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Ruan H, Gao L, Fang Z, Lei T, Xing D, Ding Y, Rashid A, Zhuang J, Zhang Q, Gu C, Qian W, Zhang N, Qian T, Li K, Xia T, Wang Y. A flavonoid metabolon: cytochrome b 5 enhances B-ring trihydroxylated flavan-3-ols synthesis in tea plants. Plant J 2024. [PMID: 38461478 DOI: 10.1111/tpj.16710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 02/02/2024] [Accepted: 02/14/2024] [Indexed: 03/12/2024]
Abstract
Flavan-3-ols are prominent phenolic compounds found abundantly in the young leaves of tea plants. The enzymes involved in flavan-3-ol biosynthesis in tea plants have been extensively investigated. However, the localization and associations of these numerous functional enzymes within cells have been largely neglected. In this study, we aimed to investigate the synthesis of flavan-3-ols in tea plants, particularly focusing on epigallocatechin gallate. Our analysis involving the DESI-MSI method to reveal a distinct distribution pattern of B-ring trihydroxylated flavonoids, primarily concentrated in the outer layer of buds. Subcellular localization showed that CsC4H, CsF3'H, and CsF3'5'H localizes endoplasmic reticulum. Protein-protein interaction studies demonstrated direct associations between CsC4H, CsF3'H, and cytoplasmic enzymes (CHS, CHI, F3H, DFR, FLS, and ANR), highlighting their interactions within the biosynthetic pathway. Notably, CsF3'5'H, the enzyme for B-ring trihydroxylation, did not directly interact with other enzymes. We identified cytochrome b5 isoform C serving as an essential redox partner, ensuring the proper functioning of CsF3'5'H. Our findings suggest the existence of distinct modules governing the synthesis of different B-ring hydroxylation compounds. This study provides valuable insights into the mechanisms underlying flavonoid diversity and efficient synthesis and enhances our understanding of the substantial accumulation of B-ring trihydroxylated flavan-3-ols in tea plants.
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Affiliation(s)
- Haixiang Ruan
- School of Life Science, Anhui Agricultural University, Hefei, Anhui, 230036, China
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Liping Gao
- School of Life Science, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Zhou Fang
- School of Life Science, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Ting Lei
- School of Life Science, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Dawei Xing
- School of Biological and Environmental Engineering, Chaohu University, Chaohu, Anhui, 238024, China
| | - Yan Ding
- School of Life Science, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Arif Rashid
- School of Life Science, Anhui Agricultural University, Hefei, Anhui, 230036, China
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, Jiangsu, 212013, China
| | - Juhua Zhuang
- College of Tea Science, Guizhou University, Guiyang, Guizhou, 550025, China
| | - Qiang Zhang
- School of Life Science, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Chunyang Gu
- School of Life Science, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Wei Qian
- School of Life Science, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Niuniu Zhang
- School of Life Science, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Tao Qian
- School of Life Science, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Kongqing Li
- College of Humanities and Social Development, Nanjing Agriculture University, Nanjing, Jiangsu, 210095, China
| | - Tao Xia
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Yunsheng Wang
- School of Life Science, Anhui Agricultural University, Hefei, Anhui, 230036, China
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui, 230036, China
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Salihovic S, Dunder L, Lind M, Lind L. Assessing the performance of a targeted absolute quantification isotope dilution liquid chromatograhy tandem mass spectrometry assay versus a commercial nontargeted relative quantification assay for detection of three major perfluoroalkyls in human blood. J Mass Spectrom 2024; 59:e4999. [PMID: 38263897 DOI: 10.1002/jms.4999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 11/29/2023] [Accepted: 12/20/2023] [Indexed: 01/25/2024]
Abstract
Isotope dilution ultrahigh-performance liquid chromatography coupled to tandem mass spectrometry (UHPLC-MS/MS) is commonly used for trace analysis of polyfluoroalkyl and perfluoroalkyl substances (PFAS) in difficult matrices. Commercial nontargeted analysis of major PFAS where relative concentrations are obtained cost effectively is rapidly emerging and is claimed to provide comparable results to that of absolute quantification using matrix matched calibration and isotope dilution UHPLC-MS/MS. However, this remains to be demonstrated on a large scale. We aimed to assess the performance of a targeted absolute quantification isotope dilution LC-MS/MS assay versus a commercial nontargeted relative quantification assay for detection of three major PFAS in human blood. We evaluated a population-based cohort of 503 individuals. Correlations were assessed using Spearman's rank correlation coefficients (rho). Precision and bias were assessed using Bland-Altman plots. For perfluorooctane sulfonic acid, the median concentrations were 5.10 ng/mL (interquartile range [IQR] 3.50-7.24 ng/mL), the two assays correlated with rho 0.83. For perfluorooctanoic acid, the median concentrations were 2.14 ng/mL (IQR 1.60-3.0 ng/mL), the two assays correlated with rho 0.92. For perfluorohexanesulfonate, the median concentrations were 5.5 ng/mL (IQR 2.50-11.61 ng/mL), the two assays correlated with rho 0.96. The Bland-Altman statistical test showed agreement of the mean difference for the majority of samples (97-98%) between the two assays. Absolute plasma concentrations of PFAS obtained using matrix matched calibration and isotope dilution UHPLC-MS/MS show agreement with relative plasma concentrations from a nontargeted commercial platform by Metabolon. We observed striking consistency between the two assays when examining the associations of the three PFAS with cholesterol, offering additional confidence in the validity of utilizing the nontargeted approach for correlations with various health phenotypes.
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Affiliation(s)
- Samira Salihovic
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Linda Dunder
- Department of Medical Sciences, Occupational and Environmental Medicine, Uppsala University, Uppsala, Sweden
- Department of Medical Sciences, Cardiovascular Epidemiology, Uppsala University, Uppsala, Sweden
| | - Monica Lind
- Department of Medical Sciences, Occupational and Environmental Medicine, Uppsala University, Uppsala, Sweden
| | - Lars Lind
- Department of Medical Sciences, Cardiovascular Epidemiology, Uppsala University, Uppsala, Sweden
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Clayton EJ, Islam NS, Pannunzio K, Kuflu K, Sirjani R, Kohalmi SE, Dhaubhadel S. Soybean AROGENATE DEHYDRATASES (GmADTs): involvement in the cytosolic isoflavonoid metabolon or trans-organelle continuity? Front Plant Sci 2024; 15:1307489. [PMID: 38322824 PMCID: PMC10845154 DOI: 10.3389/fpls.2024.1307489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 01/03/2024] [Indexed: 02/08/2024]
Abstract
Soybean (Glycine max) produces a class of phenylalanine (Phe) derived specialized metabolites, isoflavonoids. Isoflavonoids are unique to legumes and are involved in defense responses in planta, and they are also necessary for nodule formation with nitrogen-fixing bacteria. Since Phe is a precursor of isoflavonoids, it stands to reason that the synthesis of Phe is coordinated with isoflavonoid production. Two putative AROGENATE DEHYDRATASE (ADT) isoforms were previously co-purified with the soybean isoflavonoid metabolon anchor ISOFLAVONE SYNTHASE2 (GmIFS2), however the GmADT family had not been characterized. Here, we present the identification of the nine member GmADT family. We determined that the GmADTs share sequences required for enzymatic activity and allosteric regulation with other characterized plant ADTs. Furthermore, the GmADTs are differentially expressed, and multiple members have dual substrate specificity, also acting as PREPHENATE DEHYDRATASES. All GmADT isoforms were detected in the stromules of chloroplasts, and they all interact with GmIFS2 in the cytosol. In addition, GmADT12A interacts with multiple other isoflavonoid metabolon members. These data substantiate the involvement of GmADT isoforms in the isoflavonoid metabolon.
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Affiliation(s)
- Emily J. Clayton
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - Nishat S. Islam
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
| | - Kelsey Pannunzio
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - Kuflom Kuflu
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
| | - Ramtin Sirjani
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - Susanne E. Kohalmi
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - Sangeeta Dhaubhadel
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
- Department of Biology, University of Western Ontario, London, ON, Canada
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Chou MC, Wang YH, Chen FY, Kung CY, Wu KP, Kuo JC, Chan SJ, Cheng ML, Lin CY, Chou YC, Ho MC, Firestine S, Huang JR, Chen RH. PAICS ubiquitination recruits UBAP2 to trigger phase separation for purinosome assembly. Mol Cell 2023; 83:4123-4140.e12. [PMID: 37848033 DOI: 10.1016/j.molcel.2023.09.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 07/10/2023] [Accepted: 09/22/2023] [Indexed: 10/19/2023]
Abstract
Purinosomes serve as metabolons to enhance de novo purine synthesis (DNPS) efficiency through compartmentalizing DNPS enzymes during stressed conditions. However, the mechanism underpinning purinosome assembly and its pathophysiological functions remains elusive. Here, we show that K6-polyubiquitination of the DNPS enzyme phosphoribosylaminoimidazole carboxylase and phosphoribosylaminoimidazolesuccinocarboxamide synthetase (PAICS) by cullin-5/ankyrin repeat and SOCS box containing 11 (Cul5/ASB11)-based ubiquitin ligase plays a driving role in purinosome assembly. Upon several purinosome-inducing cues, ASB11 is upregulated by relieving the H3K9me3/HP1α-mediated transcriptional silencing, thus stimulating PAICS polyubiquitination. The polyubiquitinated PAICS recruits ubiquitin-associated protein 2 (UBAP2), a ubiquitin-binding protein with multiple stretches of intrinsically disordered regions, thereby inducing phase separation to trigger purinosome assembly for enhancing DNPS pathway flux. In human melanoma, ASB11 is highly expressed to facilitate a constitutive purinosome formation to which melanoma cells are addicted for supporting their proliferation, viability, and tumorigenesis in a xenograft model. Our study identifies a driving mechanism for purinosome assembly in response to cellular stresses and uncovers the impact of purinosome formation on human malignancies.
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Affiliation(s)
- Ming-Chieh Chou
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan; Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei 106, Taiwan
| | - Yi-Hsuan Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan; Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei 106, Taiwan
| | - Fei-Yun Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Chun-Ying Kung
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan; Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei 106, Taiwan
| | - Kuen-Phon Wu
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan; Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei 106, Taiwan
| | - Jean-Cheng Kuo
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
| | - Shu-Jou Chan
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Mei-Ling Cheng
- Metabolomics Core Laboratory, Healthy Aging Research Center, Chang Gung University, Taoyuan 333, Taiwan; Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan; Clinical Metabolomics Core Laboratory, Chang Gung Memorial Hospital at Linkou, Taoyuan 333, Taiwan
| | - Chih-Yu Lin
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Yu-Chi Chou
- Biomedical Translation Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Meng-Chiao Ho
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan; Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei 106, Taiwan
| | - Steven Firestine
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI 48201, USA
| | - Jie-Rong Huang
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
| | - Ruey-Hwa Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan; Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei 106, Taiwan.
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Flood D, Lee ES, Taylor CT. Intracellular energy production and distribution in hypoxia. J Biol Chem 2023; 299:105103. [PMID: 37507013 PMCID: PMC10480318 DOI: 10.1016/j.jbc.2023.105103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 07/17/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
The hydrolysis of ATP is the primary source of metabolic energy for eukaryotic cells. Under physiological conditions, cells generally produce more than sufficient levels of ATP to fuel the active biological processes necessary to maintain homeostasis. However, mechanisms underpinning the distribution of ATP to subcellular microenvironments with high local demand remain poorly understood. Intracellular distribution of ATP in normal physiological conditions has been proposed to rely on passive diffusion across concentration gradients generated by ATP producing systems such as the mitochondria and the glycolytic pathway. However, subcellular microenvironments can develop with ATP deficiency due to increases in local ATP consumption. Alternatively, ATP production can be reduced during bioenergetic stress during hypoxia. Mammalian cells therefore need to have the capacity to alter their metabolism and energy distribution strategies to compensate for local ATP deficits while also controlling ATP production. It is highly likely that satisfying the bioenergetic requirements of the cell involves the regulated distribution of ATP producing systems to areas of high ATP demand within the cell. Recently, the distribution (both spatially and temporally) of ATP-producing systems has become an area of intense investigation. Here, we review what is known (and unknown) about intracellular energy production and distribution and explore potential mechanisms through which this targeted distribution can be altered in hypoxia, with the aim of stimulating investigation in this important, yet poorly understood field of research.
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Affiliation(s)
- Darragh Flood
- Conway Institute of Biomolecular and Biomedical Research and School of Medicine, University College Dublin, Dublin, Ireland
| | - Eun Sang Lee
- Conway Institute of Biomolecular and Biomedical Research and School of Medicine, University College Dublin, Dublin, Ireland
| | - Cormac T Taylor
- Conway Institute of Biomolecular and Biomedical Research and School of Medicine, University College Dublin, Dublin, Ireland.
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Xu Y, Singer SD, Chen G. Protein interactomes for plant lipid biosynthesis and their biotechnological applications. Plant Biotechnol J 2023; 21:1734-1744. [PMID: 36762506 PMCID: PMC10440990 DOI: 10.1111/pbi.14027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/18/2023] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
Plant lipids have essential biological roles in plant development and stress responses through their functions in cell membrane formation, energy storage and signalling. Vegetable oil, which is composed mainly of the storage lipid triacylglycerol, also has important applications in food, biofuel and oleochemical industries. Lipid biosynthesis occurs in multiple subcellular compartments and involves the coordinated action of various pathways. Although biochemical and molecular biology research over the last few decades has identified many proteins associated with lipid metabolism, our current understanding of the dynamic protein interactomes involved in lipid biosynthesis, modification and channelling is limited. This review examines advances in the identification and characterization of protein interactomes involved in plant lipid biosynthesis, with a focus on protein complexes consisting of different subunits for sequential reactions such as those in fatty acid biosynthesis and modification, as well as transient or dynamic interactomes formed from enzymes in cooperative pathways such as assemblies of membrane-bound enzymes for triacylglycerol biosynthesis. We also showcase a selection of representative protein interactome structures predicted using AlphaFold2, and discuss current and prospective strategies involving the use of interactome knowledge in plant lipid biotechnology. Finally, unresolved questions in this research area and possible approaches to address them are also discussed.
