Toole
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
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34
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Maruszczak KK, Draczkowski P, Wnorowski A, Chacinska A. Structure prediction analysis of human core TIM23 complex reveals conservation of the protein translocation mechanism. FEBS Open Bio 2024. [PMID: 38837610 DOI: 10.1002/2211-5463.13840] [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: 04/17/2024] [Revised: 05/21/2024] [Accepted: 05/27/2024] [Indexed: 06/07/2024] Open
Abstract
The majority of mitochondrial proteins are encoded in the nucleus, translated on cytosolic ribosomes, and subsequently targeted to the mitochondrial surface. Their further import into the organelle is facilitated by highly specialized protein translocases. Mitochondrial precursor proteins that are destined to the mitochondrial matrix and, to some extent, the inner membrane, utilize translocase of the inner membrane (TIM23). This indispensable import machinery has been extensively studied in yeast. The translocating unit of the TIM23 complex in yeast consists of two membrane proteins, Tim17 and Tim23. In contrast to previous findings, recent reports demonstrate the primary role of Tim17, rather than Tim23, in the translocation of newly synthesized proteins. Very little is known about human TIM23 translocase. Human cells have two orthologs of yeast Tim17, TIMM17A and TIMM17B. Here, using computational tools, we present the architecture of human core TIM23 variants with either TIMM17A or TIMM17B, forming two populations of highly similar complexes. The structures reveal high conservation of the core TIM23 complex between human and yeast. Interestingly, both TIMM17A and TIMM17B variants interact with TIMM23 and reactive oxygen species modulator 1 (ROMO1); a homolog of yeast Mgr2, a protein that can create a channel-like structure with Tim17. The high structural conservation of proteins that form the core TIM23 complex in yeast and humans raises an interesting question about mechanistic and functional differences that justify existence of the two variants of TIM23 in higher eukaryotes.
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Affiliation(s)
| | - Piotr Draczkowski
- National Bioinformatics Infrastructure Sweden, SciLifeLab, Solna, Sweden
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances, Medical University of Lublin, Poland
| | - Artur Wnorowski
- Department of Biopharmacy, Medical University of Lublin, Poland
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35
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Jiang T, Wan G, Zhang H, Gyawali YP, Underbakke ES, Feng C. Mapping the Intersubunit Interdomain FMN-Heme Interactions in Neuronal Nitric Oxide Synthase by Targeted Quantitative Cross-Linking Mass Spectrometry. Biochemistry 2024; 63:1395-1411. [PMID: 38747545 DOI: 10.1021/acs.biochem.4c00157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Nitric oxide synthase (NOS) in mammals is a family of multidomain proteins in which interdomain electron transfer (IET) is controlled by domain-domain interactions. Calmodulin (CaM) binds to the canonical CaM-binding site in the linker region between the FMN and heme domains of NOS and allows tethered FMN domain motions, enabling an intersubunit FMN-heme IET in the output state for NO production. Our previous cross-linking mass spectrometric (XL MS) results demonstrated site-specific protein dynamics in the CaM-responsive regions of rat neuronal NOS (nNOS) reductase construct, a monomeric protein [Jiang et al., Biochemistry, 2023, 62, 2232-2237]. In this work, we have extended our combined approach of XL MS structural mapping and AlphaFold structural prediction to examine the homodimeric nNOS oxygenase/FMN (oxyFMN) construct, an established model of the NOS output state. We employed parallel reaction monitoring (PRM) based quantitative XL MS (qXL MS) to assess the CaM-induced changes in interdomain dynamics and interactions. Intersubunit cross-links were identified by mapping the cross-links onto top AlphaFold structural models, which was complemented by comparing their relative abundances in the cross-linked dimeric and monomeric bands. Furthermore, contrasting the CaM-free and CaM-bound nNOS samples shows that CaM enables the formation of the intersubunit FMN-heme docking complex and that CaM binding induces extensive, allosteric conformational changes across the NOS regions. Moreover, the observed cross-links sites specifically respond to changes in ionic strength. This indicates that interdomain salt bridges are responsible for stabilizing and orienting the output state for efficient FMN-heme IET. Taken together, our targeted qXL MS results have revealed that CaM and ionic strength modulate specific dynamic changes in the CaM/FMN/heme complexes, particularly in the context of intersubunit interdomain FMN-heme interactions.
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Affiliation(s)
- Ting Jiang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Guanghua Wan
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Haikun Zhang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Yadav Prasad Gyawali
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Eric S Underbakke
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011, United States
| | - Changjian Feng
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico, Albuquerque, New Mexico 87131, United States
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
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36
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Dou D, Aiken J, Holzbaur EL. RAB3 phosphorylation by pathogenic LRRK2 impairs trafficking of synaptic vesicle precursors. J Cell Biol 2024; 223:e202307092. [PMID: 38512027 PMCID: PMC10959120 DOI: 10.1083/jcb.202307092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 02/01/2024] [Accepted: 03/04/2024] [Indexed: 03/22/2024] Open
Abstract
Gain-of-function mutations in the LRRK2 gene cause Parkinson's disease (PD), characterized by debilitating motor and non-motor symptoms. Increased phosphorylation of a subset of RAB GTPases by LRRK2 is implicated in PD pathogenesis. We find that increased phosphorylation of RAB3A, a cardinal synaptic vesicle precursor (SVP) protein, disrupts anterograde axonal transport of SVPs in iPSC-derived human neurons (iNeurons) expressing hyperactive LRRK2-p.R1441H. Knockout of the opposing protein phosphatase 1H (PPM1H) in iNeurons phenocopies this effect. In these models, the compartmental distribution of synaptic proteins is altered; synaptophysin and synaptobrevin-2 become sequestered in the neuronal soma with decreased delivery to presynaptic sites along the axon. We find that RAB3A phosphorylation disrupts binding to the motor adaptor MADD, potentially preventing the formation of the RAB3A-MADD-KIF1A/1Bβ complex driving anterograde SVP transport. RAB3A hyperphosphorylation also disrupts interactions with RAB3GAP and RAB-GDI1. Our results reveal a mechanism by which pathogenic hyperactive LRRK2 may contribute to the altered synaptic homeostasis associated with characteristic non-motor and cognitive manifestations of PD.
