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Wei J, Huang CS, Shen Y, Sadre-Bazzaz K, Tong L. Sample optimizations to enable the structure determination of biotin-dependent carboxylases. Methods Enzymol 2024; 708:31-43. [PMID: 39572145 DOI: 10.1016/bs.mie.2024.10.001] [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] [Indexed: 12/08/2024]
Abstract
Biotin-dependent carboxylases have central roles in the metabolisms of fatty acids, amino acids and other compounds. Their functional importance is underscored by their strong conservation from bacteria to humans. These enzymes are large, multi-domain or multi-subunit complexes, and can have molecular weights of 500 to 750 kDa. Despite their large sizes, the first structures of most of these enzymes were determined using X-ray crystallography. This chapter presents various technical challenges that were overcome during their structure determination, which involves extensive optimization of the protein samples and their crystals. The cryo electron microscopy resolution revolution has made it easier to study these large complexes at the atomic level.
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Affiliation(s)
- Jia Wei
- Department of Biological Sciences, Columbia University, New York, NY, United States
| | - Christine S Huang
- Department of Biological Sciences, Columbia University, New York, NY, United States
| | - Yang Shen
- Department of Biological Sciences, Columbia University, New York, NY, United States
| | | | - Liang Tong
- Department of Biological Sciences, Columbia University, New York, NY, United States.
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2
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Zhou F, Zhang Y, Zhu Y, Zhou Q, Shi Y, Hu Q. Filament structures unveil the dynamic organization of human acetyl-CoA carboxylase. SCIENCE ADVANCES 2024; 10:eado4880. [PMID: 39383219 PMCID: PMC11463273 DOI: 10.1126/sciadv.ado4880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Accepted: 09/04/2024] [Indexed: 10/11/2024]
Abstract
Human acetyl-coenzyme A (CoA) carboxylases (ACCs) catalyze the carboxylation of acetyl-CoA, which is the rate-limiting step in fatty acid synthesis. The molecular mechanism underlying the dynamic organization of ACCs is largely unknown. Here, we determined the cryo-electron microscopy (EM) structure of human ACC1 in its inactive state, which forms a unique filament structure and is in complex with acetyl-CoA. We also determined the cryo-EM structure of human ACC1 activated by dephosphorylation and citrate treatment, at a resolution of 2.55 Å. Notably, the covalently linked biotin binds to a site that is distant from the acetyl-CoA binding site when acetyl-CoA is absent, suggesting a potential coordination between biotin binding and acetyl-CoA binding. These findings provide insights into the structural dynamics and regulatory mechanisms of human ACCs.
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Affiliation(s)
- Fayang Zhou
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
- School of Life Sciences, Westlake University, Hangzhou 310024, China
- Zhejiang Key Laboratory of Structural Biology, School of Life Sciences, Westlake University, Hangzhou 310024, China
- Westlake AI Therapeutics Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310058, China
| | - Yuanyuan Zhang
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
- School of Life Sciences, Westlake University, Hangzhou 310024, China
- Zhejiang Key Laboratory of Structural Biology, School of Life Sciences, Westlake University, Hangzhou 310024, China
| | - Yuyao Zhu
- School of Life Sciences, Westlake University, Hangzhou 310024, China
- Westlake AI Therapeutics Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310058, China
| | - Qiang Zhou
- School of Life Sciences, Westlake University, Hangzhou 310024, China
- Zhejiang Key Laboratory of Structural Biology, School of Life Sciences, Westlake University, Hangzhou 310024, China
| | - Yigong Shi
- School of Life Sciences, Westlake University, Hangzhou 310024, China
- Zhejiang Key Laboratory of Structural Biology, School of Life Sciences, Westlake University, Hangzhou 310024, China
| | - Qi Hu
- School of Life Sciences, Westlake University, Hangzhou 310024, China
- Westlake AI Therapeutics Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310058, China
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3
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Indelicato E, Wanschitz J, Löscher W, Boesch S. Skeletal Muscle Involvement in Friedreich Ataxia. Int J Mol Sci 2024; 25:9915. [PMID: 39337401 PMCID: PMC11432698 DOI: 10.3390/ijms25189915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2024] [Revised: 09/06/2024] [Accepted: 09/09/2024] [Indexed: 09/30/2024] Open
Abstract
Friedreich Ataxia (FRDA) is an inherited neuromuscular disorder triggered by a deficit of the mitochondrial protein frataxin. At a cellular level, frataxin deficiency results in insufficient iron-sulfur cluster biosynthesis and impaired mitochondrial function and adenosine triphosphate production. The main clinical manifestation is a progressive balance and coordination disorder which depends on the involvement of peripheral and central sensory pathways as well as of the cerebellum. Besides the neurological involvement, FRDA affects also the striated muscles. The most prominent manifestation is a hypertrophic cardiomyopathy, which also represents the major determinant of premature mortality. Moreover, FRDA displays skeletal muscle involvement, which contributes to the weakness and marked fatigue evident throughout the course of the disease. Herein, we review skeletal muscle findings in FRDA generated by functional imaging, histology, as well as multiomics techniques in both disease models and in patients. Altogether, these findings corroborate a disease phenotype in skeletal muscle and support the notion of progressive mitochondrial damage as a driver of disease progression in FRDA. Furthermore, we highlight the relevance of skeletal muscle investigations in the development of biomarkers for early-phase trials and future therapeutic strategies in FRDA.