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Affiliation(s)
- Yang Xu
- Department of Molecular and Cellular BiologyUniversity of GuelphGuelphOntarioCanada
| | - Stacy D. Singer
- Agriculture and Agri‐Food Canada, Lethbridge Research and Development CentreLethbridgeAlbertaCanada
| | - Guanqun Chen
- Department of Agricultural, Food and Nutritional ScienceUniversity of AlbertaEdmontonAlbertaCanada
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Dahmani I, Qin K, Zhang Y, Fernie AR. The formation and function of plant metabolons. Plant J 2023; 114:1080-1092. [PMID: 36906885 DOI: 10.1111/tpj.16179] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 02/26/2023] [Accepted: 03/06/2023] [Indexed: 05/31/2023]
Abstract
Metabolons are temporary structural-functional complexes of sequential enzymes of a metabolic pathway that are distinct from stable multi-enzyme complexes. Here we provide a brief history of the study of enzyme-enzyme assemblies with a particular focus on those that mediate substrate channeling in plants. Large numbers of protein complexes have been proposed for both primary and secondary metabolic pathways in plants. However, to date only four substrate channels have been demonstrated. We provide an overview of current knowledge concerning these four metabolons and explain the methodologies that are currently being applied to unravel their functions. Although the assembly of metabolons has been documented to arise through diverse mechanisms, the physical interaction within the characterized plant metabolons all appear to be driven by interaction with structural elements of the cell. We therefore pose the question as to what methodologies could be brought to bear to enhance our knowledge of plant metabolons that assemble via different mechanisms? In addressing this question, we review recent findings in non-plant systems concerning liquid droplet phase separation and enzyme chemotaxis and propose strategies via which such metabolons could be identified in plants. We additionally discuss the possibilities that could be opened up by novel approaches based on: (i) subcellular-level mass spectral imaging, (ii) proteomics, and (iii) emergent methods in structural and computational biology.
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Affiliation(s)
- Ismail Dahmani
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Kezhen Qin
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Youjun Zhang
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Center of Plant System Biology and Biotechnology, 4000, Plovdiv, Bulgaria
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Center of Plant System Biology and Biotechnology, 4000, Plovdiv, Bulgaria
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Maharjan B, Vitha S, Okumoto S. Developmental regulation and physical interaction among enzymes involved in sorgoleone biosynthesis. Plant J 2023. [PMID: 37118879 DOI: 10.1111/tpj.16263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 04/25/2023] [Indexed: 05/17/2023]
Abstract
Ammonium in the soil is converted into nitrate by nitrifying bacteria or archaea. While nitrate is readily available for plants, it is prone to leaching and contributes to eutrophication. In addition, when the soil conditions become anaerobic, nitrate can be reduced to nitrous oxide, a powerful greenhouse gas. Therefore, slowing nitrification in agricultural soil offers some benefits by reducing nitrogen loss and decreasing water and air pollution. Since nitrogen is a limiting nutrient for most ecological niches, many plants have evolved specialized compounds that reduce nitrification. One such compound, sorgoleone, which is secreted from the root hair of sorghum, has been relatively well studied due to its allelopathic function, with most enzymes involved in its biosynthesis elucidated. However, the secretion mechanisms remain unknown. Previous studies reported numerous lipidic vesicles in the sorghum root hair and speculated that they are involved in sorgoleone storage or secretion, but their roles remain unclear. Also, the subcellular organelles that are involved in sorgoleone synthesis have not been identified. In the present study, we found that the expression of sorgoleone biosynthesis enzymes is induced in a specific root zone, indicating that the secretion is developmentally regulated. The accumulation of internal vesicles preceded the peak of sorgoleone biosynthesis and secretion, indicating that the vesicles play a role in precursor storage rather than secretion. Moreover, our data suggest that enzymes that catalyze the first three steps, SbDES2, SbDES3, and SbARS1, interact with each other to form a multi-enzyme complex on the endoplasmic reticulum surface.
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Affiliation(s)
- Bal Maharjan
- Department of Soil and Crop Sciences, Texas A&M, College Station, Texas, USA
| | - Stanislav Vitha
- Microscopy and Imaging Center, Texas A&M, College Station, Texas, USA
| | - Sakiko Okumoto
- Department of Soil and Crop Sciences, Texas A&M, College Station, Texas, USA
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Del Duca S, Semenzato G, Esposito A, Liò P, Fani R. The Operon as a Conundrum of Gene Dynamics and Biochemical Constraints: What We Have Learned from Histidine Biosynthesis. Genes (Basel) 2023; 14:genes14040949. [PMID: 37107707 PMCID: PMC10138114 DOI: 10.3390/genes14040949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 04/04/2023] [Accepted: 04/20/2023] [Indexed: 04/29/2023] Open
Abstract
Operons represent one of the leading strategies of gene organization in prokaryotes, having a crucial influence on the regulation of gene expression and on bacterial chromosome organization. However, there is no consensus yet on why, how, and when operons are formed and conserved, and many different theories have been proposed. Histidine biosynthesis is a highly studied metabolic pathway, and many of the models suggested to explain operons origin and evolution can be applied to the histidine pathway, making this route an attractive model for the study of operon evolution. Indeed, the organization of his genes in operons can be due to a progressive clustering of biosynthetic genes during evolution, coupled with a horizontal transfer of these gene clusters. The necessity of physical interactions among the His enzymes could also have had a role in favoring gene closeness, of particular importance in extreme environmental conditions. In addition, the presence in this pathway of paralogous genes, heterodimeric enzymes and complex regulatory networks also support other operon evolution hypotheses. It is possible that histidine biosynthesis, and in general all bacterial operons, may result from a mixture of several models, being shaped by different forces and mechanisms during evolution.
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Affiliation(s)
- Sara Del Duca
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy
- Council for Agricultural Research and Economics, Research Centre for Agriculture and Environment (CREA-AA), Via di Lanciola 12/A, Cascine del Riccio, 50125 Firenze, Italy
| | - Giulia Semenzato
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy
| | - Antonia Esposito
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy
- Council for Agricultural Research and Economics, Research Centre for Agriculture and Environment (CREA-AA), Via di Lanciola 12/A, Cascine del Riccio, 50125 Firenze, Italy
| | - Pietro Liò
- Department of Computer Science and Technology, University of Cambridge, Cambridge CB3 0FD, UK
| | - Renato Fani
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy
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Obi CD, Dailey HA, Jami-Alahmadi Y, Wohlschlegel JA, Medlock AE. Proteomic Analysis of Ferrochelatase Interactome in Erythroid and Non-Erythroid Cells. Life (Basel) 2023; 13. [PMID: 36836934 DOI: 10.3390/life13020577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/24/2023] [Accepted: 02/13/2023] [Indexed: 02/22/2023] Open
Abstract
Heme is an essential cofactor for multiple cellular processes in most organisms. In developing erythroid cells, the demand for heme synthesis is high, but is significantly lower in non-erythroid cells. While the biosynthesis of heme in metazoans is well understood, the tissue-specific regulation of the pathway is less explored. To better understand this, we analyzed the mitochondrial heme metabolon in erythroid and non-erythroid cell lines from the perspective of ferrochelatase (FECH), the terminal enzyme in the heme biosynthetic pathway. Affinity purification of FLAG-tagged-FECH, together with mass spectrometric analysis, was carried out to identify putative protein partners in human and murine cell lines. Proteins involved in the heme biosynthetic process and mitochondrial organization were identified as the core components of the FECH interactome. Interestingly, in non-erythroid cell lines, the FECH interactome is highly enriched with proteins associated with the tricarboxylic acid (TCA) cycle. Overall, our study shows that the mitochondrial heme metabolon in erythroid and non-erythroid cells has similarities and differences, and suggests new roles for the mitochondrial heme metabolon and heme in regulating metabolic flux and key cellular processes.
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Bomba L, Walter K, Guo Q, Surendran P, Kundu K, Nongmaithem S, Karim MA, Stewart ID, Langenberg C, Danesh J, Di Angelantonio E, Roberts DJ, Ouwehand WH, Dunham I, Butterworth AS, Soranzo N. Whole-exome sequencing identifies rare genetic variants associated with human plasma metabolites. Am J Hum Genet 2022; 109:1038-1054. [PMID: 35568032 PMCID: PMC9247822 DOI: 10.1016/j.ajhg.2022.04.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 04/13/2022] [Indexed: 12/11/2022] Open
Abstract
Metabolite levels measured in the human population are endophenotypes for biological processes. We combined sequencing data for 3,924 (whole-exome sequencing, WES, discovery) and 2,805 (whole-genome sequencing, WGS, replication) donors from a prospective cohort of blood donors in England. We used multiple approaches to select and aggregate rare genetic variants (minor allele frequency [MAF] < 0.1%) in protein-coding regions and tested their associations with 995 metabolites measured in plasma by using ultra-high-performance liquid chromatography-tandem mass spectrometry. We identified 40 novel associations implicating rare coding variants (27 genes and 38 metabolites), of which 28 (15 genes and 28 metabolites) were replicated. We developed algorithms to prioritize putative driver variants at each locus and used mediation and Mendelian randomization analyses to test directionality at associations of metabolite and protein levels at the ACY1 locus. Overall, 66% of reported associations implicate gene targets of approved drugs or bioactive drug-like compounds, contributing to drug targets' validating efforts.
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Affiliation(s)
- Lorenzo Bomba
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK; Open Targets, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Klaudia Walter
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Qi Guo
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge CB1 8RN, UK
| | - Praveen Surendran
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Kousik Kundu
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK; Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Suraj Nongmaithem
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Mohd Anisul Karim
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK; Open Targets, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Isobel D Stewart
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0SL, UK
| | - Claudia Langenberg
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0SL, UK; Computational Medicine, Berlin Institute of Health at Charité - Utniversitätsmedizin Berlin, Berlin 10117, Germany
| | - John Danesh
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK; British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge CB2 0QQ, UK; National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge CB1 8RN, UK; Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge CB10 1SA, UK
| | - Emanuele Di Angelantonio
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge CB2 0QQ, UK; National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge CB1 8RN, UK; Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge CB10 1SA, UK; Human Technopole, Palazzo Italia, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
| | - David J Roberts
- National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge CB1 8RN, UK; NHS Blood and Transplant-Oxford Centre, Level 2, John Radcliffe Hospital, Oxford OX3 9BQ, UK; Radcliffe Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9BQ, UK
| | - Willem H Ouwehand
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK; Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Puddicombe Way, Cambridge CB2 0AW, UK
| | | | - Ian Dunham
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK; Open Targets, Wellcome Genome Campus, Hinxton CB10 1SD, UK; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Adam S Butterworth
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge CB2 0QQ, UK; National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge CB1 8RN, UK; Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge CB10 1SA, UK
| | - Nicole Soranzo
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK; Open Targets, Wellcome Genome Campus, Hinxton CB10 1SD, UK; Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Puddicombe Way, Cambridge CB2 0AW, UK; British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge CB2 0QQ, UK; National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge CB1 8RN, UK; Human Technopole, Palazzo Italia, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy.
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12
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Obi CD, Bhuiyan T, Dailey HA, Medlock AE. Ferrochelatase: Mapping the Intersection of Iron and Porphyrin Metabolism in the Mitochondria. Front Cell Dev Biol 2022; 10:894591. [PMID: 35646904 PMCID: PMC9133952 DOI: 10.3389/fcell.2022.894591] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 04/14/2022] [Indexed: 12/29/2022] Open
Abstract
Porphyrin and iron are ubiquitous and essential for sustaining life in virtually all living organisms. Unlike iron, which exists in many forms, porphyrin macrocycles are mostly functional as metal complexes. The iron-containing porphyrin, heme, serves as a prosthetic group in a wide array of metabolic pathways; including respiratory cytochromes, hemoglobin, cytochrome P450s, catalases, and other hemoproteins. Despite playing crucial roles in many biological processes, heme, iron, and porphyrin intermediates are potentially cytotoxic. Thus, the intersection of porphyrin and iron metabolism at heme synthesis, and intracellular trafficking of heme and its porphyrin precursors are tightly regulated processes. In this review, we discuss recent advances in understanding the physiological dynamics of eukaryotic ferrochelatase, a mitochondrially localized metalloenzyme. Ferrochelatase catalyzes the terminal step of heme biosynthesis, the insertion of ferrous iron into protoporphyrin IX to produce heme. In most eukaryotes, except plants, ferrochelatase is localized to the mitochondrial matrix, where substrates are delivered and heme is synthesized for trafficking to multiple cellular locales. Herein, we delve into the structural and functional features of ferrochelatase, as well as its metabolic regulation in the mitochondria. We discuss the regulation of ferrochelatase via post-translational modifications, transportation of substrates and product across the mitochondrial membrane, protein-protein interactions, inhibition by small-molecule inhibitors, and ferrochelatase in protozoal parasites. Overall, this review presents insight on mitochondrial heme homeostasis from the perspective of ferrochelatase.
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Affiliation(s)
- Chibuike David Obi
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Tawhid Bhuiyan
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Harry A. Dailey
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
- Department of Microbiology, University of Georgia, Athens, GA, United States
| | - Amy E. Medlock
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
- Augusta University/University of Georgia Medical Partnership, University of Georgia, Athens, GA, United States
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13
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Igelmann S, Lessard F, Ferbeyre G. Liquid-Liquid Phase Separation in Cancer Signaling, Metabolism and Anticancer Therapy. Cancers (Basel) 2022; 14:cancers14071830. [PMID: 35406602 PMCID: PMC8997759 DOI: 10.3390/cancers14071830] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 03/30/2022] [Accepted: 03/31/2022] [Indexed: 01/07/2023] Open
Abstract
The cancer state is thought to be maintained by genetic and epigenetic changes that drive a cancer-promoting gene expression program. However, recent results show that cellular states can be also stably maintained by the reorganization of cell structure leading to the formation of biological condensates via the process of liquid-liquid phase separation. Here, we review the data showing cancer-specific biological condensates initiated by mutant oncoproteins, RNA-binding proteins, or lincRNAs that regulate oncogenic gene expression programs and cancer metabolism. Effective anticancer drugs may specifically partition into oncogenic biological condensates (OBC).
