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Nolte RJM, Elemans JAAW. Artificial Processive Catalytic Systems. Chemistry 2024; 30:e202304230. [PMID: 38314967 DOI: 10.1002/chem.202304230] [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: 12/19/2023] [Revised: 02/01/2024] [Accepted: 02/02/2024] [Indexed: 02/07/2024]
Abstract
Processive catalysts remain attached to a substrate and perform multiple rounds of catalysis. They are abundant in nature. This review highlights artificial processive catalytic systems, which can be divided into (A) catalytic rings that move along a polymer chain, (B) catalytic pores that hold polymer chains and decompose them, (C) catalysts that remain attached to and move around a cyclic substrate via supramolecular interactions, and (D) anchored catalysts that remain in contact with a substrate via multiple catalytic interactions (see frontispiece).
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Affiliation(s)
- Roeland J M Nolte
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 125, 6525AJ, Nijmegen, The, Netherlands
| | - Johannes A A W Elemans
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 125, 6525AJ, Nijmegen, The, Netherlands
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2
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Li S, Hsieh KY, Kuo CI, Lin TC, Lee SH, Chen YR, Wang CH, Ho MR, Ting SY, Zhang K, Chang CI. A 5+1 assemble-to-activate mechanism of the Lon proteolytic machine. Nat Commun 2023; 14:7340. [PMID: 37957149 PMCID: PMC10643698 DOI: 10.1038/s41467-023-43035-2] [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: 09/28/2023] [Accepted: 10/26/2023] [Indexed: 11/15/2023] Open
Abstract
Many AAA+ (ATPases associated with diverse cellular activities) proteins function as protein or DNA remodelers by threading the substrate through the central pore of their hexameric assemblies. In this ATP-dependent translocating state, the substrate is gripped by the pore loops of the ATPase domains arranged in a universal right-handed spiral staircase organization. However, the process by which a AAA+ protein is activated to adopt this substrate-pore-loop arrangement remains unknown. We show here, using cryo-electron microscopy (cryo-EM), that the activation process of the Lon AAA+ protease may involve a pentameric assembly and a substrate-dependent incorporation of the sixth protomer to form the substrate-pore-loop contacts seen in the translocating state. Based on the structural results, we design truncated monomeric mutants that inhibit Lon activity by binding to the native pentamer and demonstrated that expressing these monomeric mutants in Escherichia coli cells containing functional Lon elicits specific phenotypes associated with lon deficiency, including the inhibition of persister cell formation. These findings uncover a substrate-dependent assembly process for the activation of a AAA+ protein and demonstrate a targeted approach to selectively inhibit its function within cells.
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Affiliation(s)
- Shanshan Li
- Department of Urology, The First Affiliated Hospital of USTC, MOE Key Laboratory for Cellular Dynamics, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, 230001, Hefei, China.
| | - Kan-Yen Hsieh
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan
| | - Chiao-I Kuo
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan
| | - Tzu-Chi Lin
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan
| | - Szu-Hui Lee
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan
| | - Yi-Ru Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan
| | - Chun-Hsiung Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan
| | - Meng-Ru Ho
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan
| | - See-Yeun Ting
- Institute of Molecular Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Kaiming Zhang
- Department of Urology, The First Affiliated Hospital of USTC, MOE Key Laboratory for Cellular Dynamics, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, 230001, Hefei, China.
| | - Chung-I Chang
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan.
- Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei, 10617, Taiwan.
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3
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Boutagy NE, Fowler JW, Grabinska KA, Cardone R, Sun Q, Vazquez KR, Whalen MB, Zhu X, Chakraborty R, Martin KA, Simons M, Romanoski CE, Kibbey RG, Sessa WC. TNFα increases the degradation of pyruvate dehydrogenase kinase 4 by the Lon protease to support proinflammatory genes. Proc Natl Acad Sci U S A 2023; 120:e2218150120. [PMID: 37695914 PMCID: PMC10515159 DOI: 10.1073/pnas.2218150120] [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: 10/31/2022] [Accepted: 08/07/2023] [Indexed: 09/13/2023] Open
Abstract
The endothelium is a major target of the proinflammatory cytokine, tumor necrosis factor alpha (TNFα). Exposure of endothelial cells (EC) to proinflammatory stimuli leads to an increase in mitochondrial metabolism; however, the function and regulation of elevated mitochondrial metabolism in EC in response to proinflammatory cytokines remain unclear. Studies using high-resolution metabolomics and 13C-glucose and 13C-glutamine labeling flux techniques showed that pyruvate dehydrogenase activity (PDH) and oxidative tricarboxylic acid cycle (TCA) flux are elevated in human umbilical vein ECs in response to overnight (16 h) treatment with TNFα (10 ng/mL). Mechanistic studies indicated that TNFα mediated these metabolic changes via mitochondrial-specific protein degradation of pyruvate dehydrogenase kinase 4 (PDK4, inhibitor of PDH) by the Lon protease via an NF-κB-dependent mechanism. Using RNA sequencing following siRNA-mediated knockdown of the catalytically active subunit of PDH, PDHE1α (PDHA1 gene), we show that PDH flux controls the transcription of approximately one-third of the genes that are up-regulated by TNFα stimulation. Notably, TNFα-induced PDH flux regulates a unique signature of proinflammatory mediators (cytokines and chemokines) but not inducible adhesion molecules. Metabolomics and ChIP sequencing for acetylated modification on lysine 27 of histone 3 (H3K27ac) showed that TNFα-induced PDH flux promotes histone acetylation of specific gene loci via citrate accumulation and ATP-citrate lyase-mediated generation of acetyl CoA. Together, these results uncover a mechanism by which TNFα signaling increases oxidative TCA flux of glucose to support TNFα-induced gene transcription through extramitochondrial acetyl CoA generation and histone acetylation.