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Affiliation(s)
- Dan Dou
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Neuroscience Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jayne Aiken
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Erika L.F. Holzbaur
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Neuroscience Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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37
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Cavasotto CN, Di Filippo JI, Scardino V. Lessons learnt from machine learning in early stages of drug discovery. Expert Opin Drug Discov 2024; 19:631-633. [PMID: 38727031 DOI: 10.1080/17460441.2024.2354279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 05/08/2024] [Indexed: 05/22/2024]
Affiliation(s)
- Claudio N Cavasotto
- Computational Drug Design and Biomedical Informatics Laboratory, Instituto de Investigaciones en Medicina Traslacional (IIMT), CONICET-Universidad Austral, Pilar, Buenos Aires, Argentina
- Facultad de Ciencias Biomédicas, Universidad Austral, Pilar, Buenos Aires, Argentina
- Austral Institute for Applied Artificial Intelligence, Universidad Austral, Pilar, Argentina
| | - Juan I Di Filippo
- Facultad de Ciencias Biomédicas, Universidad Austral, Pilar, Buenos Aires, Argentina
- Austral Institute for Applied Artificial Intelligence, Universidad Austral, Pilar, Argentina
- Meton AI, Inc, Wilmington, DE, USA
| | - Valeria Scardino
- Austral Institute for Applied Artificial Intelligence, Universidad Austral, Pilar, Argentina
- Meton AI, Inc, Wilmington, DE, USA
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38
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Geller AM, Shalom M, Zlotkin D, Blum N, Levy A. Identification of type VI secretion system effector-immunity pairs using structural bioinformatics. Mol Syst Biol 2024; 20:702-718. [PMID: 38658795 PMCID: PMC11148199 DOI: 10.1038/s44320-024-00035-8] [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: 01/02/2024] [Revised: 03/24/2024] [Accepted: 04/09/2024] [Indexed: 04/26/2024] Open
Abstract
The type VI secretion system (T6SS) is an important mediator of microbe-microbe and microbe-host interactions. Gram-negative bacteria use the T6SS to inject T6SS effectors (T6Es), which are usually proteins with toxic activity, into neighboring cells. Antibacterial effectors have cognate immunity proteins that neutralize self-intoxication. Here, we applied novel structural bioinformatic tools to perform systematic discovery and functional annotation of T6Es and their cognate immunity proteins from a dataset of 17,920 T6SS-encoding bacterial genomes. Using structural clustering, we identified 517 putative T6E families, outperforming sequence-based clustering. We developed a logistic regression model to reliably quantify protein-protein interaction of new T6E-immunity pairs, yielding candidate immunity proteins for 231 out of the 517 T6E families. We used sensitive structure-based annotation which yielded functional annotations for 51% of the T6E families, again outperforming sequence-based annotation. Next, we validated four novel T6E-immunity pairs using basic experiments in E. coli. In particular, we showed that the Pfam domain DUF3289 is a homolog of Colicin M and that DUF943 acts as its cognate immunity protein. Furthermore, we discovered a novel T6E that is a structural homolog of SleB, a lytic transglycosylase, and identified a specific glutamate that acts as its putative catalytic residue. Overall, this study applies novel structural bioinformatic tools to T6E-immunity pair discovery, and provides an extensive database of annotated T6E-immunity pairs.
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Affiliation(s)
- Alexander M Geller
- Department of Plant Pathology and Microbiology, The Institute of Environmental Science, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Maor Shalom
- Department of Plant Pathology and Microbiology, The Institute of Environmental Science, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - David Zlotkin
- Department of Plant Pathology and Microbiology, The Institute of Environmental Science, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Noam Blum
- Department of Plant Pathology and Microbiology, The Institute of Environmental Science, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Asaf Levy
- Department of Plant Pathology and Microbiology, The Institute of Environmental Science, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel.
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39
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Abramson J, Adler J, Dunger J, Evans R, Green T, Pritzel A, Ronneberger O, Willmore L, Ballard AJ, Bambrick J, Bodenstein SW, Evans DA, Hung CC, O'Neill M, Reiman D, Tunyasuvunakool K, Wu Z, Žemgulytė A, Arvaniti E, Beattie C, Bertolli O, Bridgland A, Cherepanov A, Congreve M, Cowen-Rivers AI, Cowie A, Figurnov M, Fuchs FB, Gladman H, Jain R, Khan YA, Low CMR, Perlin K, Potapenko A, Savy P, Singh S, Stecula A, Thillaisundaram A, Tong C, Yakneen S, Zhong ED, Zielinski M, Žídek A, Bapst V, Kohli P, Jaderberg M, Hassabis D, Jumper JM. Accurate structure prediction of biomolecular interactions with AlphaFold 3. Nature 2024; 630:493-500. [PMID: 38718835 PMCID: PMC11168924 DOI: 10.1038/s41586-024-07487-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 04/29/2024] [Indexed: 06/13/2024]
Abstract
The introduction of AlphaFold 21 has spurred a revolution in modelling the structure of proteins and their interactions, enabling a huge range of applications in protein modelling and design2-6. Here we describe our AlphaFold 3 model with a substantially updated diffusion-based architecture that is capable of predicting the joint structure of complexes including proteins, nucleic acids, small molecules, ions and modified residues. The new AlphaFold model demonstrates substantially improved accuracy over many previous specialized tools: far greater accuracy for protein-ligand interactions compared with state-of-the-art docking tools, much higher accuracy for protein-nucleic acid interactions compared with nucleic-acid-specific predictors and substantially higher antibody-antigen prediction accuracy compared with AlphaFold-Multimer v.2.37,8. Together, these results show that high-accuracy modelling across biomolecular space is possible within a single unified deep-learning framework.