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Affiliation(s)
- Elisabetta Indelicato
- Center for Rare Movement Disorders Innsbruck, Department of Neurology, Medical University of Innsbruck, 6020 Innsbruck, Austria;
| | - Julia Wanschitz
- Unit for Neuromuscular Disorders and Clinical Neurophysiology, Department of Neurology, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Wolfgang Löscher
- Unit for Neuromuscular Disorders and Clinical Neurophysiology, Department of Neurology, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Sylvia Boesch
- Center for Rare Movement Disorders Innsbruck, Department of Neurology, Medical University of Innsbruck, 6020 Innsbruck, Austria;
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4
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Bearne SL. Biochemical communication between filament-forming enzymes: Potential Regulatory Roles of Metabolites in Enzyme Co-assemblies with CTP Synthase. Bioessays 2024; 46:e2400063. [PMID: 38975656 DOI: 10.1002/bies.202400063] [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: 03/19/2024] [Revised: 05/05/2024] [Accepted: 05/08/2024] [Indexed: 07/09/2024]
Abstract
A host of metabolic enzymes reversibly self-assemble to form membrane-less, intracellular filaments under normal physiological conditions and in response to stress. Often, these enzymes reside at metabolic control points, suggesting that filament formation affords an additional regulatory mechanism. Examples include cytidine-5'-triphosphate (CTP) synthase (CTPS), which catalyzes the rate-limiting step for the de novo biosynthesis of CTP; inosine-5'-monophosphate dehydrogenase (IMPDH), which controls biosynthetic access to guanosine-5'-triphosphate (GTP); and ∆1-pyrroline-5-carboxylate (P5C) synthase (P5CS) that catalyzes the formation of P5C, which links the Krebs cycle, urea cycle, and proline metabolism. Intriguingly, CTPS can exist in co-assemblies with IMPDH or P5CS. Since GTP is an allosteric activator of CTPS, the association of CTPS and IMPDH filaments accords with the need to coordinate pyrimidine and purine biosynthesis. Herein, a hypothesis is presented furnishing a biochemical connection underlying co-assembly of CTPS and P5CS filaments - potent inhibition of CTPS by glutamate γ-semialdehyde, the open-chain form of P5C.
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Affiliation(s)
- Stephen L Bearne
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
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5
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Czajkowska A, Czajkowski M, Szczerbinski L, Jurczuk K, Reska D, Kwedlo W, Kretowski M, Zabielski P, Kretowski A. Exploring protein relative relations in skeletal muscle proteomic analysis for insights into insulin resistance and type 2 diabetes. Sci Rep 2024; 14:17631. [PMID: 39085321 PMCID: PMC11292014 DOI: 10.1038/s41598-024-68568-4] [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: 12/11/2023] [Accepted: 07/25/2024] [Indexed: 08/02/2024] Open
Abstract
The escalating prevalence of insulin resistance (IR) and type 2 diabetes mellitus (T2D) underscores the urgent need for improved early detection techniques and effective treatment strategies. In this context, our study presents a proteomic analysis of post-exercise skeletal muscle biopsies from individuals across a spectrum of glucose metabolism states: normal, prediabetes, and T2D. This enabled the identification of significant protein relationships indicative of each specific glycemic condition. Our investigation primarily leveraged the machine learning approach, employing the white-box algorithm relative evolutionary hierarchical analysis (REHA), to explore the impact of regulated, mixed mode exercise on skeletal muscle proteome in subjects with diverse glycemic status. This method aimed to advance the diagnosis of IR and T2D and elucidate the molecular pathways involved in its development and the response to exercise. Additionally, we used proteomics-specific statistical analysis to provide a comparative perspective, highlighting the nuanced differences identified by REHA. Validation of the REHA model with a comparable external dataset further demonstrated its efficacy in distinguishing between diverse proteomic profiles. Key metrics such as accuracy and the area under the ROC curve confirmed REHA's capability to uncover novel molecular pathways and significant protein interactions, offering fresh insights into the effects of exercise on IR and T2D pathophysiology of skeletal muscle. The visualizations not only underscored significant proteins and their interactions but also showcased decision trees that effectively differentiate between various glycemic states, thereby enhancing our understanding of the biomolecular landscape of T2D.
