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Nong J, Lu G, Huang Y, Liu J, Chen L, Pan H, Xiong B. Identification of cuproptosis-related subtypes, characterization of immune microenvironment infiltration, and development of a prognosis model for osteoarthritis. Front Immunol 2023; 14:1178794. [PMID: 37809099 PMCID: PMC10551149 DOI: 10.3389/fimmu.2023.1178794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 08/07/2023] [Indexed: 10/10/2023] Open
Abstract
Background Osteoarthritis (OA) is a prevalent chronic joint disease with an obscure underlying molecular signature. Cuproptosis plays a crucial role in various biological processes. However, the association between cuproptosis-mediated immune infifiltration and OA progression remains unexplored. Therefore, this study elucidates the pathological process and potential mechanisms underlying cuproptosis in OA by constructing a columnar line graph model and performing consensus clustering analysis. Methods Gene expression profifile datasets GSE12021, GSE32317, GSE55235, and GSE55457 of OA were obtained from the comprehensive gene expression database. Cuproptosis signature genes were screened by random forest (RF) and support vector machine (SVM). A nomogram was developed based on cuproptosis signature genes. A consensus clustering was used to distinguish OA patients into different cuproptosis patterns. To quantify the cuproptosis pattern, a principal component analysis was developed to generate the cuproptosis score for each sample. Single-sample gene set enrichment analysis (ssGSEA) was used to provide the abundance of immune cells in each sample and the relationship between these significant cuproptosis signature genes and immune cells.To quantify the cuproptosis pattern, a principal component analysis technique was developed to generate the cuproptosis score for each sample. Cuproptosis-related genes were extracted and subjected to differential expression analysis to construct a disease prediction model and confifirmed by RT-qPCR. Results Seven cuproptosis signature genes were screened (DBT, LIPT1, GLS, PDHB, FDX1, DLAT, and PDHA1) to predict the risk of OA disease. A column line graph model was developed based on these seven cuproptosis signature genes, which may assist patients based on decision curve analysis. A consensus clustering method was used to distinguish patients with disorder into two cuproptosis patterns (clusters A and B). To quantify the cuproptosis pattern, a principal component analysis technique was developed to generate the cuproptosis score for each sample. Furthermore, the OA characteristics of patients in cluster A were associated with the inflflammatory factors IL-1b, IL-17, IL-21, and IL-22, suggesting that the cuproptosis signature genes play a vital role in the development of OA. Discussion In this study, a risk prediction model based on cuproptosis signature genes was established for the fifirst time, and accurately predicted OA risk. In addition, patients with OA were classifified into two cuproptosis molecule subtypes (clusters A and B); cluster A was highly associated with Th17 immune responses, with higher IL-1b, IL-17, and IL-21 IL-22 expression levels, while cluster B had a higher correlation with cuproptosis. Our analysis will help facilitate future research related cuproptosis-associated OA immunotherapy. However, the specifific mechanisms remain to be elucidated.
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Affiliation(s)
- Jiao Nong
- Teaching Department, First Affiliated Hospital of the Guangxi University of Chinese Medicine, Nanning, China
| | - Guanyu Lu
- Postgraduate Schools, Guangxi University of Chinese Medicine, Nanning, China
| | - Yue Huang
- Postgraduate Schools, Guangxi University of Chinese Medicine, Nanning, China
| | - Jinfu Liu
- Postgraduate Schools, Guangxi University of Chinese Medicine, Nanning, China
| | - Lihua Chen
- Postgraduate Schools, Guangxi University of Chinese Medicine, Nanning, China
| | - Haida Pan
- Postgraduate Schools, Guangxi University of Chinese Medicine, Nanning, China
| | - Bo Xiong
- Department of Knee Arthropathy and Sports Injuries, Yulin Orthopedic Hospital of Integrated Traditional Chinese and Western Medicine, Yulin, China
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Záhonová K, Valach M, Tripathi P, Benz C, Opperdoes FR, Barath P, Lukáčová V, Danchenko M, Faktorová D, Horváth A, Burger G, Lukeš J, Škodová-Sveráková I. Subunit composition of mitochondrial dehydrogenase complexes in diplonemid flagellates. Biochim Biophys Acta Gen Subj 2023:130419. [PMID: 37451476 DOI: 10.1016/j.bbagen.2023.130419] [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: 02/02/2023] [Revised: 06/27/2023] [Accepted: 06/28/2023] [Indexed: 07/18/2023]
Abstract
In eukaryotes, pyruvate, a key metabolite produced by glycolysis, is converted by a tripartite mitochondrial pyruvate dehydrogenase (PDH) complex to acetyl-coenzyme A, which is fed into the tricarboxylic acid cycle. Two additional enzyme complexes with analogous composition catalyze similar oxidative decarboxylation reactions albeit using different substrates, the branched-chain ketoacid dehydrogenase (BCKDH) complex and the 2-oxoglutarate dehydrogenase (OGDH) complex. Comparative transcriptome analyses of diplonemids, one of the most abundant and diverse groups of oceanic protists, indicate that the conventional E1, E2, and E3 subunits of the PDH complex are lacking. E1 was apparently replaced in the euglenozoan ancestor of diplonemids by an AceE protein of archaeal type, a substitution that we also document in dinoflagellates. Here we demonstrate that the mitochondrion of the model diplonemid Paradiplonema papillatum displays pyruvate and 2-oxoglutarate dehydrogenase activities. Protein mass spectrometry of mitochondria reveal that the AceE protein is as abundant as the E1 subunit of BCKDH. This corroborates the view that the AceE subunit is a functional component of the PDH complex. We hypothesize that by acquiring AceE, the diplonemid ancestor not only lost the eukaryotic-type E1, but also the E2 and E3 subunits of the PDH complex, which are present in other euglenozoans. We posit that the PDH activity in diplonemids seems to be carried out by a complex, in which the AceE protein partners with the E2 and E3 subunits from BCKDH and/or OGDH.