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Affiliation(s)
| | - Jonas Adler
- Core Contributor, Google DeepMind, London, UK
| | - Jack Dunger
- Core Contributor, Google DeepMind, London, UK
| | | | - Tim Green
- Core Contributor, Google DeepMind, London, UK
| | | | | | | | | | | | | | | | | | | | | | | | - Zachary Wu
- Core Contributor, Google DeepMind, London, UK
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Yousuf A Khan
- Google DeepMind, London, UK
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA
| | | | | | | | | | | | | | | | | | | | - Ellen D Zhong
- Google DeepMind, London, UK
- Department of Computer Science, Princeton University, Princeton, NJ, USA
| | | | | | | | | | | | - Demis Hassabis
- Core Contributor, Google DeepMind, London, UK.
- Core Contributor, Isomorphic Labs, London, UK.
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40
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Storozhuk O, Bruekner SR, Paul A, Lebbink JHG, Sixma TK, Friedhoff P. MutL Activates UvrD by Interaction Between the MutL C-terminal Domain and the UvrD 2B Domain. J Mol Biol 2024; 436:168589. [PMID: 38677494 DOI: 10.1016/j.jmb.2024.168589] [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: 02/16/2024] [Revised: 04/14/2024] [Accepted: 04/19/2024] [Indexed: 04/29/2024]
Abstract
UvrD is a helicase vital for DNA replication and quality control processes. In its monomeric state, UvrD exhibits limited helicase activity, necessitating either dimerization or assistance from an accessory protein to efficiently unwind DNA. Within the DNA mismatch repair pathway, MutL plays a pivotal role in relaying the repair signal, enabling UvrD to unwind DNA from the strand incision site up to and beyond the mismatch. Although this interdependence is well-established, the precise mechanism of activation and the specific MutL-UvrD interactions that trigger helicase activity remain elusive. To address these questions, we employed site-specific crosslinking techniques using single-cysteine variants of MutL and UvrD followed by functional assays. Our investigation unveils that the C-terminal domain of MutL not only engages with UvrD but also acts as a self-sufficient activator of UvrD helicase activity on DNA substrates with 3'-single-stranded tails. Especially when MutL is covalently attached to the 2B or 1B domain the tail length can be reduced to a minimal substrate of 5 nucleotides without affecting unwinding efficiency.
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Affiliation(s)
- Olha Storozhuk
- Institute for Biochemistry, FB 08, Justus Liebig University, Heinrich-Buff-Ring 17, D-35392 Giessen, Germany
| | - Susanne R Bruekner
- Division of Biochemistry, Netherlands Cancer Institute and Oncode Institute, Amsterdam, the Netherlands
| | - Ankon Paul
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Joyce H G Lebbink
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands; Department of Radiotherapy, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Titia K Sixma
- Division of Biochemistry, Netherlands Cancer Institute and Oncode Institute, Amsterdam, the Netherlands
| | - Peter Friedhoff
- Institute for Biochemistry, FB 08, Justus Liebig University, Heinrich-Buff-Ring 17, D-35392 Giessen, Germany.
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41
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Chatterjee P, Garcia MA, Cote JA, Yun K, Legerme GP, Habib R, Tripepi M, Young C, Kulp D, Dyall-Smith M, Pohlschroder M. Involvement of ArlI, ArlJ, and CirA in archaeal type IV pilin-mediated motility regulation. J Bacteriol 2024:e0008924. [PMID: 38819156 DOI: 10.1128/jb.00089-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 05/06/2024] [Indexed: 06/01/2024] Open
Abstract
Many prokaryotes use swimming motility to move toward favorable conditions and escape adverse surroundings. Regulatory mechanisms governing bacterial flagella-driven motility are well-established; however, little is yet known about the regulation underlying swimming motility propelled by the archaeal cell surface structure, the archaella. Previous research showed that the deletion of the adhesion pilins (PilA1-6), subunits of the type IV pili cell surface structure, renders the model archaeon Haloferax volcanii non-motile. In this study, we used ethyl methanesulfonate mutagenesis and a motility assay to identify motile suppressors of the ∆pilA[1-6] strain. Of the eight suppressors identified, six contain missense mutations in archaella biosynthesis genes, arlI and arlJ. In trans expression of arlI and arlJ mutant constructs in the respective multi-deletion strains ∆pilA[1-6]∆arlI and ∆pilA[1-6]∆arlJ confirmed their role in suppressing the ∆pilA[1-6] motility defect. Additionally, three suppressors harbor co-occurring disruptive missense and nonsense mutations in cirA, a gene encoding a proposed regulatory protein. A deletion of cirA resulted in hypermotility, while cirA expression in trans in wild-type cells led to decreased motility. Moreover, quantitative real-time PCR analysis revealed that in wild-type cells, higher expression levels of arlI, arlJ, and the archaellin gene arlA1 were observed in motile early-log phase rod-shaped cells compared to non-motile mid-log phase disk-shaped cells. Conversely, ∆cirA cells, which form rods during both early- and mid-log phases, exhibited similar expression levels of arl genes in both growth phases. Our findings contribute to a deeper understanding of the mechanisms governing archaeal motility, highlighting the involvement of ArlI, ArlJ, and CirA in pilin-mediated motility regulation.IMPORTANCEArchaea are close relatives of eukaryotes and play crucial ecological roles. Certain behaviors, such as swimming motility, are thought to be important for archaeal environmental adaptation. Archaella, the archaeal motility appendages, are evolutionarily distinct from bacterial flagella, and the regulatory mechanisms driving archaeal motility are largely unknown. Previous research has linked the loss of type IV pili subunits to archaeal motility suppression. This study reveals three Haloferax volcanii proteins involved in pilin-mediated motility regulation, offering a deeper understanding of motility regulation in this understudied domain while also paving the way for uncovering novel mechanisms that govern archaeal motility. Understanding archaeal cellular processes will help elucidate the ecological roles of archaea as well as the evolution of these processes across domains.