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Affiliation(s)
- Sebastian Igelmann
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC H3C 3J7, Canada;
- Montreal Cancer Institute, CR-CHUM, Université de Montréal, Montréal, QC H2X 0A9, Canada
| | - Frédéric Lessard
- Laboratory of Growth and Development, St-Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre, Québec, QC G1R 2J6, Canada;
| | - Gerardo Ferbeyre
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC H3C 3J7, Canada;
- Montreal Cancer Institute, CR-CHUM, Université de Montréal, Montréal, QC H2X 0A9, Canada
- Correspondence: ; Tel.: +1-514-343-7571
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14
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Zhu Y, Jin L, Shi R, Li J, Wang Y, Zhang L, Liang CZ, Narayana VK, De Souza DP, Thorne RF, Zhang LR, Zhang XD, Wu M. The long noncoding RNA glycoLINC assembles a lower glycolytic metabolon to promote glycolysis. Mol Cell 2022; 82:542-554.e6. [PMID: 35081364 DOI: 10.1016/j.molcel.2021.11.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 08/03/2021] [Accepted: 11/15/2021] [Indexed: 01/27/2023]
Abstract
Non-covalent complexes of glycolytic enzymes, called metabolons, were postulated in the 1970s, but the concept has been controversial. Here we show that a c-Myc-responsive long noncoding RNA (lncRNA) that we call glycoLINC (gLINC) acts as a backbone for metabolon formation between all four glycolytic payoff phase enzymes (PGK1, PGAM1, ENO1, and PKM2) along with lactate dehydrogenase A (LDHA). The gLINC metabolon enhances glycolytic flux, increases ATP production, and enables cell survival under serine deprivation. Furthermore, gLINC overexpression in cancer cells promotes xenograft growth in mice fed a diet deprived of serine, suggesting that cancer cells employ gLINC during metabolic reprogramming. We propose that gLINC makes a functional contribution to cancer cell adaptation and provide the first example of a lncRNA-facilitated metabolon.
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Affiliation(s)
- Youming Zhu
- Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical Science, State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou 450003, China; Department of Dental Implant Center, Stomatologic Hospital and College, Anhui Medical University, Key Laboratory of Oral Diseases Research of Anhui Province, Hefei 230032, China
| | - Lei Jin
- Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical Science, State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou 450003, China; School of Medicine and Public Health, The University of Newcastle, Newcastle, NSW 2308, Australia
| | - Ronghua Shi
- The Chinese Academy of Sciences (CAS) Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Cell and Molecular Biology, School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Jinming Li
- Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical Science, State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou 450003, China
| | - Yan Wang
- Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical Science, State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou 450003, China
| | - Li Zhang
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei 230031, China
| | - Chao-Zhao Liang
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei 230031, China
| | - Vinod K Narayana
- Bio21 Institute and Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, VIC 3010, Australia; Metabolomics Australia, University of Melbourne, Parkville, VIC 3010, Australia
| | - David P De Souza
- Bio21 Institute and Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, VIC 3010, Australia; Metabolomics Australia, University of Melbourne, Parkville, VIC 3010, Australia
| | - Rick F Thorne
- Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical Science, State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou 450003, China; School of Environmental and Life Sciences, The University of Newcastle, Newcastle, NSW 2258, Australia
| | - Li Rong Zhang
- Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical Science, State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou 450003, China.
| | - Xu Dong Zhang
- Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical Science, State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou 450003, China; School of Biomedical Sciences and Pharmacy, The University of Newcastle, Newcastle, NSW 2308, Australia.
| | - Mian Wu
- Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical Science, State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou 450003, China; The Chinese Academy of Sciences (CAS) Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Cell and Molecular Biology, School of Life Sciences, University of Science and Technology of China, Hefei 230026, China.
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15
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Tian S, Yang Y, Wu T, Luo C, Li X, Zhao X, Xi W, Liu X, Zeng M. Functional Characterization of a Flavone Synthase That Participates in a Kumquat Flavone Metabolon. Front Plant Sci 2022; 13:826780. [PMID: 35310637 PMCID: PMC8924551 DOI: 10.3389/fpls.2022.826780] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 02/07/2022] [Indexed: 05/17/2023]
Abstract
Flavones predominantly accumulate as O- and C-glycosides in kumquat plants. Two catalytic mechanisms of flavone synthase II (FNSII) support the biosynthesis of glycosyl flavones, one involving flavanone 2-hydroxylase (which generates 2-hydroxyflavanones for C-glycosylation) and another involving the direct catalysis of flavanones to flavones for O-glycosylation. However, FNSII has not yet been characterized in kumquats. In this study, we identified two kumquat FNSII genes (FcFNSII-1 and FcFNSII-2), based on transcriptome and bioinformatics analysis. Data from in vivo and in vitro assays showed that FcFNSII-2 directly synthesized apigenin and acacetin from naringenin and isosakuranetin, respectively, whereas FcFNSII-1 showed no detectable catalytic activities with flavanones. In agreement, transient overexpression of FcFNSII-2 in kumquat peels significantly enhanced the transcription of structural genes of the flavonoid-biosynthesis pathway and the accumulation of several O-glycosyl flavones. Moreover, studying the subcellular localizations of FcFNSII-1 and FcFNSII-2 demonstrated that N-terminal membrane-spanning domains were necessary to ensure endoplasmic reticulum localization and anchoring. Protein-protein interaction analyses, using the split-ubiquitin yeast two-hybrid system and bimolecular fluorescence-complementation assays, revealed that FcFNSII-2 interacted with chalcone synthase 1, chalcone synthase 2, and chalcone isomerase-like proteins. The results provide strong evidence that FcFNSII-2 serves as a nucleation site for an O-glycosyl flavone metabolon that channels flavanones for O-glycosyl flavone biosynthesis in kumquat fruits. They have implications for guiding genetic engineering efforts aimed at enhancing the composition of bioactive flavonoids in kumquat fruits.
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Affiliation(s)
- Shulin Tian
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, Chongqing, China
| | - Yuyan Yang
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, Chongqing, China
| | - Tao Wu
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
| | - Chuan Luo
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
| | - Xin Li
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
| | - Xijuan Zhao
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, Chongqing, China
| | - Wanpeng Xi
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, Chongqing, China
| | - Xiaogang Liu
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, Chongqing, China
- *Correspondence: Xiaogang Liu,
| | - Ming Zeng
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, Chongqing, China
- Ming Zeng, ;
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16
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Abstract
Significance: Alongside well-characterized permanent multimeric enzymes and multienzyme complexes, relatively unstable transient enzyme-enzyme assemblies, including metabolons, provide an important mechanism for the regulation of energy and redox metabolism. Critical Issues: Despite the fact that enzyme-enzyme assemblies have been proposed for many decades and experimentally analyzed for at least 40 years, there are very few pathways for which unequivocal evidence for the presence of metabolite channeling, the most frequently evoked reason for their formation, has been provided. Further, in contrast to the stronger, permanent interactions for which a deep understanding of the subunit interface exists, the mechanism(s) underlying transient enzyme-enzyme interactions remain poorly studied. Recent Advances: The widespread adoption of proteomic and cell biological approaches to characterize protein-protein interaction is defining an ever-increasing number of enzyme-enzyme assemblies as well as enzyme-protein interactions that likely identify factors which stabilize such complexes. Moreover, the use of microfluidic technologies provided compelling support of a role for substrate-specific chemotaxis in complex assemblies. Future Directions: Embracing current and developing technologies should render the delineation of metabolons from other enzyme-enzyme complexes more facile. In parallel, attempts to confirm that the findings reported in microfluidic systems are, indeed, representative of the cellular situation will be critical to understanding the physiological circumstances requiring and evoking dynamic changes in the levels of the various transient enzyme-enzyme assemblies of the cell. Antioxid. Redox Signal. 35, 788-807.
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Affiliation(s)
- Youjun Zhang
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria.,Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Alisdair R Fernie
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria.,Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
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17
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Igelmann S, Lessard F, Uchenunu O, Bouchard J, Fernandez-Ruiz A, Rowell MC, Lopes-Paciencia S, Papadopoli D, Fouillen A, Ponce KJ, Huot G, Mignacca L, Benfdil M, Kalegari P, Wahba HM, Pencik J, Vuong N, Quenneville J, Guillon J, Bourdeau V, Hulea L, Gagnon E, Kenner L, Moriggl R, Nanci A, Pollak MN, Omichinski JG, Topisirovic I, Ferbeyre G. A hydride transfer complex reprograms NAD metabolism and bypasses senescence. Mol Cell 2021; 81:3848-3865.e19. [PMID: 34547241 DOI: 10.1016/j.molcel.2021.08.028] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 06/25/2021] [Accepted: 08/20/2021] [Indexed: 01/23/2023]
Abstract
Metabolic rewiring and redox balance play pivotal roles in cancer. Cellular senescence is a barrier for tumorigenesis circumvented in cancer cells by poorly understood mechanisms. We report a multi-enzymatic complex that reprograms NAD metabolism by transferring reducing equivalents from NADH to NADP+. This hydride transfer complex (HTC) is assembled by malate dehydrogenase 1, malic enzyme 1, and cytosolic pyruvate carboxylase. HTC is found in phase-separated bodies in the cytosol of cancer or hypoxic cells and can be assembled in vitro with recombinant proteins. HTC is repressed in senescent cells but induced by p53 inactivation. HTC enzymes are highly expressed in mouse and human prostate cancer models, and their inactivation triggers senescence. Exogenous expression of HTC is sufficient to bypass senescence, rescue cells from complex I inhibitors, and cooperate with oncogenic RAS to transform primary cells. Altogether, we provide evidence for a new multi-enzymatic complex that reprograms metabolism and overcomes cellular senescence.
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Affiliation(s)
- Sebastian Igelmann
- CRCHUM, 900 Saint-Denis St, Montréal, QC H2X 0A9, Canada; Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Frédéric Lessard
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Oro Uchenunu
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, QC H3T1E2, Canada; Department of Experimental Medicine, McGill University, Montreal, QC H4A3T2, Canada
| | - Jacob Bouchard
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | | | | | | | - David Papadopoli
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, QC H3T1E2, Canada; Gerald Bronfman Department of Oncology, McGill University, Montreal, QC H4A3T2, Canada
| | - Aurélien Fouillen
- Faculté de médecine dentaire, Université de Montréal, Montréal, QC H3C 3J7, Canada; Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Katia Julissa Ponce
- Faculté de médecine dentaire, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Geneviève Huot
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Lian Mignacca
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Mehdi Benfdil
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Paloma Kalegari
- CRCHUM, 900 Saint-Denis St, Montréal, QC H2X 0A9, Canada; Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Haytham M Wahba
- Department of Biochemistry, Faculty of Pharmacy, Beni-Suef University, Beni-Suef 62521, Egypt; Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Jan Pencik
- Department of Pathology, Medical University of Vienna, Vienna, Austria; Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Center for Biomarker Research in Medicine, 8010 Graz, Austria
| | - Nhung Vuong
- CRCHUM, 900 Saint-Denis St, Montréal, QC H2X 0A9, Canada
| | - Jordan Quenneville
- Institut de recherche en immunologie et en cancérologie (IRIC), Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Jordan Guillon
- CRCHUM, 900 Saint-Denis St, Montréal, QC H2X 0A9, Canada
| | - Véronique Bourdeau
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Laura Hulea
- Maisonneuve-Rosemont Hospital Research Centre, Montréal, QC H1T 2M4, Canada, Département de Médecine, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Etienne Gagnon
- Institut de recherche en immunologie et en cancérologie (IRIC), Université de Montréal, Montréal, QC H3C 3J7, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Lukas Kenner
- Department of Pathology, Medical University of Vienna, Vienna, Austria; Unit of Laboratory Animal Pathology, University of Veterinary Medicine Vienna, Vienna, Austria; Christian Doppler Laboratory for Applied Metabolomics, Vienna, Austria; CBmed GmbH - Center for Biomarker Research in Medicine, Graz, Styria, Austria
| | - Richard Moriggl
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, 1210 Vienna, Austria
| | - Antonio Nanci
- Faculté de médecine dentaire, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Michael N Pollak
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, QC H3T1E2, Canada
| | - James G Omichinski
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Ivan Topisirovic
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, QC H3T1E2, Canada; Department of Experimental Medicine, McGill University, Montreal, QC H4A3T2, Canada; Department of Biochemistry, McGill University, Montreal, QC H4A 3T2, Canada; Gerald Bronfman Department of Oncology, McGill University, Montreal, QC H4A3T2, Canada.
| | - Gerardo Ferbeyre
- CRCHUM, 900 Saint-Denis St, Montréal, QC H2X 0A9, Canada; Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC H3C 3J7, Canada.
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18
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Pareek V, Sha Z, He J, Wingreen NS, Benkovic SJ. Metabolic channeling: predictions, deductions, and evidence. Mol Cell 2021; 81:3775-3785. [PMID: 34547238 PMCID: PMC8485759 DOI: 10.1016/j.molcel.2021.08.030] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 08/18/2021] [Accepted: 08/21/2021] [Indexed: 12/19/2022]
Abstract
With the elucidation of myriad anabolic and catabolic enzyme-catalyzed cellular pathways crisscrossing each other, an obvious question arose: how could these networks operate with maximal catalytic efficiency and minimal interference? A logical answer was the postulate of metabolic channeling, which in its simplest embodiment assumes that the product generated by one enzyme passes directly to a second without diffusion into the surrounding medium. This tight coupling of activities might increase a pathway's metabolic flux and/or serve to sequester unstable/toxic/reactive intermediates as well as prevent their access to other networks. Here, we present evidence for this concept, commencing with enzymes that feature a physical molecular tunnel, to multi-enzyme complexes that retain pathway substrates through electrostatics or enclosures, and finally to metabolons that feature collections of enzymes assembled into clusters with variable stoichiometric composition. Lastly, we discuss the advantages of reversibly assembled metabolons in the context of the purinosome, the purine biosynthesis metabolon.