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Affiliation(s)
- Kristína Záhonová
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic; Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic; Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic; Division of Infectious Diseases, Department of Medicine, University of Alberta, Edmonton, Canada
| | - Matus Valach
- Department of Biochemistry and Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, Canada; Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
| | - Pragya Tripathi
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic; Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic; Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
| | - Corinna Benz
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
| | - Fred R Opperdoes
- de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Peter Barath
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia; Medirex Group Academy, Nitra, Slovakia
| | | | - Maksym Danchenko
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Drahomíra Faktorová
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic; Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Anton Horváth
- Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Gertraud Burger
- Department of Biochemistry and Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, Canada
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic; Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic.
| | - Ingrid Škodová-Sveráková
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic; Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic; Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia.
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Liu S, Pan Y, Li T, Zou M, Liu W, Li Q, Wan H, Peng J, Hao L. The Role of Regulated Programmed Cell Death in Osteoarthritis: From Pathogenesis to Therapy. Int J Mol Sci 2023; 24:ijms24065364. [PMID: 36982438 PMCID: PMC10049357 DOI: 10.3390/ijms24065364] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/08/2023] [Accepted: 03/09/2023] [Indexed: 03/14/2023] Open
Abstract
Osteoarthritis (OA) is a worldwide chronic disease that can cause severe inflammation to damage the surrounding tissue and cartilage. There are many different factors that can lead to osteoarthritis, but abnormally progressed programmed cell death is one of the most important risk factors that can induce osteoarthritis. Prior studies have demonstrated that programmed cell death, including apoptosis, pyroptosis, necroptosis, ferroptosis, autophagy, and cuproptosis, has a great connection with osteoarthritis. In this paper, we review the role of different types of programmed cell death in the generation and development of OA and how the different signal pathways modulate the different cell death to regulate the development of OA. Additionally, this review provides new insights into the radical treatment of osteoarthritis rather than conservative treatment, such as anti-inflammation drugs or surgical operation.
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Affiliation(s)
- Suqing Liu
- Department of Orthopedics, Second Affifiliated Hospital of Nanchang University, Nanchang 330006, China
- Queen Marry College, Nanchang University, Nanchang 330006, China
| | - Yurong Pan
- Department of Orthopedics, Second Affifiliated Hospital of Nanchang University, Nanchang 330006, China
- Queen Marry College, Nanchang University, Nanchang 330006, China
| | - Ting Li
- Department of Orthopedics, Second Affifiliated Hospital of Nanchang University, Nanchang 330006, China
- The Second Clinical Medical College, Nanchang University, Nanchang 330006, China
| | - Mi Zou
- Department of Orthopedics, Second Affifiliated Hospital of Nanchang University, Nanchang 330006, China
- The Second Clinical Medical College, Nanchang University, Nanchang 330006, China
| | - Wenji Liu
- Department of Orthopedics, Second Affifiliated Hospital of Nanchang University, Nanchang 330006, China
- The Second Clinical Medical College, Nanchang University, Nanchang 330006, China
| | - Qingqing Li
- Department of Orthopedics, Second Affifiliated Hospital of Nanchang University, Nanchang 330006, China
- The Second Clinical Medical College, Nanchang University, Nanchang 330006, China
| | - Huan Wan
- Department of Orthopedics, Second Affifiliated Hospital of Nanchang University, Nanchang 330006, China
- The Second Clinical Medical College, Nanchang University, Nanchang 330006, China
| | - Jie Peng
- The Second Clinical Medical College, Nanchang University, Nanchang 330006, China
- Correspondence: (J.P.); (L.H.); Tel.: +86-15983280459 (J.P.); +86-13607008562 (L.H.)
| | - Liang Hao
- Department of Orthopedics, Second Affifiliated Hospital of Nanchang University, Nanchang 330006, China
- Correspondence: (J.P.); (L.H.); Tel.: +86-15983280459 (J.P.); +86-13607008562 (L.H.)