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Affiliation(s)
- Priyanka Chatterjee
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Marco A Garcia
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jacob A Cote
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kun Yun
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Georgio P Legerme
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Rumi Habib
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, Pennsylvania, USA
| | - Manuela Tripepi
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Criston Young
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Daniel Kulp
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, Pennsylvania, USA
| | - Mike Dyall-Smith
- Computational Biology Group, Max Planck Institute of Biochemistry, Martinsried, Germany
- Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Australia
| | - Mecky Pohlschroder
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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42
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Kitta S, Kaminishi T, Higashi M, Shima T, Nishino K, Nakamura N, Kosako H, Yoshimori T, Kuma A. YIPF3 and YIPF4 regulate autophagic turnover of the Golgi apparatus. EMBO J 2024:10.1038/s44318-024-00131-3. [PMID: 38822137 DOI: 10.1038/s44318-024-00131-3] [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: 08/08/2023] [Revised: 04/21/2024] [Accepted: 05/08/2024] [Indexed: 06/02/2024] Open
Abstract
The degradation of organelles by autophagy is essential for cellular homeostasis. The Golgi apparatus has recently been demonstrated to be degraded by autophagy, but little is known about how the Golgi is recognized by the forming autophagosome. Using quantitative proteomic analysis and two novel Golgiphagy reporter systems, we found that the five-pass transmembrane Golgi-resident proteins YIPF3 and YIPF4 constitute a Golgiphagy receptor. The interaction of this complex with LC3B, GABARAP, and GABARAPL1 is dependent on a LIR motif within YIPF3 and putative phosphorylation sites immediately upstream; the stability of the complex is governed by YIPF4. Expression of a YIPF3 protein containing a mutated LIR motif caused an elongated Golgi morphology, indicating the importance of Golgi turnover via selective autophagy. The reporter assays reported here may be readily adapted to different experimental contexts to help deepen our understanding of Golgiphagy.
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Affiliation(s)
- Shinri Kitta
- Department of Genetics, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Tatsuya Kaminishi
- Department of Genetics, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Osaka, 565-0871, Japan
| | - Momoko Higashi
- Laboratory of Intracellular Membrane Dynamics, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Takayuki Shima
- Department of Genetics, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Kohei Nishino
- Division of Cell Signaling, Fujii Memorial Institute of Medical Sciences, Institute of Advanced Medical Sciences, Tokushima University, Tokushima, 770-8503, Japan
| | - Nobuhiro Nakamura
- Faculty of Life Sciences, Kyoto Sangyo University, Motoyama, Kamigamo, Kita, Kyoto, 603-8555, Japan
| | - Hidetaka Kosako
- Division of Cell Signaling, Fujii Memorial Institute of Medical Sciences, Institute of Advanced Medical Sciences, Tokushima University, Tokushima, 770-8503, Japan
| | - Tamotsu Yoshimori
- Department of Genetics, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan.
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Osaka, 565-0871, Japan.
- Laboratory of Intracellular Membrane Dynamics, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, 565-0871, Japan.
| | - Akiko Kuma
- Department of Genetics, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan.
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan.
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43
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Kadavá T, Hevler JF, Kalaidopoulou Nteak S, Yin VC, Strasser J, Preiner J, Heck AJ. Higher-order structure and proteoforms of co-occurring C4b-binding protein assemblies in human serum. EMBO J 2024:10.1038/s44318-024-00128-y. [PMID: 38811852 DOI: 10.1038/s44318-024-00128-y] [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: 12/15/2023] [Revised: 05/03/2024] [Accepted: 05/08/2024] [Indexed: 05/31/2024] Open
Abstract
The complement is a conserved cascade that plays a central role in the innate immune system. To maintain a delicate equilibrium preventing excessive complement activation, complement inhibitors are essential. One of the major fluid-phase complement inhibitors is C4b-binding protein (C4BP). Human C4BP is a macromolecular glycoprotein composed of two distinct subunits, C4BPα and C4BPβ. These associate with vitamin K-dependent protein S (ProS) forming an ensemble of co-occurring higher-order structures. Here, we characterize these C4BP assemblies. We resolve and quantify isoforms of purified human serum C4BP using distinct single-particle detection techniques: charge detection mass spectrometry, and mass photometry accompanied by high-speed atomic force microscopy. Combining cross-linking mass spectrometry, glycoproteomics, and structural modeling, we report comprehensive glycoproteoform profiles and full-length structural models of the endogenous C4BP assemblies, expanding knowledge of this key complement inhibitor's structure and composition. Finally, we reveal that an increased C4BPα to C4BPβ ratio coincides with elevated C-reactive protein levels in patient plasma samples. This observation highlights C4BP isoform variation and affirms a distinct role of co-occurring C4BP assemblies upon acute phase inflammation.