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Affiliation(s)
- Vidhi Pareek
- Huck Institutes of Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Zhou Sha
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA
| | - Jingxuan He
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA
| | - Ned S Wingreen
- Department of Molecular Biology and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Stephen J Benkovic
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA.
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19
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Streng C, Hartmann J, Leister K, Krauß N, Lamparter T, Frankenberg-Dinkel N, Weth F, Bastmeyer M, Yu Z, Fischer R. Fungal phytochrome chromophore biosynthesis at mitochondria. EMBO J 2021; 40:e108083. [PMID: 34254350 PMCID: PMC8447599 DOI: 10.15252/embj.2021108083] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 06/18/2021] [Accepted: 06/21/2021] [Indexed: 12/16/2022] Open
Abstract
Mitochondria are essential organelles because of their function in energy conservation. Here, we show an involvement of mitochondria in phytochrome‐dependent light sensing in fungi. Phytochrome photoreceptors are found in plants, bacteria, and fungi and contain a linear, heme‐derived tetrapyrrole as chromophore. Linearization of heme requires heme oxygenases (HOs) which reside inside chloroplasts in planta. Despite the poor degree of conservation of HOs, we identified two candidates in the fungus Alternaria alternata. Deletion of either one phenocopied phytochrome deletion. The two enzymes had a cooperative effect and physically interacted with phytochrome, suggesting metabolon formation. The metabolon was attached to the surface of mitochondria with a C‐terminal anchor (CTA) sequence in HoxA. The CTA was necessary and sufficient for mitochondrial targeting. The affinity of phytochrome apoprotein to HoxA was 57,000‐fold higher than the affinity of the holoprotein, suggesting a “kiss‐and‐go” mechanism for chromophore loading and a function of mitochondria as assembly platforms for functional phytochrome. Hence, two alternative approaches for chromophore biosynthesis and insertion into phytochrome evolved in plants and fungi.
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Affiliation(s)
- Christian Streng
- Department of Microbiology, Karlsruhe Institute of Technology (KIT) - South Campus, Institute for Applied Biosciences, Karlsruhe, Germany
| | - Jana Hartmann
- Department of Microbiology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Kai Leister
- Department of Microbiology, Karlsruhe Institute of Technology (KIT) - South Campus, Institute for Applied Biosciences, Karlsruhe, Germany
| | - Norbert Krauß
- Karlsruhe Institute of Technology (KIT) - South Campus, Botanical Institute, Karlsruhe, Germany
| | - Tilman Lamparter
- Karlsruhe Institute of Technology (KIT) - South Campus, Botanical Institute, Karlsruhe, Germany
| | | | - Franco Weth
- Karlsruhe Institute of Technology (KIT) - South Campus, Zoological Institute, Karlsruhe, Germany
| | - Martin Bastmeyer
- Karlsruhe Institute of Technology (KIT) - South Campus, Zoological Institute, Karlsruhe, Germany
| | - Zhenzhong Yu
- The Key Laboratory of Plant Immunity, Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Reinhard Fischer
- Department of Microbiology, Karlsruhe Institute of Technology (KIT) - South Campus, Institute for Applied Biosciences, Karlsruhe, Germany
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Zhang Y, Fernie AR. Metabolons, enzyme-enzyme assemblies that mediate substrate channeling, and their roles in plant metabolism. Plant Commun 2021; 2:100081. [PMID: 33511342 PMCID: PMC7816073 DOI: 10.1016/j.xplc.2020.100081] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/29/2020] [Accepted: 06/02/2020] [Indexed: 05/05/2023]
Abstract
Metabolons are transient multi-protein complexes of sequential enzymes that mediate substrate channeling. They differ from multi-enzyme complexes in that they are dynamic, rather than permanent, and as such have considerably lower dissociation constants. Despite the fact that a huge number of metabolons have been suggested to exist in plants, most of these claims are erroneous as only a handful of these have been proven to channel metabolites. We believe that physical protein-protein interactions between consecutive enzymes of a pathway should rather be called enzyme-enzyme assemblies. In this review, we describe how metabolons are generally assembled by transient interactions and held together by both structural elements and non-covalent interactions. Experimental evidence for their existence comes from protein-protein interaction studies, which indicate that the enzymes physically interact, and direct substrate channeling measurements, which indicate that they functionally interact. Unfortunately, advances in cell biology and proteomics have far outstripped those in classical enzymology and flux measurements, rendering most reports reliant purely on interactome studies. Recent developments in co-fractionation mass spectrometry will likely further exacerbate this bias. Given this, only dynamic enzyme-enzyme assemblies in which both physical and functional interactions have been demonstrated should be termed metabolons. We discuss the level of evidence for the manifold plant pathways that have been postulated to contain metabolons and then list examples in both primary and secondary metabolism for which strong evidence has been provided to support these claims. In doing so, we pay particular attention to experimental and mathematical approaches to study metabolons as well as complexities that arise in attempting to follow them. Finally, we discuss perspectives for improving our understanding of these fascinating but enigmatic interactions.
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Affiliation(s)
- Youjun Zhang
- Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Alisdair R. Fernie
- Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
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21
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Moss FJ, Boron WF. Carbonic anhydrases enhance activity of endogenous Na-H exchangers and not the electrogenic Na/HCO 3 cotransporter NBCe1-A, expressed in Xenopus oocytes. J Physiol 2020; 598:5821-5856. [PMID: 32969493 PMCID: PMC7747792 DOI: 10.1113/jp280143] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 09/07/2020] [Indexed: 12/16/2022] Open
Abstract
KEY POINTS According to the HCO 3 - metabolon hypothesis, direct association of cytosolic carbonic anhydrases (CAs) with the electrogenic Na/HCO3 cotransporter NBCe1-A speeds transport by regenerating/consuming HCO 3 - . The present work addresses published discrepancies as to whether cytosolic CAs stimulate NBCe1-A, heterologously expressed in Xenopus oocytes. We confirm the essential elements of the previous experimental observations, taken as support for the HCO 3 - metabolon hypothesis. However, using our own experimental protocols or those of others, we find that NBCe1-A function is unaffected by cytosolic CAs. Previous conclusions that cytosolic CAs do stimulate NBCe1-A can be explained by an unanticipated stimulatory effect of the CAs on an endogenous Na-H exchanger. Theoretical analyses show that, although CAs could stimulate non- HCO 3 - transporters (e.g. Na-H exchangers) by accelerating CO2 / HCO 3 - -mediated buffering of acid-base equivalents, they could not appreciably affect transport rates of NBCe1 or other transporters carrying HCO 3 - , CO 3 = , or NaCO 3 - ion pairs. ABSTRACT The HCO 3 - metabolon hypothesis predicts that cytosolic carbonic anhydrase (CA) binds to NBCe1-A, promotes HCO 3 - replenishment/consumption, and enhances transport. Using a short step-duration current-voltage (I-V) protocol with Xenopus oocytes expressing eGFP-tagged NBCe1-A, our group reported that neither injecting human CA II (hCA II) nor fusing hCA II to the NBCe1-A carboxy terminus affects background-subtracted NBCe1 slope conductance (GNBC ), which is a direct measure of NBCe1-A activity. Others - using bovine CA (bCA), untagged NBCe1-A, and protocols keeping holding potential (Vh ) far from NBCe1-A's reversal potential (Erev ) for prolonged periods - found that bCA increases total membrane current (ΔIm ), which apparently supports the metabolon hypothesis. We systematically investigated differences in the two protocols. In oocytes expressing untagged NBCe1-A, injected with bCA and clamped to -40 mV, CO2 / HCO 3 - exposures markedly decrease Erev , producing large transient outward currents persisting for >10 min and rapid increases in [Na+ ]i . Although the CA inhibitor ethoxzolamide (EZA) reduces both ΔIm and d[Na+ ]i /dt, it does not reduce GNBC . In oocytes not expressing NBCe1-A, CO2 / HCO 3 - triggers rapid increases in [Na+ ]i that both hCA II and bCA enhance in concentration-dependent manners. These d[Na+ ]i /dt increases are inhibited by EZA and blocked by EIPA, a Na-H exchanger (NHE) inhibitor. In oocytes expressing untagged NBCe1-A and injected with bCA, EIPA abolishes the EZA-dependent decreases in ΔIm and d[Na+ ]i /dt. Thus, CAs/EZA produce their ΔIm and d[Na+ ]i /dt effects not through NBCe1-A, but endogenous NHEs. Theoretical considerations argue against a CA stimulation of HCO 3 - transport, supporting the conclusion that an NBCe1-A- HCO 3 - metabolon does not exist in oocytes.
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Affiliation(s)
- Fraser J. Moss
- Department of Physiology and Biophysics, Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Walter F. Boron
- Department of Physiology and Biophysics, Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Department of Medicine and Department of Biochemistry Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
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22
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Faquih T, van Smeden M, Luo J, le Cessie S, Kastenmüller G, Krumsiek J, Noordam R, van Heemst D, Rosendaal FR, van Hylckama Vlieg A, Willems van Dijk K, Mook-Kanamori DO. A Workflow for Missing Values Imputation of Untargeted Metabolomics Data. Metabolites 2020; 10:metabo10120486. [PMID: 33256233 PMCID: PMC7761057 DOI: 10.3390/metabo10120486] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 11/12/2020] [Accepted: 11/25/2020] [Indexed: 01/09/2023] Open
Abstract
Metabolomics studies have seen a steady growth due to the development and implementation of affordable and high-quality metabolomics platforms. In large metabolite panels, measurement values are frequently missing and, if neglected or sub-optimally imputed, can cause biased study results. We provided a publicly available, user-friendly R script to streamline the imputation of missing endogenous, unannotated, and xenobiotic metabolites. We evaluated the multivariate imputation by chained equations (MICE) and k-nearest neighbors (kNN) analyses implemented in our script by simulations using measured metabolites data from the Netherlands Epidemiology of Obesity (NEO) study (n = 599). We simulated missing values in four unique metabolites from different pathways with different correlation structures in three sample sizes (599, 150, 50) with three missing percentages (15%, 30%, 60%), and using two missing mechanisms (completely at random and not at random). Based on the simulations, we found that for MICE, larger sample size was the primary factor decreasing bias and error. For kNN, the primary factor reducing bias and error was the metabolite correlation with its predictor metabolites. MICE provided consistently higher performance measures particularly for larger datasets (n > 50). In conclusion, we presented an imputation workflow in a publicly available R script to impute untargeted metabolomics data. Our simulations provided insight into the effects of sample size, percentage missing, and correlation structure on the accuracy of the two imputation methods.
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Affiliation(s)
- Tariq Faquih
- Department of Clinical Epidemiology, Leiden University Medical Center, Postal Zone C7-P, PO Box 9600, 2300 RC Leiden, The Netherlands; (T.F.); (J.L.); (S.l.C.); (F.R.R.); (A.v.H.V.)
| | - Maarten van Smeden
- Julius Center for Health Sciences and Primary Care, University Medical Centre Utrecht, Utrecht University, 8, 3584 Utrecht, The Netherlands;
| | - Jiao Luo
- Department of Clinical Epidemiology, Leiden University Medical Center, Postal Zone C7-P, PO Box 9600, 2300 RC Leiden, The Netherlands; (T.F.); (J.L.); (S.l.C.); (F.R.R.); (A.v.H.V.)
| | - Saskia le Cessie
- Department of Clinical Epidemiology, Leiden University Medical Center, Postal Zone C7-P, PO Box 9600, 2300 RC Leiden, The Netherlands; (T.F.); (J.L.); (S.l.C.); (F.R.R.); (A.v.H.V.)
- Department of Biomedical Data Sciences, Section Medical Statistics and Bioinformatics, Leiden University Medical Center, 2, 2333 Leiden, The Netherlands
| | - Gabi Kastenmüller
- Institute of Bioinformatics and Systems Biology, Helmholtz-Zentrum München, 85764 Neuherberg, Germany;
- Institute of Experimental Genetics, Genome Analysis Center, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Jan Krumsiek
- Department of Physiology, Institute for Computational Biomedicine, Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10065, USA;
| | - Raymond Noordam
- Department of Internal Medicine, Section of Gerontology and Geriatrics, Leiden University Medical Center, 2333ZA Leiden, The Netherlands; (R.N.); (D.v.H.)
| | - Diana van Heemst
- Department of Internal Medicine, Section of Gerontology and Geriatrics, Leiden University Medical Center, 2333ZA Leiden, The Netherlands; (R.N.); (D.v.H.)
| | - Frits R. Rosendaal
- Department of Clinical Epidemiology, Leiden University Medical Center, Postal Zone C7-P, PO Box 9600, 2300 RC Leiden, The Netherlands; (T.F.); (J.L.); (S.l.C.); (F.R.R.); (A.v.H.V.)
| | - Astrid van Hylckama Vlieg
- Department of Clinical Epidemiology, Leiden University Medical Center, Postal Zone C7-P, PO Box 9600, 2300 RC Leiden, The Netherlands; (T.F.); (J.L.); (S.l.C.); (F.R.R.); (A.v.H.V.)
| | - Ko Willems van Dijk
- Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2, 2333 Leiden, The Netherlands;
- Department of Internal Medicine, Division of Endocrinology, Leiden University Medical Center, 2, 2333 Leiden, The Netherlands
- Department of Human Genetics, Leiden University Medical Center, 2, 2333 Leiden, The Netherlands
| | - Dennis O. Mook-Kanamori
- Department of Clinical Epidemiology, Leiden University Medical Center, Postal Zone C7-P, PO Box 9600, 2300 RC Leiden, The Netherlands; (T.F.); (J.L.); (S.l.C.); (F.R.R.); (A.v.H.V.)