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Affiliation(s)
- Anna Czajkowska
- Clinical Research Centre, Medical University of Bialystok, Białystok, Poland.
- Department of Medical Biology, Medical University of Bialystok, A. Mickiewicza 2C, 15-369, Białystok, Poland.
| | - Marcin Czajkowski
- Faculty of Computer Science, Bialystok University of Technology, Białystok, Poland
| | - Lukasz Szczerbinski
- Clinical Research Centre, Medical University of Bialystok, Białystok, Poland
- Department of Endocrinology, Diabetology and Internal Medicine, Medical University of Bialystok, Białystok, Poland
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Krzysztof Jurczuk
- Faculty of Computer Science, Bialystok University of Technology, Białystok, Poland
| | - Daniel Reska
- Faculty of Computer Science, Bialystok University of Technology, Białystok, Poland
| | - Wojciech Kwedlo
- Faculty of Computer Science, Bialystok University of Technology, Białystok, Poland
| | - Marek Kretowski
- Faculty of Computer Science, Bialystok University of Technology, Białystok, Poland
| | - Piotr Zabielski
- Department of Medical Biology, Medical University of Bialystok, A. Mickiewicza 2C, 15-369, Białystok, Poland
| | - Adam Kretowski
- Clinical Research Centre, Medical University of Bialystok, Białystok, Poland
- Department of Endocrinology, Diabetology and Internal Medicine, Medical University of Bialystok, Białystok, Poland
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6
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Plaza-Pegueroles A, Aphasizheva I, Aphasizhev R, Fernández-Tornero C, Ruiz FM. The cryo-EM structure of trypanosome 3-methylcrotonyl-CoA carboxylase provides mechanistic and dynamic insights into its enzymatic function. Structure 2024; 32:930-940.e3. [PMID: 38593794 PMCID: PMC11246232 DOI: 10.1016/j.str.2024.03.010] [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: 11/16/2023] [Revised: 02/15/2024] [Accepted: 03/13/2024] [Indexed: 04/11/2024]
Abstract
3-Methylcrotonyl-CoA carboxylase (MCC) catalyzes the two-step, biotin-dependent production of 3-methylglutaconyl-CoA, an essential intermediate in leucine catabolism. Given the critical metabolic role of MCC, deficiencies in this enzyme lead to organic aciduria, while its overexpression is linked to tumor development. MCC is a dodecameric enzyme composed of six copies of each α- and β-subunit. We present the cryo-EM structure of the endogenous MCC holoenzyme from Trypanosoma brucei in a non-filamentous state at 2.4 Å resolution. Biotin is covalently bound to the biotin carboxyl carrier protein domain of α-subunits and positioned in a non-canonical pocket near the active site of neighboring β-subunit dimers. Moreover, flexibility of key residues at α-subunit interfaces and loops enables pivoting of α-subunit trimers to partly reduce the distance between α- and β-subunit active sites, required for MCC catalysis. Our results provide a structural framework to understand the enzymatic mechanism of eukaryotic MCCs and to assist drug discovery against trypanosome infections.
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Affiliation(s)
| | - Inna Aphasizheva
- Department of Molecular and Cell Biology, Boston University Medical Campus (BUMC), Boston, MA 02118, USA
| | - Ruslan Aphasizhev
- Department of Molecular and Cell Biology, Boston University Medical Campus (BUMC), Boston, MA 02118, USA
| | | | - Federico M Ruiz
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, 28040 Madrid, Spain.