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Affiliation(s)
- Nabil E Boutagy
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT 06520
| | - Joseph W Fowler
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT 06520
| | - Kariona A Grabinska
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT 06520
| | - Rebecca Cardone
- Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520
- Department Cellular & Molecular Physiology, Yale University School of Medicine, New Haven, CT 06520
| | - Qiushi Sun
- Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520
- Department Cellular & Molecular Physiology, Yale University School of Medicine, New Haven, CT 06520
| | - Kyla R Vazquez
- Department of Cellular & Molecular Medicine, Bioscience Research Laboratories, University of Arizona, College of Medicine, Tucson, AZ 85724
| | - Michael B Whalen
- Department of Cellular & Molecular Medicine, Bioscience Research Laboratories, University of Arizona, College of Medicine, Tucson, AZ 85724
| | - Xiaolong Zhu
- Department of Cardiology, Yale University School of Medicine, New Haven, CT 06520
| | - Raja Chakraborty
- Department of Cardiology, Yale University School of Medicine, New Haven, CT 06520
| | - Kathleen A Martin
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT 06520
- Department of Cardiology, Yale University School of Medicine, New Haven, CT 06520
| | - Michael Simons
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT 06520
- Department of Cardiology, Yale University School of Medicine, New Haven, CT 06520
| | - Casey E Romanoski
- Department of Cardiology, Yale University School of Medicine, New Haven, CT 06520
| | - Richard G Kibbey
- Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520
- Department Cellular & Molecular Physiology, Yale University School of Medicine, New Haven, CT 06520
| | - William C Sessa
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT 06520
- Department of Cardiology, Yale University School of Medicine, New Haven, CT 06520
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4
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Chen SY, Feilen LP, Chávez-Gutiérrez L, Steiner H, Zacharias M. Enzyme-substrate hybrid β-sheet controls geometry and water access to the γ-secretase active site. Commun Biol 2023; 6:670. [PMID: 37355752 PMCID: PMC10290658 DOI: 10.1038/s42003-023-05039-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 06/12/2023] [Indexed: 06/26/2023] Open
Abstract
γ-Secretase is an aspartyl intramembrane protease that cleaves the amyloid precursor protein (APP) involved in Alzheimer's disease pathology and other transmembrane proteins. Substrate-bound structures reveal a stable hybrid β-sheet immediately following the substrate scissile bond consisting of β1 and β2 from the enzyme and β3 from the substrate. Molecular dynamics simulations and enhanced sampling simulations demonstrate that the hybrid β-sheet stability is strongly correlated with the formation of a stable cleavage-compatible active geometry and it also controls water access to the active site. The hybrid β-sheet is only stable for substrates with 3 or more C-terminal residues beyond the scissile bond. The simulation model allowed us to predict the effect of Pro and Phe mutations that weaken the formation of the hybrid β-sheet which were confirmed by experimental testing. Our study provides a direct explanation why γ-secretase preferentially cleaves APP in steps of 3 residues and how the hybrid β-sheet facilitates γ-secretase proteolysis.
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Affiliation(s)
- Shu-Yu Chen
- Center of Functional Protein Assemblies, Technical University of Munich, Garching, Germany
| | - Lukas P Feilen
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Lucía Chávez-Gutiérrez
- VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium
- Department of Neurosciences, Leuven Research Institute for Neuroscience and Disease (LIND), KU Leuven, Leuven, Belgium
| | - Harald Steiner
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Biomedical Center (BMC), Division of Metabolic Biochemistry, Faculty of Medicine, LMU Munich, Germany
| | - Martin Zacharias
- Center of Functional Protein Assemblies, Technical University of Munich, Garching, Germany.