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How evolution dismantles and reassembles multienzyme complexes. Proc Natl Acad Sci U S A 2022; 119:2120286118. [PMID: 34996854 PMCID: PMC8740704 DOI: 10.1073/pnas.2120286118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Echeverri Ruiz NP, Mohan V, Wu J, Scott S, Kreamer M, Benej M, Golias T, Papandreou I, Denko NC. Dynamic regulation of mitochondrial pyruvate metabolism is necessary for orthotopic pancreatic tumor growth. Cancer Metab 2021; 9:39. [PMID: 34749809 PMCID: PMC8577026 DOI: 10.1186/s40170-021-00275-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 10/18/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Pyruvate dehydrogenase complex (PDC) plays a central role in carbohydrate metabolism, linking cytoplasmic glycolysis to the mitochondrial tricarboxylic acid (TCA) cycle. PDC is a conserved E1-E2-E3 dehydrogenase with a PDHA1 and PDHB heterotetramer functioning as the E1 subunit. PDHA1 contains three serine residues that can be reversibly phosphorylated by a dedicated family of four inhibitory pyruvate dehydrogenase kinases (PDHK1-4) and two reactivating phosphatases (PDP1, 2). Hypoxia induces the expression of PDHK1 and PDHK3 and hyperphosphorylates PDHA1. The role of PDC in metabolic reprogramming and tumor progression appears to be for the integration of oncogenic and environmental signals which supports tumor growth. METHODS To isolate the function of the serine-dependent regulation of PDC, we engineered MiaPaca2 cells to express PDHA1 protein with either intact serines at positions 232, 293, and 300 or all the combinations of non-phosphorylatable alanine substitution mutations. These lines were compared in vitro for biochemical response to hypoxia by western blot, metabolic activity by biochemical assay and Seahorse XF flux analysis, and growth in media with reduced exogenous metabolites. The lines were also tested for growth in vivo after orthotopic injection into the pancreata of immune-deficient mice. RESULTS In this family of cells with non-phosphorylatable PDHA1, we found reduced hypoxic phosphorylation of PDHA1, decreased PDH enzymatic activity in normoxia and hypoxia, decreased mitochondrial function by Seahorse flux assay, reduced in vitro growth of cells in media depleted of lipids, and reduced growth of tumors after orthotopic transplantation of cells into the pancreata of immune-deficient mice. CONCLUSIONS We found that any substitution of alanine for serine at regulatory sites generated a hypomorphic PDC. However, the reduced PDC activity was insensitive to further reduction in hypoxia. These cells had a very modest reduction of growth in vitro, but failed to grow as tumors indicating that dynamic PDC adaptation to microenvironmental conditions is necessary to support pancreatic cancer growth in vivo.
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Affiliation(s)
- Nancy P Echeverri Ruiz
- Department of Radiation Oncology, OSUCCC and Wexner Medical Center, The Ohio State University, Columbus, Ohio, 43210, USA
- Current address: Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Vijay Mohan
- Department of Radiation Oncology, OSUCCC and Wexner Medical Center, The Ohio State University, Columbus, Ohio, 43210, USA
| | - Jinghai Wu
- Department of Radiation Oncology, OSUCCC and Wexner Medical Center, The Ohio State University, Columbus, Ohio, 43210, USA
| | - Sabina Scott
- Department of Radiation Oncology, OSUCCC and Wexner Medical Center, The Ohio State University, Columbus, Ohio, 43210, USA
| | - McKenzie Kreamer
- Department of Radiation Oncology, OSUCCC and Wexner Medical Center, The Ohio State University, Columbus, Ohio, 43210, USA
| | - Martin Benej
- Department of Radiation Oncology, OSUCCC and Wexner Medical Center, The Ohio State University, Columbus, Ohio, 43210, USA
| | - Tereza Golias
- Institute of Virology, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, 84505, Slovak Republic
| | - Ioanna Papandreou
- Department of Radiation Oncology, OSUCCC and Wexner Medical Center, The Ohio State University, Columbus, Ohio, 43210, USA
| | - Nicholas C Denko
- Department of Radiation Oncology, OSUCCC and Wexner Medical Center, The Ohio State University, Columbus, Ohio, 43210, USA.
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Sandor A, Fricker MD, Kriechbaumer V, Sweetlove LJ. IntEResting structures: formation and applications of organized smooth endoplasmic reticulum in plant cells. PLANT PHYSIOLOGY 2021; 185:550-561. [PMID: 33822222 PMCID: PMC8892044 DOI: 10.1104/pp.20.00719] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 07/21/2020] [Indexed: 06/12/2023]
Abstract
The endoplasmic reticulum (ER) is an organelle with remarkable plasticity, capable of rapidly changing its structure to accommodate different functions based on intra- and extracellular cues. One of the ER structures observed in plants is known as "organized smooth endoplasmic reticulum" (OSER), consisting of symmetrically stacked ER membrane arrays. In plants, these structures were first described in certain specialized tissues, e.g. the sieve elements of the phloem, and more recently in transgenic plants overexpressing ER membrane resident proteins. To date, much of the investigation of OSER focused on yeast and animal cells but research into plant OSER has started to grow. In this update, we give a succinct overview of research into the OSER phenomenon in plant cells with case studies highlighting both native and synthetic occurrences of OSER. We also assess the primary driving forces that trigger the formation of OSER, collating evidence from the literature to compare two competing theories for the origin of OSER: that OSER formation is initiated by oligomerizing protein accumulation in the ER membrane or that OSER is the result of ER membrane proliferation. This has long been a source of controversy in the field and here we suggest a way to integrate arguments from both sides into a single unifying theory. Finally, we discuss the potential biotechnological uses of OSER as a tool for the nascent plant synthetic biology field with possible applications as a synthetic microdomain for metabolic engineering and as an extensive membrane surface for synthetic chemistry or protein accumulation.