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7
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Xu X, de Sousa AS, Boram TJ, Jiang W, Lohman JR. Active E. coli heteromeric acetyl-CoA carboxylase forms polymorphic helical tubular filaments. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.28.596234. [PMID: 38854064 PMCID: PMC11160672 DOI: 10.1101/2024.05.28.596234] [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
The Escherichia coli heteromeric acetyl-CoA carboxylase (ACC) has four subunits assumed to form an elusive catalytic complex and are involved in allosteric and transcriptional regulation. The E. coli ACC represents almost all ACCs from pathogenic bacteria making it a key antibiotic development target to fight growing antibiotic resistance. Furthermore, it is a model for cyanobacterial and plant plastid ACCs as biofuel engineering targets. Here we report the catalytic E. coli ACC complex surprisingly forms tubes rather than dispersed particles. The cryo-EM structure reveals key protein-protein interactions underpinning efficient catalysis and how transcriptional regulatory roles are masked during catalysis. Discovering the protein-protein interaction interfaces that facilitate catalysis, allosteric and transcriptional regulation provides new routes to engineering catalytic activity and new targets for drug discovery.
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Affiliation(s)
- Xueyong Xu
- Department of Biological Sciences, Purdue University; West Lafayette, IN 47907 USA
| | - Amanda Silva de Sousa
- Department of Biochemistry and Molecular Biology, Michigan State University; East Lansing, MI 48824 USA
- Department of Biochemistry, Purdue University; West Lafayette, IN 47907 USA
| | - Trevor J. Boram
- Department of Biochemistry, Purdue University; West Lafayette, IN 47907 USA
| | - Wen Jiang
- Department of Biological Sciences, Purdue University; West Lafayette, IN 47907 USA
| | - Jeremy R. Lohman
- Department of Biochemistry and Molecular Biology, Michigan State University; East Lansing, MI 48824 USA
- Department of Biochemistry, Purdue University; West Lafayette, IN 47907 USA
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8
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Liu S, Wang H, Li X, Zhang F, Lee JKJ, Li Z, Yu C, Hu JJ, Zhao X, Suematsu T, Alvarez-Cabrera AL, Liu Q, Zhang L, Huang L, Aphasizheva I, Aphasizhev R, Zhou ZH. Structural basis of gRNA stabilization and mRNA recognition in trypanosomal RNA editing. Science 2023; 381:eadg4725. [PMID: 37410820 DOI: 10.1126/science.adg4725] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 05/17/2023] [Indexed: 07/08/2023]
Abstract
In Trypanosoma brucei, the editosome, composed of RNA-editing substrate-binding complex (RESC) and RNA-editing catalytic complex (RECC), orchestrates guide RNA (gRNA)-programmed editing to recode cryptic mitochondrial transcripts into messenger RNAs (mRNAs). The mechanism of information transfer from gRNA to mRNA is unclear owing to a lack of high-resolution structures for these complexes. With cryo-electron microscopy and functional studies, we have captured gRNA-stabilizing RESC-A and gRNA-mRNA-binding RESC-B and RESC-C particles. RESC-A sequesters gRNA termini, thus promoting hairpin formation and blocking mRNA access. The conversion of RESC-A into RESC-B or -C unfolds gRNA and allows mRNA selection. The ensuing gRNA-mRNA duplex protrudes from RESC-B, likely exposing editing sites to RECC-catalyzed cleavage, uridine insertion or deletion, and ligation. Our work reveals a remodeling event facilitating gRNA-mRNA hybridization and assembly of a macromolecular substrate for the editosome's catalytic modality.