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Affiliation(s)
- Tereza Kadavá
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, Utrecht, 3584 CH, the Netherlands
- Netherlands Proteomics Center, Padualaan 8, Utrecht, 3584 CH, the Netherlands
| | - Johannes F Hevler
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, Utrecht, 3584 CH, the Netherlands
- Netherlands Proteomics Center, Padualaan 8, Utrecht, 3584 CH, the Netherlands
| | - Sofia Kalaidopoulou Nteak
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, Utrecht, 3584 CH, the Netherlands
- Netherlands Proteomics Center, Padualaan 8, Utrecht, 3584 CH, the Netherlands
| | - Victor C Yin
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, Utrecht, 3584 CH, the Netherlands
- Netherlands Proteomics Center, Padualaan 8, Utrecht, 3584 CH, the Netherlands
| | - Juergen Strasser
- University of Applied Sciences Upper Austria, 4020, Linz, Austria
| | - Johannes Preiner
- University of Applied Sciences Upper Austria, 4020, Linz, Austria
| | - Albert Jr Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, Utrecht, 3584 CH, the Netherlands.
- Netherlands Proteomics Center, Padualaan 8, Utrecht, 3584 CH, the Netherlands.
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44
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Jänes J, Müller M, Selvaraj S, Manoel D, Stephenson J, Gonçalves C, Lafita A, Polacco B, Obernier K, Alasoo K, Lemos MC, Krogan N, Martin M, Saraiva LR, Burke D, Beltrao P. Predicted mechanistic impacts of human protein missense variants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.29.596373. [PMID: 38854010 PMCID: PMC11160786 DOI: 10.1101/2024.05.29.596373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Genome sequencing efforts have led to the discovery of tens of millions of protein missense variants found in the human population with the majority of these having no annotated role and some likely contributing to trait variation and disease. Sequence-based artificial intelligence approaches have become highly accurate at predicting variants that are detrimental to the function of proteins but they do not inform on mechanisms of disruption. Here we combined sequence and structure-based methods to perform proteome-wide prediction of deleterious variants with information on their impact on protein stability, protein-protein interactions and small-molecule binding pockets. AlphaFold2 structures were used to predict approximately 100,000 small-molecule binding pockets and stability changes for over 200 million variants. To inform on protein-protein interfaces we used AlphaFold2 to predict structures for nearly 500,000 protein complexes. We illustrate the value of mechanism-aware variant effect predictions to study the relation between protein stability and abundance and the structural properties of interfaces underlying trans protein quantitative trait loci (pQTLs). We characterised the distribution of mechanistic impacts of protein variants found in patients and experimentally studied example disease linked variants in FGFR1.
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Affiliation(s)
- Jürgen Jänes
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Marc Müller
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Senthil Selvaraj
- Sidra Medicine, Doha, Qatar
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Diogo Manoel
- Sidra Medicine, Doha, Qatar
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - James Stephenson
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge CB10 1SD, UK
- Open Targets, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Catarina Gonçalves
- Sidra Medicine, Doha, Qatar
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | | | - Benjamin Polacco
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
| | - Kirsten Obernier
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
| | - Kaur Alasoo
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Manuel C. Lemos
- CICS-UBI, Health Sciences Research Centre, University of Beira Interior, 6200-506, Covilhã, Portugal
| | - Nevan Krogan
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
| | - Maria Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge CB10 1SD, UK
- Open Targets, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Luis R. Saraiva
- Sidra Medicine, Doha, Qatar
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - David Burke
- Faculty of Life Sciences and Medicine, King’s College, London, UK
| | - Pedro Beltrao
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge CB10 1SD, UK
- Open Targets, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
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45
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Agbavor C, Zimnicka A, Kumar A, George JL, Torres M, Prehna G, Alonzo F, Durrant JD, Freitag NE, Cahoon LA. The chaperone PrsA2 regulates the secretion, stability, and folding of listeriolysin O during Listeria monocytogenes infection. mBio 2024:e0074324. [PMID: 38809022 DOI: 10.1128/mbio.00743-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Accepted: 04/22/2024] [Indexed: 05/30/2024] Open
Abstract
Pathogenic bacteria rely on secreted virulence factors to cause disease in susceptible hosts. However, in Gram-positive bacteria, the mechanisms underlying secreted protein activation and regulation post-membrane translocation remain largely unknown. Using proteomics, we identified several proteins that are dependent on the secreted chaperone PrsA2. We followed with phenotypic, biochemical, and biophysical assays and computational analyses to examine the regulation of a detected key secreted virulence factor, listeriolysin O (LLO), and its interaction with PrsA2 from the bacterial pathogen Listeria monocytogenes (Lm). Critical to Lm virulence is internalization by host cells and the subsequent action of the cholesterol-dependent pore-forming toxin, LLO, which enables bacterial escape from the host cell phagosome. Since Lm is a Gram-positive organism, the space between the cell membrane and wall is solvent exposed. Therefore, we hypothesized that the drop from neutral to acidic pH as the pathogen is internalized into a phagosome is critical to regulating the interaction of PrsA2 with LLO. Here, we demonstrate that PrsA2 directly interacts with LLO in a pH-dependent manner. We show that PrsA2 protects and sequesters LLO under neutral pH conditions where LLO can be observed to aggregate. In addition, we identify molecular features of PrsA2 that are required for interaction and ultimately the folding and activity of LLO. Moreover, protein-complex modeling suggests that PrsA2 interacts with LLO via its cholesterol-binding domain. These findings highlight a mechanism by which a Gram-positive secretion chaperone regulates the secretion, stability, and folding of a pore-forming toxin under conditions relevant to host cell infection. IMPORTANCE Lm is a ubiquitous food-borne pathogen that can cause severe disease to vulnerable populations. During infection, Lm relies on a wide repertoire of secreted virulence factors including the LLO that enables the bacterium to invade the host and spread from cell to cell. After membrane translocation, secreted factors must become active in the challenging bacterial cell membrane-wall interface. However, the mechanisms required for secreted protein folding and function are largely unknown. Lm encodes a chaperone, PrsA2, that is critical for the activity of secreted factors. Here, we show that PrsA2 directly associates and protects the major Lm virulence factor, LLO, under conditions corresponding to the host cytosol, where LLO undergoes irreversible denaturation. Additionally, we identify molecular features of PrsA2 that enable its interaction with LLO. Together, our results suggest that Lm and perhaps other Gram-positive bacteria utilize secreted chaperones to regulate the activity of pore-forming toxins during infection.