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Affiliation(s)
- Andras Sandor
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, UK
| | - Mark D Fricker
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, UK
| | - Verena Kriechbaumer
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Lee J Sweetlove
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, UK
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Research progress and the biotechnological applications of multienzyme complex. Appl Microbiol Biotechnol 2021; 105:1759-1777. [PMID: 33564922 DOI: 10.1007/s00253-021-11121-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 01/07/2021] [Accepted: 01/16/2021] [Indexed: 11/26/2022]
Abstract
The multienzyme complex system has become a research focus in synthetic biology due to its highly efficient overall catalytic ability and has been applied to various fields. Multienzyme complexes are formed by cascading complexes, which are multiple functionally related enzymes that continuously and efficiently catalyze the production of substrates. Compared with current mainstream microbial cell catalytic systems, in vitro multienzyme molecular machines have many advantages, such as fewer side reactions, a high product yield, a fast reaction speed, easy product separation, a tolerable toxic environment, and robust system operability, showing increasing competitiveness in the field of biomanufacturing. In this review, the research progress of multienzyme complexes in nature and multienzyme cascades in vivo or in vitro will be introduced, and the discovered enzyme cascades concerning scaffolding proteins will also be discussed. This review is expected to provide a more theoretical basis for the modification of multienzyme complexes and broaden their application in the field of synthetic biology. KEY POINTS: • The cascade reactions of some natural multienzyme complexes are reviewed. • The main approaches of constructing artificial multienzyme complexes are summarized. • The structure and application of cellulosomes are discussed and prospected.
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8
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Vanderstraeten J, Briers Y. Synthetic protein scaffolds for the colocalisation of co-acting enzymes. Biotechnol Adv 2020; 44:107627. [DOI: 10.1016/j.biotechadv.2020.107627] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 08/17/2020] [Accepted: 08/25/2020] [Indexed: 02/06/2023]
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9
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Wang Y, Gong Z, Fang H, Zhi D, Tao H. The N-terminal 1-55 residues domain of pyruvate dehydrogenase from Escherichia coli assembles as a dimer in solution. Protein Eng Des Sel 2019; 32:271-276. [PMID: 31828348 DOI: 10.1093/protein/gzz044] [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: 04/28/2019] [Revised: 09/14/2019] [Indexed: 11/12/2022] Open
Abstract
The pyruvate dehydrogenase complex (PDHc) from Escherichia coli is a large protein complex consisting of multiple copies of the pyruvate dehydrogenase (E1ec), dihydrolipoamide acetyltransferase (E2ec) and dihydrolipoamide dehydrogenase (E3ec). The N-terminal domain (NTD, residues 1-55) of E1ec plays a critical role in the interaction between E1ec and E2ec and the whole PDHc activity. Using circular dichroism, size-exclusion chromatography and dynamic light scattering spectroscopy, we show that the NTD of E1ec presents dimeric assembly under physiological condition. Pull-down and isothermal titration calorimetry binding assays revealed that the E2ec peripheral subunit-binding domain (PSBD) forms a very stable complex with the NTD, indicating the isolated NTD functionally interacts with PSBD and the truncated E1ec (E1ec∆NTD) does not interact with PSBD. These findings are important to understand the mechanism of PDHc and other thiamine-based multi-component enzymes.
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Affiliation(s)
- Yuanyuan Wang
- College of Life Sciences, Northwest A&F University, Yangling, China
| | - Zemao Gong
- College of Chemistry and Pharmacy, Northwest A&F University, Yangling, China
| | - Han Fang
- College of Life Sciences, Northwest A&F University, Yangling, China
| | - Dongming Zhi
- College of Life Sciences, Northwest A&F University, Yangling, China
| | - Hu Tao
- College of Chemistry and Pharmacy, Northwest A&F University, Yangling, China
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Myocardial Adaptation in Pseudohypoxia: Signaling and Regulation of mPTP via Mitochondrial Connexin 43 and Cardiolipin. Cells 2019; 8:cells8111449. [PMID: 31744200 PMCID: PMC6912244 DOI: 10.3390/cells8111449] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 11/15/2019] [Indexed: 12/26/2022] Open
Abstract
Therapies intended to mitigate cardiovascular complications cannot be applied in practice without detailed knowledge of molecular mechanisms. Mitochondria, as the end-effector of cardioprotection, represent one of the possible therapeutic approaches. The present review provides an overview of factors affecting the regulation processes of mitochondria at the level of mitochondrial permeability transition pores (mPTP) resulting in comprehensive myocardial protection. The regulation of mPTP seems to be an important part of the mechanisms for maintaining the energy equilibrium of the heart under pathological conditions. Mitochondrial connexin 43 is involved in the regulation process by inhibition of mPTP opening. These individual cardioprotective mechanisms can be interconnected in the process of mitochondrial oxidative phosphorylation resulting in the maintenance of adenosine triphosphate (ATP) production. In this context, the degree of mitochondrial membrane fluidity appears to be a key factor in the preservation of ATP synthase rotation required for ATP formation. Moreover, changes in the composition of the cardiolipin’s structure in the mitochondrial membrane can significantly affect the energy system under unfavorable conditions. This review aims to elucidate functional and structural changes of cardiac mitochondria subjected to preconditioning, with an emphasis on signaling pathways leading to mitochondrial energy maintenance during partial oxygen deprivation.