- Department of Public Health and Primary Care, Leiden University Medical Center, 2, 233 Leiden, The Netherlands
- Metabolon Inc., Morrisville, NC 27560, USA
- Correspondence:
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23
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Wolfe K, Kamata R, Coutinho K, Inoue T, Sasaki AT. Metabolic Compartmentalization at the Leading Edge of Metastatic Cancer Cells. Front Oncol 2020; 10:554272. [PMID: 33224873 PMCID: PMC7667250 DOI: 10.3389/fonc.2020.554272] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 09/29/2020] [Indexed: 12/30/2022] Open
Abstract
Despite advances in targeted therapeutics and understanding in molecular mechanisms, metastasis remains a substantial obstacle for cancer treatment. Acquired genetic mutations and transcriptional changes can promote the spread of primary tumor cells to distant tissues. Additionally, recent studies have uncovered that metabolic reprogramming of cancer cells is tightly associated with cancer metastasis. However, whether intracellular metabolism is spatially and temporally regulated for cancer cell migration and invasion is understudied. In this review, we highlight the emergence of a concept, termed “membraneless metabolic compartmentalization,” as one of the critical mechanisms that determines the metastatic capacity of cancer cells. In particular, we focus on the compartmentalization of purine nucleotide metabolism (e.g., ATP and GTP) at the leading edge of migrating cancer cells through the uniquely phase-separated microdomains where dynamic exchange of nucleotide metabolic enzymes takes place. We will discuss how future insights may usher in a novel class of therapeutics specifically targeting the metabolic compartmentalization that drives tumor metastasis.
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Affiliation(s)
- Kara Wolfe
- Division of Hematology and Oncology, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, United States.,Department of Cancer Biology, University of Cincinnati College of Medicine, OH, United States
| | - Ryo Kamata
- Division of Inflammation Research, Center for Molecular Medicine, Jichi Medical University, Tochigi, Japan.,Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
| | - Kester Coutinho
- Department of Cell Biology and Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Takanari Inoue
- Department of Cell Biology and Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Atsuo T Sasaki
- Division of Hematology and Oncology, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, United States.,Department of Cancer Biology, University of Cincinnati College of Medicine, OH, United States.,Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan.,Department of Neurosurgery, Brain Tumor Center at UC Gardner Neuroscience Institute, Cincinnati, OH, United States
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24
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Imaizumi R, Mameda R, Takeshita K, Kubo H, Sakai N, Nakata S, Takahashi S, Kataoka K, Yamamoto M, Nakayama T, Yamashita S, Waki T. Crystal structure of chalcone synthase, a key enzyme for isoflavonoid biosynthesis in soybean. Proteins 2020; 89:126-131. [PMID: 32725893 DOI: 10.1002/prot.25988] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 07/12/2020] [Accepted: 07/26/2020] [Indexed: 01/02/2023]
Abstract
Isoflavonoid is one of the groups of flavonoids that play pivotal roles in the survival of land plants. Chalcone synthase (CHS), the first enzyme of the isoflavonoid biosynthetic pathway, catalyzes the formation of a common isoflavonoid precursor. We have previously reported that an isozyme of soybean CHS (termed GmCHS1) is a key component of the isoflavonoid metabolon, a protein complex to enhance efficiency of isoflavonoid production. Here, we determined the crystal structure of GmCHS1 as a first step of understanding the metabolon structure, as well as to better understand the catalytic mechanism of GmCHS1.
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Affiliation(s)
- Riki Imaizumi
- Department of Material Chemistry, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa, Japan
| | - Ryo Mameda
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Miyagi, Japan
| | | | - Hiroki Kubo
- Department of Material Chemistry, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa, Japan
| | - Naoki Sakai
- RIKEN SPring-8 Center, Sayo-cho, Sayo-gun, Hyogo, Japan
| | - Shun Nakata
- Department of Material Chemistry, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa, Japan
| | - Seiji Takahashi
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Miyagi, Japan
| | - Kunishige Kataoka
- Department of Material Chemistry, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa, Japan
| | | | - Toru Nakayama
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Miyagi, Japan
| | - Satoshi Yamashita
- Department of Material Chemistry, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa, Japan
| | - Toshiyuki Waki
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Miyagi, Japan
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25
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Doigneaux C, Pedley AM, Mistry IN, Papayova M, Benkovic SJ, Tavassoli A. Hypoxia drives the assembly of the multienzyme purinosome complex. J Biol Chem 2020; 295:9551-9566. [PMID: 32439803 PMCID: PMC7363121 DOI: 10.1074/jbc.ra119.012175] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 05/18/2020] [Indexed: 01/20/2023] Open
Abstract
The purinosome is a dynamic metabolic complex composed of enzymes responsible for de novo purine biosynthesis, whose formation has been associated with elevated purine demand. However, the physiological conditions that govern purinosome formation in cells remain unknown. Here, we report that purinosome formation is up-regulated in cells in response to a low-oxygen microenvironment (hypoxia). We demonstrate that increased purinosome assembly in hypoxic human cells requires the activation of hypoxia inducible factor 1 (HIF-1) and not HIF-2. Hypoxia-driven purinosome assembly was inhibited in cells lacking 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase (ATIC), a single enzyme in de novo purine biosynthesis, and in cells treated with a small molecule inhibitor of ATIC homodimerization. However, despite the increase in purinosome assembly in hypoxia, we observed no associated increase in de novo purine biosynthesis in cells. Our results indicate that this was likely due to a reduction in mitochondrial one-carbon metabolism, resulting in reduced mitochondrion-derived one-carbon units needed for de novo purine biosynthesis. The findings of our study further clarify and deepen our understanding of purinosome formation by revealing that this process does not solely depend on cellular purine demand.
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Affiliation(s)
- Cyrielle Doigneaux
- School of Chemistry, University of Southampton, Southampton, United Kingdom
| | - Anthony M Pedley
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Ishna N Mistry
- School of Chemistry, University of Southampton, Southampton, United Kingdom
| | - Monika Papayova
- School of Chemistry, University of Southampton, Southampton, United Kingdom
| | - Stephen J Benkovic
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Ali Tavassoli
- School of Chemistry, University of Southampton, Southampton, United Kingdom
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26
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Abstract
For millennia, humans have used plants for food, raw materials, and medicines, but only within the past two centuries have we begun to connect particular plant metabolites with specific properties and utilities. Since the utility of classical molecular genetics beyond model species is limited, the vast specialized metabolic systems present in the Earth's flora remain largely unstudied. With an explosion in genomics resources and a rapidly expanding toolbox over the past decade, exploration of plant specialized metabolism in nonmodel species is becoming more feasible than ever before. We review the state-of-the-art tools that have enabled this rapid progress. We present recent examples of de novo biosynthetic pathway discovery that employ various innovative approaches. We also draw attention to the higher-order organization of plant specialized metabolism at subcellular, cellular, tissue, interorgan, and interspecies levels, which will have important implications for the future design of comprehensive metabolic engineering strategies.
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Affiliation(s)
- Joseph R Jacobowitz
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA;
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Jing-Ke Weng
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA;
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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27
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Ono E, Waki T, Oikawa D, Murata J, Shiraishi A, Toyonaga H, Kato M, Ogata N, Takahashi S, Yamaguchi MA, Horikawa M, Nakayama T. Glycoside-specific glycosyltransferases catalyze regio-selective sequential glucosylations for a sesame lignan, sesaminol triglucoside. Plant J 2020; 101:1221-1233. [PMID: 31654577 DOI: 10.1111/tpj.14586] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 10/07/2019] [Accepted: 10/16/2019] [Indexed: 05/10/2023]
Abstract
Sesame (Sesamum indicum) seeds contain a large number of lignans, phenylpropanoid-related plant specialized metabolites. (+)-Sesamin and (+)-sesamolin are major hydrophobic lignans, whereas (+)-sesaminol primarily accumulates as a water-soluble sesaminol triglucoside (STG) with a sugar chain branched via β1→2 and β1→6-O-glucosidic linkages [i.e. (+)-sesaminol 2-O-β-d-glucosyl-(1→2)-O-β-d-glucoside-(1→6)-O-β-d-glucoside]. We previously reported that the 2-O-glucosylation of (+)-sesaminol aglycon and β1→6-O-glucosylation of (+)-sesaminol 2-O-β-d-glucoside (SMG) are mediated by UDP-sugar-dependent glucosyltransferases (UGT), UGT71A9 and UGT94D1, respectively. Here we identified a distinct UGT, UGT94AG1, that specifically catalyzes the β1→2-O-glucosylation of SMG and (+)-sesaminol 2-O-β-d-glucosyl-(1→6)-O-β-d-glucoside [termed SDG(β1→6)]. UGT94AG1 was phylogenetically related to glycoside-specific glycosyltransferases (GGTs) and co-ordinately expressed with UGT71A9 and UGT94D1 in the seeds. The role of UGT94AG1 in STG biosynthesis was further confirmed by identification of a STG-deficient sesame mutant that predominantly accumulates SDG(β1→6) due to a destructive insertion in the coding sequence of UGT94AG1. We also identified UGT94AA2 as an alternative UGT potentially involved in sugar-sugar β1→6-O-glucosylation, in addition to UGT94D1, during STG biosynthesis. Yeast two-hybrid assays showed that UGT71A9, UGT94AG1, and UGT94AA2 were found to interact with a membrane-associated P450 enzyme, CYP81Q1 (piperitol/sesamin synthase), suggesting that these UGTs are components of a membrane-bound metabolon for STG biosynthesis. A comparison of kinetic parameters of these UGTs further suggested that the main β-O-glucosylation sequence of STG biosynthesis is β1→2-O-glucosylation of SMG by UGT94AG1 followed by UGT94AA2-mediated β1→6-O-glucosylation. These findings together establish the complete biosynthetic pathway of STG and shed light on the evolvability of regio-selectivity of sequential glucosylations catalyzed by GGTs.
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Affiliation(s)
- Eiichiro Ono
- Suntory Global Innovation Center (SIC) Ltd., Research Institute, Soraku-gun, Kyoto, 619-0284, Japan
| | - Toshiyuki Waki
- Graduate School of Engineering, Tohoku University, Sendai, Miyagi, 980-8579, Japan
| | - Daiki Oikawa
- Graduate School of Engineering, Tohoku University, Sendai, Miyagi, 980-8579, Japan
| | - Jun Murata
- Suntory Bioorganic Research Institute (SUNBOR), Suntory Foundation for Life Sciences, Soraku-gun, Kyoto, 619-0284, Japan
| | - Akira Shiraishi
- Suntory Bioorganic Research Institute (SUNBOR), Suntory Foundation for Life Sciences, Soraku-gun, Kyoto, 619-0284, Japan
| | - Hiromi Toyonaga
- Suntory Global Innovation Center (SIC) Ltd., Research Institute, Soraku-gun, Kyoto, 619-0284, Japan
| | - Masako Kato
- National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, 305-8517, Japan
| | - Naoki Ogata
- National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, 305-8517, Japan
| | - Seiji Takahashi
- Graduate School of Engineering, Tohoku University, Sendai, Miyagi, 980-8579, Japan
| | | | - Manabu Horikawa
- Suntory Bioorganic Research Institute (SUNBOR), Suntory Foundation for Life Sciences, Soraku-gun, Kyoto, 619-0284, Japan
| | - Toru Nakayama
- Graduate School of Engineering, Tohoku University, Sendai, Miyagi, 980-8579, Japan
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28
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Behrendorff JBYH, Borràs-Gas G, Pribil M. Synthetic Protein Scaffolding at Biological Membranes. Trends Biotechnol 2020; 38:432-46. [PMID: 31718802 DOI: 10.1016/j.tibtech.2019.10.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 10/18/2019] [Accepted: 10/21/2019] [Indexed: 02/07/2023]
Abstract
Protein scaffolding is a natural phenomenon whereby proteins colocalize into macromolecular complexes via specific protein-protein interactions. In the case of metabolic enzymes, protein scaffolding drives metabolic flux through specific pathways by colocalizing enzyme active sites. Synthetic protein scaffolding is increasingly used as a mechanism to improve product specificity and yields in metabolic engineering projects. To date, synthetic scaffolding has focused primarily on soluble enzyme systems, but many metabolic pathways for high-value secondary metabolites depend on membrane-bound enzymes. The compositional diversity of biological membranes and general challenges associated with modifying membrane proteins complicate scaffolding with membrane-requiring enzymes. Several recent studies have introduced new approaches to protein scaffolding at membrane surfaces, with notable success in improving product yields from specific metabolic pathways.
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Blakeslee JJ, Spatola Rossi T, Kriechbaumer V. Auxin biosynthesis: spatial regulation and adaptation to stress. J Exp Bot 2019; 70:5041-5049. [PMID: 31198972 DOI: 10.1093/jxb/erz283] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 06/03/2019] [Indexed: 05/25/2023]
Abstract
The plant hormone auxin is essential for plant growth and development, controlling both organ development and overall plant architecture. Auxin homeostasis is regulated by coordination of biosynthesis, transport, conjugation, sequestration/storage, and catabolism to optimize concentration-dependent growth responses and adaptive responses to temperature, water stress, herbivory, and pathogens. At present, the best defined pathway of auxin biosynthesis is the TAA/YUC route, in which the tryptophan aminotransferases TAA and TAR and YUCCA flavin-dependent monooxygenases produce the auxin indole-3-acetic acid from tryptophan. This review highlights recent advances in our knowledge of TAA/YUC-dependent auxin biosynthesis focusing on membrane localization of auxin biosynthetic enzymes, differential regulation in root and shoot tissue, and auxin biosynthesis during abiotic stress.
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Affiliation(s)
- Joshua J Blakeslee
- Department of Horticulture and Crop Science, The Ohio State University, Wooster, OH, USA
| | - Tatiana Spatola Rossi
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
| | - Verena Kriechbaumer
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
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e Silva KSF, Lima RM, Baeza LC, Lima PDS, Cordeiro TDM, Charneau S, da Silva RA, Soares CMDA, Pereira M. Interactome of Glyceraldehyde-3-Phosphate Dehydrogenase Points to the Existence of Metabolons in Paracoccidioides lutzii. Front Microbiol 2019; 10:1537. [PMID: 31338083 PMCID: PMC6629890 DOI: 10.3389/fmicb.2019.01537] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 06/20/2019] [Indexed: 11/13/2022] Open
Abstract
Paracoccidioides is a dimorphic fungus, the causative agent of paracoccidioidomycosis. The disease is endemic within Latin America and prevalent in Brazil. The treatment is based on azoles, sulfonamides and amphotericin B. The seeking for new treatment approaches is a real necessity for neglected infections. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is an essential glycolytic enzyme, well known for its multitude of functions within cells, therefore categorized as a moonlight protein. To our knowledge, this is the first approach performed on the Paracoccidioides genus regarding the description of PPIs having GAPDH as a target. Here, we show an overview of experimental GAPDH interactome in different phases of Paracoccidioides lutzii and an in silico analysis of 18 proteins partners. GAPDH interacted with 207 proteins in P. lutzii. Several proteins bound to GAPDH in mycelium, transition and yeast phases are common to important pathways such as glycolysis and TCA. We performed a co-immunoprecipitation assay to validate the complex formed by GAPDH with triose phosphate isomerase, enolase, isocitrate lyase and 2-methylcitrate synthase. We found GAPDH participating in complexes with proteins of specific pathways, indicating the existence of a glycolytic and a TCA metabolon in P. lutzii. GAPDH interacted with several proteins that undergoes regulation by nitrosylation. In addition, we modeled the GAPDH 3-D structure, performed molecular dynamics and molecular docking in order to identify the interacting interface between GAPDH and the interacting proteins. Despite the large number of interacting proteins, GAPDH has only four main regions of contact with interacting proteins, reflecting its ancestrality and conservation over evolution.