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5
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Bremer E, Calteau A, Danchin A, Harwood C, Helmann JD, Médigue C, Palsson BO, Sekowska A, Vallenet D, Zuniga A, Zuniga C. A model industrial workhorse:
Bacillus subtilis
strain 168 and its genome after a quarter of a century. Microb Biotechnol 2023; 16:1203-1231. [PMID: 37002859 DOI: 10.1111/1751-7915.14257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 03/20/2023] [Indexed: 04/04/2023] Open
Abstract
The vast majority of genomic sequences are automatically annotated using various software programs. The accuracy of these annotations depends heavily on the very few manual annotation efforts that combine verified experimental data with genomic sequences from model organisms. Here, we summarize the updated functional annotation of Bacillus subtilis strain 168, a quarter century after its genome sequence was first made public. Since the last such effort 5 years ago, 1168 genetic functions have been updated, allowing the construction of a new metabolic model of this organism of environmental and industrial interest. The emphasis in this review is on new metabolic insights, the role of metals in metabolism and macromolecule biosynthesis, functions involved in biofilm formation, features controlling cell growth, and finally, protein agents that allow class discrimination, thus allowing maintenance management, and accuracy of all cell processes. New 'genomic objects' and an extensive updated literature review have been included for the sequence, now available at the International Nucleotide Sequence Database Collaboration (INSDC: AccNum AL009126.4).
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Affiliation(s)
- Erhard Bremer
- Department of Biology, Laboratory for Microbiology and Center for Synthetic Microbiology (SYNMIKRO) Philipps‐University Marburg Marburg Germany
| | - Alexandra Calteau
- LABGeM, Génomique Métabolique, CEA, Genoscope, Institut de Biologie François Jacob Université d'Évry, Université Paris‐Saclay, CNRS Évry France
| | - Antoine Danchin
- School of Biomedical Sciences, Li KaShing Faculty of Medicine Hong Kong University Pokfulam SAR Hong Kong China
| | - Colin Harwood
- Centre for Bacterial Cell Biology, Biosciences Institute Newcastle University Baddiley Clark Building Newcastle upon Tyne UK
| | - John D. Helmann
- Department of Microbiology Cornell University Ithaca New York USA
| | - Claudine Médigue
- LABGeM, Génomique Métabolique, CEA, Genoscope, Institut de Biologie François Jacob Université d'Évry, Université Paris‐Saclay, CNRS Évry France
| | - Bernhard O. Palsson
- Department of Bioengineering University of California San Diego La Jolla USA
| | | | - David Vallenet
- LABGeM, Génomique Métabolique, CEA, Genoscope, Institut de Biologie François Jacob Université d'Évry, Université Paris‐Saclay, CNRS Évry France
| | - Abril Zuniga
- Department of Biology San Diego State University San Diego California USA
| | - Cristal Zuniga
- Bioinformatics and Medical Informatics Graduate Program San Diego State University San Diego California USA
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6
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Gustchina A, Li M, Andrianova AG, Kudzhaev AM, Lountos GT, Sekula B, Cherry S, Tropea JE, Smirnov IV, Wlodawer A, Rotanova TV. Unique Structural Fold of LonBA Protease from Bacillus subtilis, a Member of a Newly Identified Subfamily of Lon Proteases. Int J Mol Sci 2022; 23:11425. [PMID: 36232729 PMCID: PMC9569914 DOI: 10.3390/ijms231911425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/21/2022] [Accepted: 09/22/2022] [Indexed: 11/16/2022] Open
Abstract
ATP-dependent Lon proteases are key participants in the quality control system that supports the homeostasis of the cellular proteome. Based on their unique structural and biochemical properties, Lon proteases have been assigned in the MEROPS database to three subfamilies (A, B, and C). All Lons are single-chain, multidomain proteins containing an ATPase and protease domains, with different additional elements present in each subfamily. LonA and LonC proteases are soluble cytoplasmic enzymes, whereas LonBs are membrane-bound. Based on an analysis of the available sequences of Lon proteases, we identified a number of enzymes currently assigned to the LonB subfamily that, although presumably membrane-bound, include structural features more similar to their counterparts in the LonA subfamily. This observation was confirmed by the crystal structure of the proteolytic domain of the enzyme previously assigned as Bacillus subtilis LonB, combined with the modeled structure of its ATPase domain. Several structural features present in both domains differ from their counterparts in either LonA or LonB subfamilies. We thus postulate that this enzyme is the founding member of a newly identified LonBA subfamily, so far found only in the gene sequences of firmicutes.