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Ozbakir HF, Garcia KE, Banta S. Creation of a formate: malate oxidoreductase by fusion of dehydrogenase enzymes with PEGylated cofactor swing arms. Protein Eng Des Sel 2018; 31:103-108. [PMID: 29660073 DOI: 10.1093/protein/gzy005] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Accepted: 03/16/2018] [Indexed: 11/13/2022] Open
Abstract
Enzymatic biocatalysis can be limited by the necessity of soluble cofactors. Here, we introduced PEGylated nicotinamide adenine dinucleotide (NAD(H)) swing arms to two covalently fused dehydrogenase enzymes to eliminate their nicotinamide cofactor requirements. A formate dehydrogenase and cytosolic malate dehydrogenase were connected via SpyCatcher-SpyTag fusions. Bifunctionalized polyethylene glycol chains tethered NAD(H) to the fusion protein. This produced a formate:malate oxidoreductase that exhibited cofactor-independent ping-pong kinetics with predictable Michaelis constants. Kinetic modeling was used to explore the effective cofactor concentrations available for electron transfer in the complexes. This approach could be used to create additional cofactor-independent transhydrogenase biocatalysts by swapping fused dehydrogenases.
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Affiliation(s)
- Harun F Ozbakir
- Department of Chemical Engineering, Columbia University, New York, NY, USA
| | - Kristen E Garcia
- Department of Chemical Engineering, Columbia University, New York, NY, USA
| | - Scott Banta
- Department of Chemical Engineering, Columbia University, New York, NY, USA
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Compulsive methamphetamine taking in the presence of punishment is associated with increased oxytocin expression in the nucleus accumbens of rats. Sci Rep 2017; 7:8331. [PMID: 28827541 PMCID: PMC5566486 DOI: 10.1038/s41598-017-08898-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 07/19/2017] [Indexed: 12/24/2022] Open
Abstract
Methamphetamine addiction is mimicked in rats that self-administer the drug. However, these self-administration (SA) models do not include adverse consequences that are necessary to reach a diagnosis of addiction in humans. Herein, we measured genome-wide transcriptional consequences of methamphetamine SA and footshocks in the rat brain. We trained rats to self-administer methamphetamine for 20 days. Thereafter, lever-presses for methamphetamine were punished by mild footshocks for 5 days. Response-contingent punishment significantly reduced methamphetamine taking in some rats (shock-sensitive, SS) but not in others (shock-resistant, SR). Rats also underwent extinction test at one day and 30 days after the last shock session. Rats were euthanized one day after the second extinction test and the nucleus accumbens (NAc) and dorsal striatum were collected to measure gene expression with microarray analysis. In the NAc, there were changes in the expression of 13 genes in the SRvsControl and 9 genes in the SRvsSS comparison. In the striatum, there were 9 (6 up, 3 down) affected genes in the SRvsSS comparison. Among the upregulated genes was oxytocin in the NAc and CARTpt in the striatum of SR rats. These observations support a regional role of neuropeptides in the brain after a long withdrawal interval when animals show incubation of methamphetamine craving.
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Wheeldon I, Minteer SD, Banta S, Barton SC, Atanassov P, Sigman M. Substrate channelling as an approach to cascade reactions. Nat Chem 2016; 8:299-309. [DOI: 10.1038/nchem.2459] [Citation(s) in RCA: 422] [Impact Index Per Article: 52.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 01/15/2016] [Indexed: 12/22/2022]
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Pröschel M, Detsch R, Boccaccini AR, Sonnewald U. Engineering of Metabolic Pathways by Artificial Enzyme Channels. Front Bioeng Biotechnol 2015; 3:168. [PMID: 26557643 PMCID: PMC4617052 DOI: 10.3389/fbioe.2015.00168] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 10/06/2015] [Indexed: 11/13/2022] Open
Abstract
Application of industrial enzymes for production of valuable chemical compounds has greatly benefited from recent developments in Systems and Synthetic Biology. Both, in vivo and in vitro systems have been established, allowing conversion of simple into complex compounds. Metabolic engineering in living cells needs to be balanced which is achieved by controlling gene expression levels, translation, scaffolding, compartmentation, and flux control. In vitro applications are often hampered by limited protein stability/half-life and insufficient rates of substrate conversion. To improve stability and catalytic activity, proteins are post-translationally modified and arranged in artificial metabolic channels. Within the review article, we will first discuss the supramolecular organization of enzymes in living systems and second summarize current and future approaches to design artificial metabolic channels by additive manufacturing for the efficient production of desired products.