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Affiliation(s)
- Charles Agbavor
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Adriana Zimnicka
- Department of Pharmaceutical Sciences, University of Illinois Chicago, Chicago, Illinois, USA
| | - Allison Kumar
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Jada L George
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Madeline Torres
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Gerd Prehna
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Francis Alonzo
- Department of Microbiology and Immunology, University of Illinois Chicago, Chicago, Illinois, USA
| | - Jacob D Durrant
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Nancy E Freitag
- Department of Pharmaceutical Sciences, University of Illinois Chicago, Chicago, Illinois, USA
| | - Laty A Cahoon
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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46
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Johnson LG, Zhai C, Brown K, Prenni JE, N Nair M, Huff-Lonergan E, Lonergan SM. Secondary Lipid Oxidation Products as Modulators of Calpain-2 Functionality In Vitro. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:12229-12239. [PMID: 38743679 DOI: 10.1021/acs.jafc.4c00335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The objective was to understand the impacts of secondary lipid oxidation products on calpain-2 activity and autolysis and, subsequently, to determine the quantity and localization of modification sites. 2-Hexenal and 4-hydroxynonenal incubation significantly decreased calpain-2 activity and slowed the progression of autolysis, while malondialdehyde had minimal impact on calpain-2 activity and autolysis. Specific modification sites were determined with LC-MS/MS, including distinct malondialdehyde modification sites on the calpain-2 catalytic and regulatory subunits. 2-Hexenal modification sites were observed on the calpain-2 catalytic subunit. Intact protein mass analysis with MALDI-MS revealed that a significant number of modifications on the calpain-2 catalytic and regulatory subunits are likely to exist. These observations confirm that specific lipid oxidation products modify calpain-2 and may affect the calpain-2 functionality. The results of these novel experiments have implications for healthy tissue metabolism, skeletal muscle growth, and post-mortem meat tenderness development.
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Affiliation(s)
- Logan G Johnson
- Department of Animal Science, Iowa State University, Ames, Iowa 50011, United States
| | - Chaoyu Zhai
- Department of Animal Science, University of Connecticut, Storrs, Connecticut 06269, United States
- Department of Animal Sciences, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Kitty Brown
- Analytical Resources Core- Bioanalysis & Omics, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Jessica E Prenni
- Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Mahesh N Nair
- Department of Animal Sciences, Colorado State University, Fort Collins, Colorado 80523, United States
| | | | - Steven M Lonergan
- Department of Animal Science, Iowa State University, Ames, Iowa 50011, United States
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47
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Gao S, Carrasquillo Rodríguez JW, Bahmanyar S, Airola MV. Structure and mechanism of the human CTDNEP1-NEP1R1 membrane protein phosphatase complex necessary to maintain ER membrane morphology. Proc Natl Acad Sci U S A 2024; 121:e2321167121. [PMID: 38776370 PMCID: PMC11145253 DOI: 10.1073/pnas.2321167121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 04/12/2024] [Indexed: 05/25/2024] Open
Abstract
C-terminal Domain Nuclear Envelope Phosphatase 1 (CTDNEP1) is a noncanonical protein serine/threonine phosphatase that has a conserved role in regulating ER membrane biogenesis. Inactivating mutations in CTDNEP1 correlate with the development of medulloblastoma, an aggressive childhood cancer. The transmembrane protein Nuclear Envelope Phosphatase 1 Regulatory Subunit 1 (NEP1R1) binds CTDNEP1, but the molecular details by which NEP1R1 regulates CTDNEP1 function are unclear. Here, we find that knockdown of NEP1R1 generates identical phenotypes to reported loss of CTDNEP1 in mammalian cells, establishing CTDNEP1-NEP1R1 as an evolutionarily conserved membrane protein phosphatase complex that restricts ER expansion. Mechanistically, NEP1R1 acts as an activating regulatory subunit that directly binds and increases the phosphatase activity of CTDNEP1. By defining a minimal NEP1R1 domain sufficient to activate CTDNEP1, we determine high-resolution crystal structures of the CTDNEP1-NEP1R1 complex bound to a peptide sequence acting as a pseudosubstrate. Structurally, NEP1R1 engages CTDNEP1 at a site distant from the active site to stabilize and allosterically activate CTDNEP1. Substrate recognition is facilitated by a conserved Arg residue in CTDNEP1 that binds and orients the substrate peptide in the active site. Together, this reveals mechanisms for how NEP1R1 regulates CTDNEP1 and explains how cancer-associated mutations inactivate CTDNEP1.