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Affiliation(s)
- Alla Gustchina
- Center for Structural Biology, National Cancer Institute, Frederick, MD 21702, USA
| | - Mi Li
- Center for Structural Biology, National Cancer Institute, Frederick, MD 21702, USA
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Anna G Andrianova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Arsen M Kudzhaev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - George T Lountos
- Center for Structural Biology, National Cancer Institute, Frederick, MD 21702, USA
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Bartosz Sekula
- Center for Structural Biology, National Cancer Institute, Frederick, MD 21702, USA
- Institute of Molecular and Industrial Biotechnology, Lodz University of Technology, 90-573 Lodz, Poland
| | - Scott Cherry
- Center for Structural Biology, National Cancer Institute, Frederick, MD 21702, USA
| | - Joseph E Tropea
- Center for Structural Biology, National Cancer Institute, Frederick, MD 21702, USA
| | - Ivan V Smirnov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Alexander Wlodawer
- Center for Structural Biology, National Cancer Institute, Frederick, MD 21702, USA
| | - Tatyana V Rotanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
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7
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Catalytic cycling of human mitochondrial Lon protease. Structure 2022; 30:1254-1268.e7. [PMID: 35870450 DOI: 10.1016/j.str.2022.06.006] [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: 12/16/2021] [Revised: 03/21/2022] [Accepted: 06/28/2022] [Indexed: 11/20/2022]
Abstract
The mitochondrial Lon protease (LonP1) regulates mitochondrial health by removing redundant proteins from the mitochondrial matrix. We determined LonP1 in eight nucleotide-dependent conformational states by cryoelectron microscopy (cryo-EM). The flexible assembly of N-terminal domains had 3-fold symmetry, and its orientation depended on the conformational state. We show that a conserved structural motif around T803 with a high similarity to the trypsin catalytic triad is essential for proteolysis. We show that LonP1 is not regulated by redox potential, despite the presence of two conserved cysteines at disulfide-bonding distance in its unfoldase core. Our data indicate how sequential ATP hydrolysis controls substrate protein translocation in a 6-fold binding change mechanism. Substrate protein translocation, rather than ATP hydrolysis, is a rate-limiting step, suggesting that LonP1 is a Brownian ratchet with ATP hydrolysis preventing translocation reversal. 3-fold rocking motions of the flexible N-domain assembly may assist thermal unfolding of the substrate protein.
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8
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Wlodawer A, Sekula B, Gustchina A, Rotanova TV. Structure and the mode of activity of Lon proteases from diverse organisms. J Mol Biol 2022; 434:167504. [PMID: 35183556 PMCID: PMC9013511 DOI: 10.1016/j.jmb.2022.167504] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 02/14/2022] [Accepted: 02/14/2022] [Indexed: 11/19/2022]
Abstract
Lon proteases, members of the AAA+ superfamily of enzymes, are key components of the protein quality control system in bacterial cells, as well as in the mitochondria and other specialized organelles of higher organisms. These enzymes have been subject of extensive biochemical and structural investigations, resulting in 72 crystal and solution structures, including structures of the individual domains, multi-domain constructs, and full-length proteins. However, interpretation of the latter structures still leaves some questions unanswered. Based on their amino acid sequence and details of their structure, Lon proteases can be divided into at least three subfamilies, designated as LonA, LonB, and LonC. Protomers of all Lons are single-chain polypeptides and contain two functional domains, ATPase and protease. The LonA enzymes additionally include a large N-terminal region, and different Lons may also include non-conserved inserts in the principal domains. These ATP-dependent proteases function as homohexamers, in which unfolded substrates are translocated to a large central chamber where they undergo proteolysis by a processive mechanism. X-ray crystal structures provided high-resolution models which verified that Lons are hydrolases with the rare Ser-Lys catalytic dyad. Full-length LonA enzymes have been investigated by cryo-electron microscopy (cryo-EM), providing description of the functional enzyme at different stages of the catalytic cycle, indicating extensive flexibility of their N-terminal domains, and revealing insights into the substrate translocation mechanism. Structural studies of Lon proteases provide an interesting case for symbiosis of X-ray crystallography and cryo-EM, currently the two principal techniques for determination of macromolecular structures.
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Affiliation(s)
- Alexander Wlodawer
- Protein Structure Section, Center for Structural Biology, National Cancer Institute, Frederick, MD 21702, USA.
| | - Bartosz Sekula
- Protein Structure Section, Center for Structural Biology, National Cancer Institute, Frederick, MD 21702, USA
| | - Alla Gustchina
- Protein Structure Section, Center for Structural Biology, National Cancer Institute, Frederick, MD 21702, USA
| | - Tatyana V Rotanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
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