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Affiliation(s)
- Marlene Pröschel
- Department of Biology, Biochemistry Division, Friedrich-Alexander-University Erlangen-Nuremberg , Erlangen , Germany
| | - Rainer Detsch
- Department of Materials Science and Engineering, Institute of Biomaterials, Friedrich-Alexander-University Erlangen-Nuremberg , Erlangen , Germany
| | - Aldo R Boccaccini
- Department of Materials Science and Engineering, Institute of Biomaterials, Friedrich-Alexander-University Erlangen-Nuremberg , Erlangen , Germany
| | - Uwe Sonnewald
- Department of Biology, Biochemistry Division, Friedrich-Alexander-University Erlangen-Nuremberg , Erlangen , Germany
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15
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Component co-expression and purification of recombinant human pyruvate dehydrogenase complex from baculovirus infected SF9 cells. Protein Expr Purif 2014; 97:9-16. [PMID: 24534072 DOI: 10.1016/j.pep.2014.02.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Revised: 02/05/2014] [Accepted: 02/06/2014] [Indexed: 11/21/2022]
Abstract
The mammalian pyruvate dehydrogenase complex (PDC) is a multi-component mitochondrial enzyme that plays a key role in the conversion of pyruvate to acetyl-CoA connecting glycolysis to the citric acid cycle. Recent studies indicate that targeting the regulation of PDC enzymatic activity might offer therapeutic opportunities by inhibiting cancer cell metabolism. To facilitate drug discovery in this area, a well defined PDC sample is needed. Here, we report a new method of producing functional, recombinant, high quality human PDC complex. All five components were co-expressed in the cytoplasm of baculovirus-infected SF9 cells by deletion of the mitochondrial localization signal sequences of all the components and E1a was FLAG-tagged to facilitate purification. The protein FLAG tagged E1a complex was purified using FLAG-M2 affinity resin, followed by Superdex 200 sizing chromatography. The E2 and E3BP components were then Lipoylated using an enzyme based in vitro process. The resulting PDC is over 90% pure and homogenous. This non-phosphorylated, lipoylated human PDC was demonstrated to produce a robust detection window when used to develop an enzyme coupled assay of PDHK.
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Jia F, Narasimhan B, Mallapragada S. Materials-based strategies for multi-enzyme immobilization and co-localization: A review. Biotechnol Bioeng 2013; 111:209-22. [DOI: 10.1002/bit.25136] [Citation(s) in RCA: 190] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 09/13/2013] [Accepted: 10/16/2013] [Indexed: 12/12/2022]
Affiliation(s)
- Feng Jia
- Department of Chemical and Biological Engineering; Iowa State University; Ames Iowa 50011-2230
| | - Balaji Narasimhan
- Department of Chemical and Biological Engineering; Iowa State University; Ames Iowa 50011-2230
| | - Surya Mallapragada
- Department of Chemical and Biological Engineering; Iowa State University; Ames Iowa 50011-2230
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18
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Padrick SB, Deka RK, Chuang JL, Wynn RM, Chuang DT, Norgard MV, Rosen MK, Brautigam CA. Determination of protein complex stoichiometry through multisignal sedimentation velocity experiments. Anal Biochem 2010; 407:89-103. [PMID: 20667444 PMCID: PMC3089910 DOI: 10.1016/j.ab.2010.07.017] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2010] [Revised: 07/19/2010] [Accepted: 07/20/2010] [Indexed: 01/21/2023]
Abstract
Determination of the stoichiometry of macromolecular assemblies is fundamental to an understanding of how they function. Many different biophysical methodologies may be used to determine stoichiometry. In the past, both sedimentation equilibrium and sedimentation velocity analytical ultracentrifugation have been employed to determine component stoichiometries. Recently, a method of globally analyzing multisignal sedimentation velocity data was introduced by Schuck and coworkers. This global analysis removes some of the experimental inconveniences and inaccuracies that could occur in the previously used strategies. This method uses spectral differences between the macromolecular components to decompose the well-known c(s) distribution into component distributions c(k)(s); that is, each component k has its own c(k)(s) distribution. Integration of these distributions allows the calculation of the populations of each component in cosedimenting complexes, yielding their stoichiometry. In our laboratories, we have used this method extensively to determine the component stoichiometries of several protein-protein complexes involved in cytoskeletal remodeling, sugar metabolism, and host-pathogen interactions. The overall method is described in detail in this work, as are experimental examples and caveats.