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Affiliation(s)
- Shiheng Liu
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA, USA
- California NanoSystems Institute, University of California, Los Angeles, CA, USA
| | - Hong Wang
- Department of Molecular and Cell Biology, Boston University Medical Campus, Boston, MA, USA
| | - Xiaorun Li
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA, USA
- California NanoSystems Institute, University of California, Los Angeles, CA, USA
| | - Fan Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Jane K J Lee
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA, USA
- California NanoSystems Institute, University of California, Los Angeles, CA, USA
| | - Zihang Li
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA, USA
- California NanoSystems Institute, University of California, Los Angeles, CA, USA
| | - Clinton Yu
- Department of Physiology and Biophysics, University of California, Irvine, CA, USA
| | - Jason J Hu
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA, USA
- California NanoSystems Institute, University of California, Los Angeles, CA, USA
| | - Xiaojing Zhao
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Takuma Suematsu
- Department of Molecular and Cell Biology, Boston University Medical Campus, Boston, MA, USA
| | - Ana L Alvarez-Cabrera
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA, USA
- California NanoSystems Institute, University of California, Los Angeles, CA, USA
| | - Qiushi Liu
- Department of Molecular and Cell Biology, Boston University Medical Campus, Boston, MA, USA
| | - Liye Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Shanghai Clinical Research and Trial Center, Shanghai 201210, China
| | - Lan Huang
- Department of Physiology and Biophysics, University of California, Irvine, CA, USA
| | - Inna Aphasizheva
- Department of Molecular and Cell Biology, Boston University Medical Campus, Boston, MA, USA
| | - Ruslan Aphasizhev
- Department of Molecular and Cell Biology, Boston University Medical Campus, Boston, MA, USA
- Department of Biochemistry, Boston University Medical Campus, Boston, MA, USA
| | - Z Hong Zhou
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA, USA
- California NanoSystems Institute, University of California, Los Angeles, CA, USA
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9
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Lee JK, Liu YT, Hu JJ, Aphasizheva I, Aphasizhev R, Zhou ZH. CryoEM reveals oligomeric isomers of a multienzyme complex and assembly mechanics. J Struct Biol X 2023; 7:100088. [PMID: 37128595 PMCID: PMC10148081 DOI: 10.1016/j.yjsbx.2023.100088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 03/13/2023] [Accepted: 04/07/2023] [Indexed: 05/03/2023] Open
Abstract
Propionyl-CoA carboxylase (PCC) is a multienzyme complex consisting of up to six α-subunits and six β-subunits. Belonging to a metabolic pathway converging on the citric acid cycle, it is present in most forms of life and irregularities in its assembly lead to serious illness in humans, known as propionic acidemia. Here, we report the cryogenic electron microscopy (cryoEM) structures and assembly of different oligomeric isomers of endogenous PCC from the parasitic protozoan Leishmania tarentolae (LtPCC). These structures and their statistical distribution reveal the mechanics of PCC assembly and disassembly at equilibrium. We show that, in solution, endogenous LtPCC β-subunits form stable homohexamers, to which different numbers of α-subunits attach. Sorting LtPCC particles into seven classes (i.e., oligomeric formulae α0β6, α1β6, α2β6, α3β6, α4β6, α5β6, α6β6) enables formulation of a model for PCC assembly. Our results suggest how multimerization regulates PCC enzymatic activity and showcase the utility of cryoEM in revealing the statistical mechanics of reaction pathways.
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Affiliation(s)
- Jane K.J. Lee
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
- California NanoSystems Institute, UCLA, Los Angeles, CA 90095, USA
- Department of Psychology, UCLA, Los Angeles, CA 90095, USA
| | - Yun-Tao Liu
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
- California NanoSystems Institute, UCLA, Los Angeles, CA 90095, USA
| | - Jason J. Hu
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
- California NanoSystems Institute, UCLA, Los Angeles, CA 90095, USA
- Department of Mathematics, UCLA, Los Angeles, CA 90095, USA
| | - Inna Aphasizheva
- Department of Molecular and Cell Biology, Boston University Medical Campus (BUMC), Boston, MA 02118, USA
| | - Ruslan Aphasizhev
- Department of Molecular and Cell Biology, Boston University Medical Campus (BUMC), Boston, MA 02118, USA
- Department of Biochemistry, BUMC, Boston, MA 02118, USA
| | - Z. Hong Zhou
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
- California NanoSystems Institute, UCLA, Los Angeles, CA 90095, USA
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10
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Hvorecny KL, Kollman JM. Greater than the sum of parts: Mechanisms of metabolic regulation by enzyme filaments. Curr Opin Struct Biol 2023; 79:102530. [PMID: 36709625 PMCID: PMC10023394 DOI: 10.1016/j.sbi.2023.102530] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 11/28/2022] [Accepted: 12/19/2022] [Indexed: 01/28/2023]
Abstract
Recent work in structural biology is shedding light on how many of the enzymes of intermediary metabolism are self- and co-assembling into large, filamentous polymers or agglomerates to organize and regulate the complex and essential biochemical pathways in cells. Filament assembly provides an additional layer of regulation by modulating the intrinsic allostery of the enzyme protomers which tunes activity in response to a variety of environmental cues. Enzyme filaments dynamically assemble and disassemble in response to changes in metabolite levels and environmental cues, shifting metabolic flux on a more rapid timescale than transcriptional or translational reprogramming. Here we present recent examples of high-resolution structures of filaments from proteins in intermediary metabolism and we discuss how filament assembly modulates the activities of these and other proteins.
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Affiliation(s)
- Kelli L Hvorecny
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Justin M Kollman
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
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