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Affiliation(s)
- Shujuan Gao
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY11794
| | | | - Shirin Bahmanyar
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT06511
| | - Michael V. Airola
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY11794
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48
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Xie C, Chen G, Li M, Huang P, Chen Z, Lei K, Li D, Wang Y, Cleetus A, Mohamed MA, Sonar P, Feng W, Ökten Z, Ou G. Neurons dispose of hyperactive kinesin into glial cells for clearance. EMBO J 2024:10.1038/s44318-024-00118-0. [PMID: 38806659 DOI: 10.1038/s44318-024-00118-0] [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: 11/22/2023] [Revised: 04/06/2024] [Accepted: 04/25/2024] [Indexed: 05/30/2024] Open
Abstract
Microtubule-based kinesin motor proteins are crucial for intracellular transport, but their hyperactivation can be detrimental for cellular functions. This study investigated the impact of a constitutively active ciliary kinesin mutant, OSM-3CA, on sensory cilia in C. elegans. Surprisingly, we found that OSM-3CA was absent from cilia but underwent disposal through membrane abscission at the tips of aberrant neurites. Neighboring glial cells engulf and eliminate the released OSM-3CA, a process that depends on the engulfment receptor CED-1. Through genetic suppressor screens, we identified intragenic mutations in the OSM-3CA motor domain and mutations inhibiting the ciliary kinase DYF-5, both of which restored normal cilia in OSM-3CA-expressing animals. We showed that conformational changes in OSM-3CA prevent its entry into cilia, and OSM-3CA disposal requires its hyperactivity. Finally, we provide evidence that neurons also dispose of hyperactive kinesin-1 resulting from a clinic variant associated with amyotrophic lateral sclerosis, suggesting a widespread mechanism for regulating hyperactive kinesins.
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Affiliation(s)
- Chao Xie
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
- Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China
- McGovern Institute for Brain Research, Tsinghua University, Beijing, China
- State Key Laboratory for Membrane Biology, Beijing, China
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Guanghan Chen
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
- Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China
- McGovern Institute for Brain Research, Tsinghua University, Beijing, China
- State Key Laboratory for Membrane Biology, Beijing, China
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Ming Li
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
- Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China
- McGovern Institute for Brain Research, Tsinghua University, Beijing, China
- State Key Laboratory for Membrane Biology, Beijing, China
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Peng Huang
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
- Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China
- McGovern Institute for Brain Research, Tsinghua University, Beijing, China
- State Key Laboratory for Membrane Biology, Beijing, China
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Zhe Chen
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
- Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China
- McGovern Institute for Brain Research, Tsinghua University, Beijing, China
- State Key Laboratory for Membrane Biology, Beijing, China
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Kexin Lei
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
- Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China
- McGovern Institute for Brain Research, Tsinghua University, Beijing, China
- State Key Laboratory for Membrane Biology, Beijing, China
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Dong Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, 100101, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Yuhe Wang
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
- Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China
- McGovern Institute for Brain Research, Tsinghua University, Beijing, China
- State Key Laboratory for Membrane Biology, Beijing, China
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Augustine Cleetus
- Physik Department E22, Technische Universitat Munchen, James-Franck-Strasse, Garching, 85748, Germany
| | - Mohamed Aa Mohamed
- Physik Department E22, Technische Universitat Munchen, James-Franck-Strasse, Garching, 85748, Germany
| | - Punam Sonar
- Physik Department E22, Technische Universitat Munchen, James-Franck-Strasse, Garching, 85748, Germany
| | - Wei Feng
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, 100101, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Zeynep Ökten
- Physik Department E22, Technische Universitat Munchen, James-Franck-Strasse, Garching, 85748, Germany
| | - Guangshuo Ou
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China.
- Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China.
- McGovern Institute for Brain Research, Tsinghua University, Beijing, China.
- State Key Laboratory for Membrane Biology, Beijing, China.
- School of Life Sciences, Tsinghua University, Beijing, China.
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49
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Hsiao MH, Miao Y, Liu Z, Schütze K, Limjunyawong N, Chien DCC, Monteiro WD, Chu LS, Morgenlander W, Jayaraman S, Jang SE, Gray JJ, Zhu H, Dong X, Steinegger M, Larman HB. Molecular Display of the Animal Meta-Venome for Discovery of Novel Therapeutic Peptides. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.27.595990. [PMID: 38854075 PMCID: PMC11160688 DOI: 10.1101/2024.05.27.595990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Animal venoms, distinguished by their unique structural features and potent bioactivities, represent a vast and relatively untapped reservoir of therapeutic molecules. However, limitations associated with extracting or expressing large numbers of individual venoms and venom-like molecules have precluded their therapeutic evaluation via high throughput screening. Here, we developed an innovative computational approach to design a highly diverse library of animal venoms and "metavenoms". We employed programmable M13 hyperphage display to preserve critical disulfide-bonded structures for highly parallelized single-round biopanning with quantitation via high-throughput DNA sequencing. Our approach led to the discovery of Kunitz type domain containing proteins that target the human itch receptor Mas-related G protein-coupled receptor X4 (MRGPRX4), which plays a crucial role in itch perception. Deep learning-based structural homology mining identified two endogenous human homologs, tissue factor pathway inhibitor (TFPI) and serine peptidase inhibitor, Kunitz type 2 (SPINT2), which exhibit agonist-dependent potentiation of MRGPRX4. Highly multiplexed screening of animal venoms and metavenoms is therefore a promising approach to uncover new drug candidates.