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Affiliation(s)
- Shae B. Padrick
- Department of Biochemistry, The University of Texas, Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd., Dallas, TX 75390-8816
| | - Ranjit K. Deka
- Department of Microbiology, The University of Texas, Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd., Dallas, TX 75390-8816
| | - Jacinta L. Chuang
- Department of Biochemistry, The University of Texas, Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd., Dallas, TX 75390-8816
| | - R. Max Wynn
- Department of Biochemistry, The University of Texas, Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd., Dallas, TX 75390-8816
- Department of Internal Medicine, The University of Texas, Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd., Dallas, TX 75390-8816
| | - David T. Chuang
- Department of Biochemistry, The University of Texas, Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd., Dallas, TX 75390-8816
- Department of Internal Medicine, The University of Texas, Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd., Dallas, TX 75390-8816
| | - Michael V. Norgard
- Department of Microbiology, The University of Texas, Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd., Dallas, TX 75390-8816
| | - Michael K. Rosen
- Department of Biochemistry, The University of Texas, Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd., Dallas, TX 75390-8816
- Howard Hughes Medical Institute, The University of Texas, Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd., Dallas, TX 75390-8816
| | - Chad A. Brautigam
- Department of Biochemistry, The University of Texas, Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd., Dallas, TX 75390-8816
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19
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Rapoport M, Salman L, Sabag O, Patel MS, Lorberboum-Galski H. Successful TAT-mediated enzyme replacement therapy in a mouse model of mitochondrial E3 deficiency. J Mol Med (Berl) 2010; 89:161-70. [PMID: 21079907 DOI: 10.1007/s00109-010-0693-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2010] [Revised: 10/21/2010] [Accepted: 10/26/2010] [Indexed: 11/25/2022]
Abstract
Medicine today offers no cure for patients suffering from mitochondrial disorders, such as lipoamide dehydrogenase (LAD; also known as E3) deficiency, and treatment is limited to symptomatic care. LAD is one of the components of the α-ketoacid dehydrogenase complexes, which are mitochondrial multienzyme complexes crucial for the metabolism of carbohydrates and amino acids. Recently, we tested the therapeutic approach for treating mitochondrial disorders whereby the activity of multicomponent complexes in the mitochondria is restored by TAT-mediated enzyme replacement therapy (ERT). The LAD deficiency disease was used before as a proof-of-principle in vitro, in patients' cells, utilizing the TAT-LAD fusion protein. In this report, we present successful TAT-mediated ERT in an in vivo mouse model using E3-deficient mice. We demonstrate the delivery of TAT-LAD into E3-deficient mice tissues and that a single administration of TAT-LAD results in a significant increase in the enzymatic activity of the mitochondrial multienzyme complex pyruvate dehydrogenase complex within the liver, heart and, most importantly, the brain of TAT-LAD-treated E3-deficient mice. We believe that this TAT-mediated ERT approach could change the management of mitochondrial disorders and of other metabolic diseases in modern medicine.
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Affiliation(s)
- Matan Rapoport
- Department of Biochemistry and Molecular Biology, Institute for Medical Research-Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, 91120, Israel
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20
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Strecker V, Wumaier Z, Wittig I, Schägger H. Large pore gels to separate mega protein complexes larger than 10 MDa by blue native electrophoresis: Isolation of putative respiratory strings or patches. Proteomics 2010; 10:3379-87. [DOI: 10.1002/pmic.201000343] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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21
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Park YH, Patel MS. Characterization of interactions of dihydrolipoamide dehydrogenase with its binding protein in the human pyruvate dehydrogenase complex. Biochem Biophys Res Commun 2010; 395:416-9. [PMID: 20385101 DOI: 10.1016/j.bbrc.2010.04.038] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2010] [Accepted: 04/05/2010] [Indexed: 10/19/2022]
Abstract
Unlike pyruvate dehydrogenase complexes (PDCs) from prokaryotes, PDCs from higher eukaryotes have an additional structural component, E3-binding protein (BP), for binding of dihydrolipoamide dehydrogenase (E3) in the complex. Based on the 3D structure of the subcomplex of human (h) E3 with the di-domain (L3S1) of hBP, the amino acid residues (H348, D413, Y438, and R447) of hE3 for binding to hBP were substituted singly by alanine or other residues. These substitutions did not have large effects on hE3 activity when measured in its free form. However, when these hE3 mutants were reconstituted in the complex, the PDC activity was significantly reduced to 9% for Y438A, 20% for Y438H, and 18% for D413A. The binding of hE3 mutants with L3S1 determined by isothermal titration calorimetry revealed that the binding affinities of the Y438A, Y438H, and D413A mutants to L3S1 were severely reduced (1019-, 607-, and 402-fold, respectively). Unlike wild-type hE3 the binding of the Y438A mutant to L3S1 was accompanied by an unfavorable enthalpy change and a large positive entropy change. These results indicate that hE3-Y438 and hE3-D413 play important roles in binding of hE3 to hBP.