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Affiliation(s)
| | - Raisa Melo Lima
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Brazil
| | - Lilian Cristiane Baeza
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Brazil
| | - Patrícia de Sousa Lima
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Brazil
| | - Thuany de Moura Cordeiro
- Laboratório de Bioquímica e Química de Proteínas, Departamento de Biologia Celular, Universidade de Brasília, Brasília, Brazil
| | - Sébastien Charneau
- Laboratório de Bioquímica e Química de Proteínas, Departamento de Biologia Celular, Universidade de Brasília, Brasília, Brazil
| | - Roosevelt Alves da Silva
- Núcleo Colaborativo de Biossistemas, Instituto de Ciências Exatas, Universidade Federal de Jataí, Goiás, Brazil
| | | | - Maristela Pereira
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Brazil
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Xia C, Fu Z, Battaile KP, Kim JP. Crystal structure of human mitochondrial trifunctional protein, a fatty acid β-oxidation metabolon. Proc Natl Acad Sci U S A 2019; 116:6069-74. [PMID: 30850536 DOI: 10.1073/pnas.1816317116] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Membrane-bound mitochondrial trifunctional protein (TFP) catalyzes β-oxidation of long chain fatty acyl-CoAs, employing 2-enoyl-CoA hydratase (ECH), 3-hydroxyl-CoA dehydrogenase (HAD), and 3-ketothiolase (KT) activities consecutively. Inherited deficiency of TFP is a recessive genetic disease, manifesting in hypoketotic hypoglycemia, cardiomyopathy, and sudden death. We have determined the crystal structure of human TFP at 3.6-Å resolution. The biological unit of the protein is α2β2 The overall structure of the heterotetramer is the same as that observed by cryo-EM methods. The two β-subunits make a tightly bound homodimer at the center, and two α-subunits are bound to each side of the β2 dimer, creating an arc, which binds on its concave side to the mitochondrial innermembrane. The catalytic residues in all three active sites are arranged similarly to those of the corresponding, soluble monofunctional enzymes. A structure-based, substrate channeling pathway from the ECH active site to the HAD and KT sites is proposed. The passage from the ECH site to the HAD site is similar to those found in the two bacterial TFPs. However, the passage from the HAD site to the KT site is unique in that the acyl-CoA intermediate can be transferred between the two sites by passing along the mitochondrial inner membrane using the hydrophobic nature of the acyl chain. The 3'-AMP-PPi moiety is guided by the positively charged residues located along the "ceiling" of the channel, suggesting that membrane integrity is an essential part of the channel and is required for the activity of the enzyme.
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Norris V. Successive Paradigm Shifts in the Bacterial Cell Cycle and Related Subjects. Life (Basel) 2019; 9:E27. [PMID: 30866455 PMCID: PMC6462897 DOI: 10.3390/life9010027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 02/28/2019] [Accepted: 03/04/2019] [Indexed: 11/26/2022] Open
Abstract
A paradigm shift in one field can trigger paradigm shifts in other fields. This is illustrated by the paradigm shifts that have occurred in bacterial physiology following the discoveries that bacteria are not unstructured, that the bacterial cell cycle is not controlled by the dynamics of peptidoglycan, and that the growth rates of bacteria in the same steady-state population are not at all the same. These paradigm shifts are having an effect on longstanding hypotheses about the regulation of the bacterial cell cycle, which appear increasingly to be inadequate. I argue that, just as one earthquake can trigger others, an imminent paradigm shift in the regulation of the bacterial cell cycle will have repercussions or "paradigm quakes" on hypotheses about the origins of life and about the regulation of the eukaryotic cell cycle.
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Affiliation(s)
- Vic Norris
- Laboratory of Microbiology Signals and Microenvironment, University of Rouen, 76821 Mont Saint Aignan, France.
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Hajj Chehade M, Pelosi L, Fyfe CD, Loiseau L, Rascalou B, Brugière S, Kazemzadeh K, Vo CDT, Ciccone L, Aussel L, Couté Y, Fontecave M, Barras F, Lombard M, Pierrel F. A Soluble Metabolon Synthesizes the Isoprenoid Lipid Ubiquinone. Cell Chem Biol 2019; 26:482-492.e7. [PMID: 30686758 DOI: 10.1016/j.chembiol.2018.12.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 11/14/2018] [Accepted: 11/29/2018] [Indexed: 01/03/2023]
Abstract
Ubiquinone (UQ) is a polyprenylated lipid that is conserved from bacteria to humans and is crucial to cellular respiration. How the cell orchestrates the efficient synthesis of UQ, which involves the modification of extremely hydrophobic substrates by multiple sequential enzymes, remains an unresolved issue. Here, we demonstrate that seven Ubi proteins form the Ubi complex, a stable metabolon that catalyzes the last six reactions of the UQ biosynthetic pathway in Escherichia coli. The SCP2 domain of UbiJ forms an extended hydrophobic cavity that binds UQ intermediates inside the 1-MDa Ubi complex. We purify the Ubi complex from cytoplasmic extracts and demonstrate that UQ biosynthesis occurs in this fraction, challenging the current thinking of a membrane-associated biosynthetic process. Collectively, our results document a rare case of stable metabolon and highlight how the supramolecular organization of soluble enzymes allows the modification of hydrophobic substrates in a hydrophilic environment.
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Affiliation(s)
| | - Ludovic Pelosi
- Univ. Grenoble Alpes, CNRS, Grenoble INP, TIMC-IMAG, 38000 Grenoble, France
| | - Cameron David Fyfe
- Laboratoire de Chimie des Processus Biologiques, Collège de France, Université Pierre et Marie Curie, CNRS UMR 8229, PSL Research University, 11 Place Marcelin Berthelot, 75005 Paris, France
| | - Laurent Loiseau
- Aix Marseille Université, CNRS, Laboratoire Chimie Bactérienne, Institut Microbiologie de la Méditerranée, 31 Chemin Joseph Aiguier, Marseille 13009, France
| | - Bérengère Rascalou
- Univ. Grenoble Alpes, CNRS, Grenoble INP, TIMC-IMAG, 38000 Grenoble, France
| | - Sabine Brugière
- Univ. Grenoble Alpes, CEA, Inserm, BIG-BGE, 38000 Grenoble, France
| | | | - Chau-Duy-Tam Vo
- Laboratoire de Chimie des Processus Biologiques, Collège de France, Université Pierre et Marie Curie, CNRS UMR 8229, PSL Research University, 11 Place Marcelin Berthelot, 75005 Paris, France
| | - Lidia Ciccone
- SOLEIL Synchrotron, L'Orme des Merisiers, 91198 Gif-sur-Yvette, France
| | - Laurent Aussel
- Aix Marseille Université, CNRS, Laboratoire Chimie Bactérienne, Institut Microbiologie de la Méditerranée, 31 Chemin Joseph Aiguier, Marseille 13009, France
| | - Yohann Couté
- Univ. Grenoble Alpes, CEA, Inserm, BIG-BGE, 38000 Grenoble, France
| | - Marc Fontecave
- Laboratoire de Chimie des Processus Biologiques, Collège de France, Université Pierre et Marie Curie, CNRS UMR 8229, PSL Research University, 11 Place Marcelin Berthelot, 75005 Paris, France
| | - Frédéric Barras
- Aix Marseille Université, CNRS, Laboratoire Chimie Bactérienne, Institut Microbiologie de la Méditerranée, 31 Chemin Joseph Aiguier, Marseille 13009, France; SAMe Unit, Department de Microbiologie, Institut Pasteur, 25 Rue du Dr Roux, 75015 Paris, France
| | - Murielle Lombard
- Laboratoire de Chimie des Processus Biologiques, Collège de France, Université Pierre et Marie Curie, CNRS UMR 8229, PSL Research University, 11 Place Marcelin Berthelot, 75005 Paris, France
| | - Fabien Pierrel
- Univ. Grenoble Alpes, CNRS, Grenoble INP, TIMC-IMAG, 38000 Grenoble, France.
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Nakayama T, Takahashi S, Waki T. Formation of Flavonoid Metabolons: Functional Significance of Protein-Protein Interactions and Impact on Flavonoid Chemodiversity. Front Plant Sci 2019; 10:821. [PMID: 31338097 PMCID: PMC6629762 DOI: 10.3389/fpls.2019.00821] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 06/07/2019] [Indexed: 05/21/2023]
Abstract
Flavonoids are a class of plant specialized metabolites with more than 6,900 known structures and play important roles in plant survival and reproduction. These metabolites are derived from p-coumaroyl-CoA via the sequential actions of a variety of flavonoid enzymes, which have been proposed to form weakly bound, ordered protein complexes termed flavonoid metabolons. This review discusses the impacts of the formation of flavonoid metabolons on the chemodiversity of flavonoids. Specific protein-protein interactions in the metabolons of Arabidopsis thaliana and other plant species have been studied for two decades. In many cases, metabolons are associated with the ER membrane, with ER-bound cytochromes P450 hypothesized to serve as nuclei for metabolon formation. Indeed, cytochromes P450 have been found to be components of flavonoid metabolons in rice, snapdragon, torenia, and soybean. Recent studies illustrate the importance of specific interactions for the efficient production and temporal/spatial distribution of flavonoids. For example, in diverse plant species, catalytically inactive type-IV chalcone isomerase-like protein serves as an enhancer of flavonoid production via its involvement in flavonoid metabolons. In soybean roots, a specific isozyme of chalcone reductase (CHR) interacts with 2-hydroxyisoflavanone synthase, to which chalcone synthase (CHS) can also bind, providing a mechanism to prevent the loss of the unstable CHR substrate during its transfer from CHS to CHR. Thus, diversification in chemical structures and temporal/spatial distribution patterns of flavonoids in plants is likely to be mediated by the formation of specific flavonoid metabolons via specific protein-protein interactions.
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Chan CY, Pedley AM, Kim D, Xia C, Zhuang X, Benkovic SJ. Microtubule-directed transport of purine metabolons drives their cytosolic transit to mitochondria. Proc Natl Acad Sci U S A 2018; 115:13009-14. [PMID: 30509995 DOI: 10.1073/pnas.1814042115] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
To meet their purine demand, cells activate the de novo purine biosynthetic pathway and transiently cluster the pathway enzymes into metabolons called purinosomes. Recently, we have shown that purinosomes were spatially colocalized with mitochondria and microtubules, yet it remained unclear as to what drives these associations and whether a relationship between them exist. Here, we employed superresolution imaging methods to describe purinosome transit in the context of subcellular localization. Time-resolved imaging of purinosomes showed that these assemblies exhibit directed motion as they move along a microtubule toward mitochondria, where upon colocalization, a change in purinosome motion was observed. A majority of purinosomes colocalized with mitochondria were also deemed colocalized with microtubules. Nocodazole-dependent microtubule depolymerization resulted in a loss in the purinosome-mitochondria colocalization, suggesting that the association of purinosomes with mitochondria is facilitated by microtubule-directed transport, and thereby supporting our notion of an interdependency between these subcellular components in maximizing purine production through the de novo purine biosynthetic pathway.
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Mameda R, Waki T, Kawai Y, Takahashi S, Nakayama T. Involvement of chalcone reductase in the soybean isoflavone metabolon: identification of GmCHR5, which interacts with 2-hydroxyisoflavanone synthase. Plant J 2018; 96:56-74. [PMID: 29979476 DOI: 10.1111/tpj.14014] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 06/08/2018] [Accepted: 06/20/2018] [Indexed: 05/02/2023]
Abstract
Soybean (Glycine max) 5-deoxyisoflavonoids (daidzein and its conjugates) are precursors of glyceollin phytoalexins. They are also converted to equol by microbes in the human intestine, resulting in health benefits. 5-Deoxyisoflavonoids accumulate in the roots (93% mol/mol of the total root isoflavonoids) and seeds of unstressed soybean plants. Chalcone reductase (CHR) is a key enzyme mediating 5-deoxyisoflavonoid biosynthesis because it catalyzes the production of 6'-deoxychalcone through its effects on the chalcone synthase (CHS)-catalyzed reaction. The soybean genome encodes at least 11 CHR-related homologs, but it is unclear which ones are functionally important for daidzein accumulation in unstressed plants. Among the CHR homologs, the temporal and spatial expression patterns of GmCHR5 were the most correlated with the distribution patterns of 5-deoxyisoflavonoids. The CHR activity of GmCHR5 was confirmed in vitro and in planta. In the in vitro assays, the ratio of CHR products (6'-deoxychalcone) to total CHS products (R value) was dependent on GmCHR5 and CHS concentrations, with higher concentrations resulting in higher R values (i.e. approaching 90%). Subcellular localization analyses revealed that GmCHR5 was present in the cytoplasm and nucleus. Protein-protein interaction assays indicated that GmCHR5, but not GmCHR1 and GmCHR6, interacted with 2-hydroxyisoflavanone synthase (IFS) isozymes. The CHS isozymes also interacted with IFS isozymes but not with GmCHR5. The proposed micro-compartmentalization of isoflavone biosynthesis through the formation of an IFS-mediated metabolon is probably involved in positioning GmCHR5 close to CHS, resulting in an R value that is high enough for the accumulation of abundant 5-deoxyisoflavonoids in soybean roots.