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Affiliation(s)
- Meng-Hsuan Hsiao
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- These authors contributed equally to this work
| | - Yang Miao
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Biomedical Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- These authors contributed equally to this work
| | - Zixing Liu
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Biology, Zanvyl Krieger School of Arts and Sciences, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Konstantin Schütze
- School of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Nathachit Limjunyawong
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Center of Research Excellence in Allergy and Immunology, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Thailand
| | - Daphne Chun-Che Chien
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Wayne Denis Monteiro
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Lee-Shin Chu
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - William Morgenlander
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Sahana Jayaraman
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Sung-eun Jang
- School of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Jeffrey J. Gray
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Heng Zhu
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Viral Oncology Program, Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Xinzhong Dong
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Martin Steinegger
- School of Biological Sciences, Seoul National University, Seoul, South Korea
- Artificial Intelligence Institute, Seoul National University, Seoul, South Korea
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea
| | - H. Benjamin Larman
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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50
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Nechushtai R, Rowland L, Karmi O, Marjault HB, Nguyen TT, Mittal S, Ahmed RS, Grant D, Manrique-Acevedo C, Morcos F, Onuchic JN, Mittler R. CISD3/MiNT is required for complex I function, mitochondrial integrity, and skeletal muscle maintenance. Proc Natl Acad Sci U S A 2024; 121:e2405123121. [PMID: 38781208 PMCID: PMC11145280 DOI: 10.1073/pnas.2405123121] [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: 03/12/2024] [Accepted: 04/23/2024] [Indexed: 05/25/2024] Open
Abstract
Mitochondria play a central role in muscle metabolism and function. A unique family of iron-sulfur proteins, termed CDGSH Iron Sulfur Domain-containing (CISD/NEET) proteins, support mitochondrial function in skeletal muscles. The abundance of these proteins declines during aging leading to muscle degeneration. Although the function of the outer mitochondrial CISD/NEET proteins, CISD1/mitoNEET and CISD2/NAF-1, has been defined in skeletal muscle cells, the role of the inner mitochondrial CISD protein, CISD3/MiNT, is currently unknown. Here, we show that CISD3 deficiency in mice results in muscle atrophy that shares proteomic features with Duchenne muscular dystrophy. We further reveal that CISD3 deficiency impairs the function and structure of skeletal muscles, as well as their mitochondria, and that CISD3 interacts with, and donates its [2Fe-2S] clusters to, complex I respiratory chain subunit NADH Ubiquinone Oxidoreductase Core Subunit V2 (NDUFV2). Using coevolutionary and structural computational tools, we model a CISD3-NDUFV2 complex with proximal coevolving residue interactions conducive of [2Fe-2S] cluster transfer reactions, placing the clusters of the two proteins 10 to 16 Å apart. Taken together, our findings reveal that CISD3/MiNT is important for supporting the biogenesis and function of complex I, essential for muscle maintenance and function. Interventions that target CISD3 could therefore impact different muscle degeneration syndromes, aging, and related conditions.
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Affiliation(s)
- Rachel Nechushtai
- Plant & Environmental Sciences, The Alexander Silberman Institute of Life Science and The Wolfson Centre for Applied Structural Biology, Faculty of Science and Mathematics, The Edmond J. Safra Campus at Givat Ram, The Hebrew University of Jerusalem, Jerusalem91904, Israel
| | - Linda Rowland
- Department of Surgery, University of Missouri School of Medicine, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO65201
| | - Ola Karmi
- Plant & Environmental Sciences, The Alexander Silberman Institute of Life Science and The Wolfson Centre for Applied Structural Biology, Faculty of Science and Mathematics, The Edmond J. Safra Campus at Givat Ram, The Hebrew University of Jerusalem, Jerusalem91904, Israel
| | - Henri-Baptiste Marjault
- Department of Surgery, University of Missouri School of Medicine, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO65201
| | - Thi Thao Nguyen
- Gehrke Proteomics Center, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO65211
| | - Shubham Mittal
- Department of Biological Sciences, University of Texas at Dallas, Richardson, TX75080
| | - Raheel S. Ahmed
- Department of Biological Sciences, University of Texas at Dallas, Richardson, TX75080
| | - DeAna Grant
- Electron Microscopy Core Facility, University of Missouri, NextGen Precision Health Institute, Columbia, MO65211
| | - Camila Manrique-Acevedo
- Division of Endocrinology and Metabolism, Department of Medicine, University of Missouri, Columbia, MO 65201
- NextGen Precision Health, University of Missouri, Columbia, MO 65201
- Harry S. Truman Memorial Veterans’ Hospital, Columbia, MO 65201
| | - Faruck Morcos
- Department of Biological Sciences, University of Texas at Dallas, Richardson, TX75080
- Department of Bioengineering, University of Texas at Dallas, Richardson, TX75080
- Department of Physics, University of Texas at Dallas, Richardson, TX75080
- Center for Systems Biology, University of Texas at Dallas, Richardson, TX75080
| | - José N. Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, TX77005
- Department of Physics and Astronomy, Rice University, Houston, TX77005
- Department of Chemistry, Rice University, Houston, TX77005
- Department of Biosciences, Rice University, Houston, TX77005
| | - Ron Mittler
- Department of Surgery, University of Missouri School of Medicine, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO65201
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