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Affiliation(s)
- Yun-Hee Park
- Department of Biochemistry, School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, Buffalo, NY 14214, USA
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22
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Brautigam CA, Wynn RM, Chuang JL, Chuang DT. Subunit and catalytic component stoichiometries of an in vitro reconstituted human pyruvate dehydrogenase complex. J Biol Chem 2009; 284:13086-98. [PMID: 19240034 DOI: 10.1074/jbc.m806563200] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The human pyruvate dehydrogenase complex (PDC) is a 9.5-megadalton catalytic machine that employs three catalytic components, i.e. pyruvate dehydrogenase (E1p), dihydrolipoyl transacetylase (E2p), and dihydrolipoamide dehydrogenase (E3), to carry out the oxidative decarboxylation of pyruvate. The human PDC is organized around a 60-meric dodecahedral core comprising the C-terminal domains of E2p and a noncatalytic component, E3-binding protein (E3BP), which specifically tethers E3 dimers to the PDC. A central issue concerning the PDC structure is the subunit stoichiometry of the E2p/E3BP core; recent studies have suggested that the core is composed of 48 copies of E2p and 12 copies of E3BP. Here, using an in vitro reconstituted PDC, we provide densitometry, isothermal titration calorimetry, and analytical ultracentrifugation evidence that there are 40 copies of E2p and 20 copies of E3BP in the E2p/E3BP core. Reconstitution with saturating concentrations of E1p and E3 demonstrated 40 copies of E1p heterotetramers and 20 copies of E3 dimers associated with the E2p/E3BP core. To corroborate the 40/20 model of this core, the stoichiometries of E3 and E1p binding to their respective binding domains were reexamined. In these binding studies, the stoichiometries were found to be 1:1, supporting the 40/20 model of the core. The overall maximal stoichiometry of this in vitro assembled PDC for E2p:E3BP:E1p:E3 is 40:20:40:20. These findings contrast a previous report that implicated that two E3-binding domains of E3BP bind simultaneously to a single E3 dimer (Smolle, M., Prior, A. E., Brown, A. E., Cooper, A., Byron, O., and Lindsay, J. G. (2006) J. Biol. Chem. 281, 19772-19780).
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Affiliation(s)
- Chad A Brautigam
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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23
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Bunik VI, Degtyarev D. Structure-function relationships in the 2-oxo acid dehydrogenase family: substrate-specific signatures and functional predictions for the 2-oxoglutarate dehydrogenase-like proteins. Proteins 2008; 71:874-90. [PMID: 18004749 DOI: 10.1002/prot.21766] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Structural relationship within the family of the thiamine diphosphate-dependent 2-oxo acid dehydrogenases was analyzed by combining different methods of sequence alignment with crystallographic and enzymological studies of the family members. For the first time, the sequence similarity of the homodimeric 2-oxoglutarate dehydrogenase to heterotetrameric 2-oxo acid dehydrogenases is established. The presented alignment of the catalytic domains of the dehydrogenases of pyruvate, branched-chain 2-oxo acids and 2-oxoglutarate unravels the sequence markers of the substrate specificity and the essential residues of the family members without the 3D structures resolved. Predicted dual substrate specificity of some of the 2-oxo acid dehydrogenases was confirmed experimentally. The results were used to decipher functions of the two hypothetical proteins of animal genomes, OGDHL and DHTKD1, similar to the 2-oxoglutarate dehydrogenase. Conservation of all the essential residues confirmed their catalytic competence. Sequence analysis indicated that OGDHL represents a previously unknown isoform of the 2-oxoglutarate dehydrogenase, whereas DHTKD1 differs from the homologs at the N-terminus and substrate binding pocket. The differences suggest changes in heterologous protein interactions and accommodation of more polar and/or bulkier structural analogs of 2-oxoglutarate, such as 2-oxoadipate, 2-oxo-4-hydroxyglutarate, or products of the carboligase reaction between a 2-oxodicarboxylate and glyoxylate or acetaldehyde. The signatures of the Ca2+-binding sites were found in the Ca2+-activated 2-oxoglutarate dehydrogenase and OGDHL, but not in DHTKD1. Mitochondrial localization was predicted for OGDHL and DHTKD1, with DHTKD1 probably localized also to nuclei. Medical implications of the obtained results are discussed in view of the possible associations of the 2-oxo acid dehydrogenases and DHTKD1 with neurodegeneration and cancer.
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Affiliation(s)
- Victoria I Bunik
- School of Bioinformatics and Bioengineering, Lomonosov Moscow State University, Moscow 119992, Russian Federation.
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TAT-mediated Delivery of LAD Restores Pyruvate Dehydrogenase Complex Activity in the Mitochondria of Patients with LAD Deficiency. Mol Ther 2008; 16:691-7. [DOI: 10.1038/mt.2008.4] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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25
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Rapoport M, Saada A, Elpeleg O, Lorberboum-Galski H. TAT-mediated Delivery of LAD Restores Pyruvate Dehydrogenase Complex Activity in the Mitochondria of Patients with LAD Deficiency. Mol Ther 2008. [DOI: 10.1038/sj.mt.6300410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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