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Affiliation(s)
- Ryo Mameda
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aobayama 6-6-11, Sendai, 980-8579, Japan
| | - Toshiyuki Waki
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aobayama 6-6-11, Sendai, 980-8579, Japan
| | - Yosuke Kawai
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Seiji Takahashi
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aobayama 6-6-11, Sendai, 980-8579, Japan
| | - Toru Nakayama
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aobayama 6-6-11, Sendai, 980-8579, Japan
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Hsu K. Exploring the Potential Roles of Band 3 and Aquaporin-1 in Blood CO 2 Transport-Inspired by Comparative Studies of Glycophorin B-A-B Hybrid Protein GP.Mur. Front Physiol 2018; 9:733. [PMID: 29971013 PMCID: PMC6018491 DOI: 10.3389/fphys.2018.00733] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 05/25/2018] [Indexed: 12/15/2022] Open
Abstract
The Cl—/HCO3— exchanger band 3 is functionally relevant to blood CO2 transport. Band 3 is the most abundant membrane protein in human red blood cells (RBCs). Our understanding of its physiological functions mainly came from clinical cases associated with band 3 mutations. Severe reduction in band 3 expression affects blood HCO3—/CO2 metabolism. What could happen physiologically if band 3 expression is elevated instead? In some areas of Southeast Asia, about 1–10% of the populations express GP.Mur, a glycophorin B-A-B hybrid membrane protein important in the field of transfusion medicine. GP.Mur functions to promote band 3 expression, and GP.Mur red cells can be deemed as a naturally occurred model for higher band 3 expression. This review first compares the functional consequences of band 3 at different levels, and suggests a critical role of band 3 in postnatal CO2 respiration. The second part of the review explores the transport of water, which is the other substrate for intra-erythrocytic CO2/HCO3— conversion (an essential step in blood CO2 transport). Despite that water is considered unlimited physiologically, it is unclear whether water channel aquaporin-1 (AQP1) abundantly expressed in RBCs is functionally involved in CO2 transport. Research in this area is complicated by the fact that the H2O/CO2-transporting function of AQP1 is replaceable by other erythrocyte channels/transporters (e.g., UT-B/GLUT1 for H2O; RhAG for CO2). Recently, using carbonic anhydrase II (CAII)-filled erythrocyte vesicles, AQP1 has been demonstrated to transport water for the CAII-mediated reaction, CO2(g) + H2O ⇌ HCO3—(aq) + H+(aq). AQP1 is structurally associated with some population of band 3 complexes on the erythrocyte membrane in an osmotically responsive fashion. The current findings reveal transient interaction among components within the band 3-central, CO2-transport metabolon (AQP1, band 3, CAII and deoxygenated hemoglobin). Their dynamic interaction is envisioned to facilitate blood CO2 respiration, in the presence of constantly changing osmotic and hemodynamic stresses during circulation.
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Affiliation(s)
- Kate Hsu
- Transfusion Medicine and Immunogenetics Laboratories, MacKay Memorial Hospital, Tamsui, Taiwan
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Fujino N, Tenma N, Waki T, Ito K, Komatsuzaki Y, Sugiyama K, Yamazaki T, Yoshida S, Hatayama M, Yamashita S, Tanaka Y, Motohashi R, Denessiouk K, Takahashi S, Nakayama T. Physical interactions among flavonoid enzymes in snapdragon and torenia reveal the diversity in the flavonoid metabolon organization of different plant species. Plant J 2018; 94:372-392. [PMID: 29421843 DOI: 10.1111/tpj.13864] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 01/04/2018] [Accepted: 01/31/2018] [Indexed: 05/02/2023]
Abstract
Flavonoid metabolons (weakly-bound multi-enzyme complexes of flavonoid enzymes) are believed to occur in diverse plant species. However, how flavonoid enzymes are organized to form a metabolon is unknown for most plant species. We analyzed the physical interaction partnerships of the flavonoid enzymes from two lamiales plants (snapdragon and torenia) that produce flavones and anthocyanins. In snapdragon, protein-protein interaction assays using yeast and plant systems revealed the following binary interactions: flavone synthase II (FNSII)/chalcone synthase (CHS); FNSII/chalcone isomerase (CHI); FNSII/dihydroflavonol 4-reductase (DFR); CHS/CHI; CHI/DFR; and flavonoid 3'-hydroxylase/CHI. These results along with the subcellular localizations and membrane associations of snapdragon flavonoid enzymes suggested that FNSII serves as a component of the flavonoid metabolon tethered to the endoplasmic reticulum (ER). The observed interaction partnerships and temporal gene expression patterns of flavonoid enzymes in red snapdragon petal cells suggested the flower stage-dependent formation of the flavonoid metabolon, which accounted for the sequential flavone and anthocyanin accumulation patterns therein. We also identified interactions between FNSII and other flavonoid enzymes in torenia, in which the co-suppression of FNSII expression was previously reported to diminish petal anthocyanin contents. The observed physical interactions among flavonoid enzymes of these plant species provided further evidence supporting the long-suspected organization of flavonoid metabolons as enzyme complexes tethered to the ER via cytochrome P450, and illustrated how flavonoid metabolons mediate flower coloration. Moreover, the observed interaction partnerships were distinct from those previously identified in other plant species (Arabidopsis thaliana and soybean), suggesting that the organization of flavonoid metabolons may differ among plant species.
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Affiliation(s)
- Naoto Fujino
- Graduate School of Engineering, Tohoku University, Aza Aoba, Aramaki, Aoba 6-6-11, Sendai, Miyagi, 980-8579, Japan
| | - Natsuki Tenma
- Graduate School of Engineering, Tohoku University, Aza Aoba, Aramaki, Aoba 6-6-11, Sendai, Miyagi, 980-8579, Japan
| | - Toshiyuki Waki
- Graduate School of Engineering, Tohoku University, Aza Aoba, Aramaki, Aoba 6-6-11, Sendai, Miyagi, 980-8579, Japan
| | - Keisuke Ito
- Graduate School of Engineering, Tohoku University, Aza Aoba, Aramaki, Aoba 6-6-11, Sendai, Miyagi, 980-8579, Japan
| | - Yuki Komatsuzaki
- Graduate School of Engineering, Tohoku University, Aza Aoba, Aramaki, Aoba 6-6-11, Sendai, Miyagi, 980-8579, Japan
| | - Keigo Sugiyama
- Graduate School of Engineering, Tohoku University, Aza Aoba, Aramaki, Aoba 6-6-11, Sendai, Miyagi, 980-8579, Japan
| | - Tatsuya Yamazaki
- Graduate School of Engineering, Tohoku University, Aza Aoba, Aramaki, Aoba 6-6-11, Sendai, Miyagi, 980-8579, Japan
| | - Saori Yoshida
- Graduate School of Engineering, Tohoku University, Aza Aoba, Aramaki, Aoba 6-6-11, Sendai, Miyagi, 980-8579, Japan
| | - Masayoshi Hatayama
- Graduate School of Engineering, Tohoku University, Aza Aoba, Aramaki, Aoba 6-6-11, Sendai, Miyagi, 980-8579, Japan
| | - Satoshi Yamashita
- Graduate School of Engineering, Tohoku University, Aza Aoba, Aramaki, Aoba 6-6-11, Sendai, Miyagi, 980-8579, Japan
| | - Yoshikazu Tanaka
- Suntory World Research Center, Suntory Holdings Ltd., Soraku-gun, Kyoto, 619-0284, Japan
| | - Reiko Motohashi
- Department of Biological and Environmental Science, Faculty of Agriculture, Shizuoka University, Shizuoka, 422-8529, Japan
| | | | - Seiji Takahashi
- Graduate School of Engineering, Tohoku University, Aza Aoba, Aramaki, Aoba 6-6-11, Sendai, Miyagi, 980-8579, Japan
| | - Toru Nakayama
- Graduate School of Engineering, Tohoku University, Aza Aoba, Aramaki, Aoba 6-6-11, Sendai, Miyagi, 980-8579, Japan
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Guo H, Zhong Y, Jackson AL, Clark LH, Kilgore J, Zhang L, Han J, Sheng X, Gilliam TP, Gehrig PA, Zhou C, Bae-Jump VL. Everolimus exhibits anti-tumorigenic activity in obesity-induced ovarian cancer. Oncotarget 2018; 7:20338-56. [PMID: 26959121 PMCID: PMC4991459 DOI: 10.18632/oncotarget.7934] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 01/24/2016] [Indexed: 01/21/2023] Open
Abstract
Everolimus inhibits mTOR kinase activity and its downstream targets by acting on mTORC1 and has anti-tumorigenic activity in ovarian cancer. Clinical and epidemiologic data find that obesity is associated with worse outcomes in ovarian cancer. In addition, obesity leads to hyperactivation of the mTOR pathway in epithelial tissues, suggesting that mTOR inhibitors may be a logical choice for treatment in obesity-driven cancers. However, it remains unclear if obesity impacts the effect of everolimus on tumor growth in ovarian cancer. The present study was aimed at evaluating the effects of everolimus on cytotoxicity, cell metabolism, apoptosis, cell cycle, cell stress and invasion in human ovarian cancer cells. A genetically engineered mouse model of serous ovarian cancer fed a high fat diet or low fat diet allowed further investigation into the inter-relationship between everolimus and obesity in vivo. Everolimus significantly inhibited cellular proliferation, induced cell cycle G1 arrest and apoptosis, reduced invasion and caused cellular stress via inhibition of mTOR pathways in vitro. Hypoglycemic conditions enhanced the sensitivity of cells to everolimus through the disruption of glycolysis. Moreover, everolimus was found to inhibit ovarian tumor growth in both obese and lean mice. This reduction coincided with a decrease in expression of Ki-67 and phosphorylated-S6, as well as an increase in cleaved caspase 3 and phosphorylated-AKT. Metabolite profiling revealed that everolimus was able to alter tumor metabolism through different metabolic pathways in the obese and lean mice. Our findings support that everolimus may be a promising therapeutic agent for obesity-driven ovarian cancers.
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Affiliation(s)
- Hui Guo
- Department of Gynecologic Oncology, Shandong Cancer Hospital and Institute, Jinan University, Jinan, P.R. China.,Division of Gynecologic Oncology, University of North Carolina, Chapel Hill, NC, USA.,School of Medicine and Life Sciences, University of Jinan, Shandong Academy of Medical Sciences, Shandong, P.R. China
| | - Yan Zhong
- Division of Gynecologic Oncology, University of North Carolina, Chapel Hill, NC, USA.,Department of Gynecologic Oncology, Linyi Cancer Hospital, Linyi, P.R. China
| | - Amanda L Jackson
- Division of Gynecologic Oncology, University of North Carolina, Chapel Hill, NC, USA
| | - Leslie H Clark
- Division of Gynecologic Oncology, University of North Carolina, Chapel Hill, NC, USA
| | - Josh Kilgore
- Division of Gynecologic Oncology, University of North Carolina, Chapel Hill, NC, USA
| | - Lu Zhang
- Department of Gynecologic Oncology, Shandong Cancer Hospital and Institute, Jinan University, Jinan, P.R. China.,Division of Gynecologic Oncology, University of North Carolina, Chapel Hill, NC, USA.,School of Medicine and Life Sciences, University of Jinan, Shandong Academy of Medical Sciences, Shandong, P.R. China
| | - Jianjun Han
- Division of Gynecologic Oncology, University of North Carolina, Chapel Hill, NC, USA.,Department of Surgical Oncology, Shandong Cancer Hospital and Institute, Jinan, P.R. China
| | - Xiugui Sheng
- Department of Gynecologic Oncology, Shandong Cancer Hospital and Institute, Jinan University, Jinan, P.R. China
| | - Timothy P Gilliam
- Division of Gynecologic Oncology, University of North Carolina, Chapel Hill, NC, USA
| | - Paola A Gehrig
- Division of Gynecologic Oncology, University of North Carolina, Chapel Hill, NC, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Chunxiao Zhou
- Division of Gynecologic Oncology, University of North Carolina, Chapel Hill, NC, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Victoria L Bae-Jump
- Division of Gynecologic Oncology, University of North Carolina, Chapel Hill, NC, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
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40
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Stefely JA, Pagliarini DJ. Biochemistry of Mitochondrial Coenzyme Q Biosynthesis. Trends Biochem Sci 2017; 42:824-843. [PMID: 28927698 DOI: 10.1016/j.tibs.2017.06.008] [Citation(s) in RCA: 194] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Revised: 06/14/2017] [Accepted: 06/22/2017] [Indexed: 11/16/2022]
Abstract
Coenzyme Q (CoQ, ubiquinone) is a redox-active lipid produced across all domains of life that functions in electron transport and oxidative phosphorylation and whose deficiency causes human diseases. Yet, CoQ biosynthesis has not been fully defined in any organism. Several proteins with unclear molecular functions facilitate CoQ biosynthesis through unknown means, and multiple steps in the pathway are catalyzed by currently unidentified enzymes. Here we highlight recent progress toward filling these knowledge gaps through both traditional biochemistry and cutting-edge 'omics' approaches. To help fill the remaining gaps, we present questions framed by the recently discovered CoQ biosynthetic complex and by putative biophysical barriers. Mapping CoQ biosynthesis, metabolism, and transport pathways has great potential to enhance treatment of numerous human diseases.
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Affiliation(s)
- Jonathan A Stefely
- Morgridge Institute for Research, Madison, WI, USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA; School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - David J Pagliarini
- Morgridge Institute for Research, Madison, WI, USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA.
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41
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Kastritis PL, O'Reilly FJ, Bock T, Li Y, Rogon MZ, Buczak K, Romanov N, Betts MJ, Bui KH, Hagen WJ, Hennrich ML, Mackmull MT, Rappsilber J, Russell RB, Bork P, Beck M, Gavin AC. Capturing protein communities by structural proteomics in a thermophilic eukaryote. Mol Syst Biol 2017; 13:936. [PMID: 28743795 PMCID: PMC5527848 DOI: 10.15252/msb.20167412] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The arrangement of proteins into complexes is a key organizational principle for many cellular functions. Although the topology of many complexes has been systematically analyzed in isolation, their molecular sociology in situ remains elusive. Here, we show that crude cellular extracts of a eukaryotic thermophile, Chaetomium thermophilum, retain basic principles of cellular organization. Using a structural proteomics approach, we simultaneously characterized the abundance, interactions, and structure of a third of the C. thermophilum proteome within these extracts. We identified 27 distinct protein communities that include 108 interconnected complexes, which dynamically associate with each other and functionally benefit from being in close proximity in the cell. Furthermore, we investigated the structure of fatty acid synthase within these extracts by cryoEM and this revealed multiple, flexible states of the enzyme in adaptation to its association with other complexes, thus exemplifying the need for in situ studies. As the components of the captured protein communities are known—at both the protein and complex levels—this study constitutes another step forward toward a molecular understanding of subcellular organization.
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Affiliation(s)
- Panagiotis L Kastritis
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Francis J O'Reilly
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany.,Chair of Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Thomas Bock
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Yuanyue Li
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Matt Z Rogon
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Katarzyna Buczak
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Natalie Romanov
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Matthew J Betts
- Cell Networks, Bioquant & Biochemie Zentrum Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Khanh Huy Bui
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany.,Department of Anatomy and Cell Biology, McGill University, Montreal, QC, Canada
| | - Wim J Hagen
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Marco L Hennrich
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Marie-Therese Mackmull
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Juri Rappsilber
- Chair of Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany.,Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Robert B Russell
- Cell Networks, Bioquant & Biochemie Zentrum Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Peer Bork
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Martin Beck
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Anne-Claude Gavin
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
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42
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Cohen RD, Pielak GJ. A cell is more than the sum of its (dilute) parts: A brief history of quinary structure. Protein Sci 2017; 26:403-413. [PMID: 27977883 PMCID: PMC5326556 DOI: 10.1002/pro.3092] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 12/02/2016] [Accepted: 12/02/2016] [Indexed: 01/01/2023]
Abstract
Most knowledge of protein structure and function is derived from experiments performed with purified protein resuspended in dilute, buffered solutions. However, proteins function in the crowded, complex cellular environment. Although the first four levels of protein structure provide important information, a complete understanding requires consideration of quinary structure. Quinary structure comprises the transient interactions between macromolecules that provides organization and compartmentalization inside cells. We review the history of quinary structure in the context of several metabolic pathways, and the technological advances that have yielded recent insight into protein behavior in living cells. The evidence demonstrates that protein behavior in isolated solutions deviates from behavior in the physiological environment.
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Affiliation(s)
- Rachel D. Cohen
- Department of ChemistryUniversity of North CarolinaChapel HillNorth Carolina27599
| | - Gary J. Pielak
- Department of ChemistryUniversity of North CarolinaChapel HillNorth Carolina27599
- Department of Biochemistry and BiophysicsUniversity of North CarolinaChapel HillNorth Carolina27599
- Lineberger Comprehensive Cancer Center, University of North CarolinaChapel HillNorth Carolina27599
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43
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Pedley AM, Benkovic SJ. A New View into the Regulation of Purine Metabolism: The Purinosome. Trends Biochem Sci 2016; 42:141-154. [PMID: 28029518 DOI: 10.1016/j.tibs.2016.09.009] [Citation(s) in RCA: 311] [Impact Index Per Article: 38.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 09/23/2016] [Accepted: 09/26/2016] [Indexed: 10/20/2022]
Abstract
Other than serving as building blocks for DNA and RNA, purine metabolites provide a cell with the necessary energy and cofactors to promote cell survival and proliferation. A renewed interest in how purine metabolism may fuel cancer progression has uncovered a new perspective into how a cell regulates purine need. Under cellular conditions of high purine demand, the de novo purine biosynthetic enzymes cluster near mitochondria and microtubules to form dynamic multienzyme complexes referred to as 'purinosomes'. In this review, we highlight the purinosome as a novel level of metabolic organization of enzymes in cells, its consequences for regulation of purine metabolism, and the extent that purine metabolism is being targeted for the treatment of cancers.
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Affiliation(s)
- Anthony M Pedley
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Stephen J Benkovic
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA.
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44
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Yasid NA, Rolfe MD, Green J, Williamson MP. Homeostasis of metabolites in Escherichia coli on transition from anaerobic to aerobic conditions and the transient secretion of pyruvate. R Soc Open Sci 2016; 3:160187. [PMID: 27853594 PMCID: PMC5108944 DOI: 10.1098/rsos.160187] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 07/29/2016] [Indexed: 06/06/2023]
Abstract
We have developed a method for rapid quenching of samples taken from chemostat cultures of Escherichia coli that gives reproducible and reliable measurements of extracellular and intracellular metabolites by 1H NMR and have applied it to study the major central metabolites during the transition from anaerobic to aerobic growth. Almost all metabolites showed a gradual change after perturbation with air, consistent with immediate inhibition of pyruvate formate-lyase, dilution of overflow metabolites and induction of aerobic enzymes. Surprisingly, although pyruvate showed almost no change in intracellular concentration, the extracellular concentration transiently increased. The absence of intracellular accumulation of pyruvate suggested that one or more glycolytic enzymes might relocate to the cell membrane. To test this hypothesis, chromosomal pyruvate kinase (pykF) was modified to express either PykF-green fluorescent protein or PykF-FLAG fusion proteins. Measurements showed that PykF-FLAG relocates to the cell membrane within 5 min of aeration and then slowly returns to the cytoplasm, suggesting that on aeration, PykF associates with the membrane to facilitate secretion of pyruvate to maintain constant intracellular levels.
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45
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Kriechbaumer V, Botchway SW, Hawes C. Localization and interactions between Arabidopsis auxin biosynthetic enzymes in the TAA/YUC-dependent pathway. J Exp Bot 2016; 67:4195-207. [PMID: 27208541 DOI: 10.1093/jxb/erw195] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The growth regulator auxin is involved in all key developmental processes in plants. A complex network of a multiplicity of potential biosynthetic pathways as well as transport, signalling plus conjugation and deconjugation lead to a complex and multifaceted system system for auxin function. This raises the question how such a system can be effectively organized and controlled. Here we report that a subset of auxin biosynthetic enzymes in the TAA/YUC route of auxin biosynthesis is localized to the endoplasmic reticulum (ER). ER microsomal fractions also contain a significant percentage of auxin biosynthetic activity. This could point toward a model of auxin function using ER membrane location and subcellular compartmentation for supplementary layers of regulation. Additionally we show specific protein-protein interactions between some of the enzymes in the TAA/YUC route of auxin biosynthesis.
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Affiliation(s)
- Verena Kriechbaumer
- Plant Cell Biology, Biological and Medical Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Stanley W Botchway
- Central Laser Facility, Science and Technology Facilities Council (STFC) Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot OX11 0QX, UK
| | - Chris Hawes
- Plant Cell Biology, Biological and Medical Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
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46
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Dastmalchi M, Bernards MA, Dhaubhadel S. Twin anchors of the soybean isoflavonoid metabolon: evidence for tethering of the complex to the endoplasmic reticulum by IFS and C4H. Plant J 2016; 85:689-706. [PMID: 26856401 DOI: 10.1111/tpj.13137] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 01/26/2016] [Accepted: 02/01/2016] [Indexed: 05/02/2023]
Abstract
Isoflavonoids are specialized plant metabolites, almost exclusive to legumes, and their biosynthesis forms a branch of the diverse phenylpropanoid pathway. Plant metabolism may be coordinated at many levels, including formation of protein complexes, or 'metabolons', which represent the molecular level of organization. Here, we have confirmed the existence of the long-postulated isoflavonoid metabolon by identifying elements of the complex, their subcellular localizations and their interactions. Isoflavone synthase (IFS) and cinnamate 4-hydroxylase (C4H) have been shown to be tandem P450 enzymes that are anchored in the ER, interacting with soluble enzymes of the phenylpropanoid and isoflavonoid pathways (chalcone synthase, chalcone reductase and chalcone isomerase). The soluble enzymes of these pathways, whether localized to the cytoplasm or nucleus, are tethered to the ER through interaction with these P450s. The complex is also held together by interactions between the soluble elements. We provide evidence for IFS interaction with upstream and non-consecutive enzymes. The existence of such a protein complex suggests a possible mechanism for flux of metabolites into the isoflavonoid pathway. Further, through interaction studies, we identified several candidates that are associated with GmIFS2, an isoform of IFS, in soybean hairy roots. This list provides additional candidates for various biosynthetic and structural elements that are involved in isoflavonoid production. Our interaction studies provide valuable information about isoform specificity among isoflavonoid enzymes, which may guide future engineering of the pathway in legumes or help overcome bottlenecks in heterologous expression.
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Affiliation(s)
- Mehran Dastmalchi
- Department of Biology, University of Western Ontario, London, Ontario, Canada
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, Ontario, Canada
| | - Mark A Bernards
- Department of Biology, University of Western Ontario, London, Ontario, Canada
| | - Sangeeta Dhaubhadel
- Department of Biology, University of Western Ontario, London, Ontario, Canada
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, Ontario, Canada
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47
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Abstract
In the past century, few areas of biology advanced as much as our understanding of the pathways of intermediary metabolism. Initially considered unimportant in terms of gene regulation, crucial cellular fate changes, cell differentiation, or malignant transformation are now known to involve 'metabolic remodeling' with profound changes in the expression of many metabolic enzyme genes. This review focuses on the recent identification of RNA-binding activity of numerous metabolic enzymes. We discuss possible roles of this unexpected second activity in feedback gene regulation ('moonlighting') and/or in the control of enzymatic function. We also consider how metabolism-driven post-translational modifications could regulate enzyme-RNA interactions. Thus, RNA emerges as a new partner of metabolic enzymes with far-reaching possible consequences to be unraveled in the future.
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Affiliation(s)
- Alfredo Castello
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Matthias W Hentze
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
| | - Thomas Preiss
- EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Acton (Canberra), ACT 2601, Australia; Victor Chang Cardiac Research Institute, Darlinghurst (Sydney), New South Wales 2010, Australia
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48
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Aleshin VA, Artiukhov AV, Oppermann H, Kazantsev AV, Lukashev NV, Bunik VI. Mitochondrial Impairment May Increase Cellular NAD(P)H: Resazurin Oxidoreductase Activity, Perturbing the NAD(P)H-Based Viability Assays. Cells 2015; 4:427-51. [PMID: 26308058 DOI: 10.3390/cells4030427] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 08/11/2015] [Accepted: 08/12/2015] [Indexed: 01/10/2023] Open
Abstract
Cellular NAD(P)H-dependent oxidoreductase activity with artificial dyes (NAD(P)H-OR) is an indicator of viability, as the cellular redox state is important for biosynthesis and antioxidant defense. However, high NAD(P)H due to impaired mitochondrial oxidation, known as reductive stress, should increase NAD(P)H-OR yet perturb viability. To better understand this complex behavior, we assayed NAD(P)H-OR with resazurin (Alamar Blue) in glioblastoma cell lines U87 and T98G, treated with inhibitors of central metabolism, oxythiamin, and phosphonate analogs of 2-oxo acids. Targeting the thiamin diphosphate (ThDP)-dependent enzymes, the inhibitors are known to decrease the NAD(P)H production in the pentose phosphate shuttle and/or upon mitochondrial oxidation of 2-oxo acids. Nevertheless, the inhibitors elevated NAD(P)H-OR with resazurin in a time- and concentration-dependent manner, suggesting impaired NAD(P)H oxidation rather than increased viability. In particular, inhibition of the ThDP-dependent enzymes affects metabolism of malate, which mediates mitochondrial oxidation of cytosolic NAD(P)H. We showed that oxythiamin not only inhibited mitochondrial 2-oxo acid dehydrogenases, but also induced cell-specific changes in glutamate and malate dehydrogenases and/or malic enzyme. As a result, inhibition of the 2-oxo acid dehydrogenases compromises mitochondrial metabolism, with the dysregulated electron fluxes leading to increases in cellular NAD(P)H-OR. Perturbed mitochondrial oxidation of NAD(P)H may thus complicate the NAD(P)H-based viability assay.
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49
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Wang N, McCammon JA. Substrate channeling between the human dihydrofolate reductase and thymidylate synthase. Protein Sci 2015; 25:79-86. [PMID: 26096018 DOI: 10.1002/pro.2720] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 06/02/2015] [Accepted: 06/05/2015] [Indexed: 12/17/2022]
Abstract
In vivo, as an advanced catalytic strategy, transient non-covalently bound multi-enzyme complexes can be formed to facilitate the relay of substrates, i. e. substrate channeling, between sequential enzymatic reactions and to enhance the throughput of multi-step enzymatic pathways. The human thymidylate synthase and dihydrofolate reductase catalyze two consecutive reactions in the folate metabolism pathway, and experiments have shown that they are very likely to bind in the same multi-enzyme complex in vivo. While reports on the protozoa thymidylate synthase-dihydrofolate reductase bifunctional enzyme give substantial evidences of substrate channeling along a surface "electrostatic highway," attention has not been paid to whether the human thymidylate synthase and dihydrofolate reductase, if they are in contact with each other in the multi-enzyme complex, are capable of substrate channeling employing surface electrostatics. This work utilizes protein-protein docking, electrostatics calculations, and Brownian dynamics to explore the existence and mechanism of the substrate channeling between the human thymidylate synthase and dihydrofolate reductase. The results show that the bound human thymidylate synthase and dihydrofolate reductase are capable of substrate channeling and the formation of the surface "electrostatic highway." The substrate channeling efficiency between the two can be reasonably high and comparable to that of the protozoa.
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Affiliation(s)
- Nuo Wang
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, 92037
| | - J Andrew McCammon
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, 92037.,Department of Pharmacology, University of California San Diego, La Jolla, California, 92037.,Howard Hughes Medical Institute, University of California San Diego, La Jolla, California, 92037
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50
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Weis C, Hildebrandt U, Hoffmann T, Hemetsberger C, Pfeilmeier S, König C, Schwab W, Eichmann R, Hückelhoven R. CYP83A1 is required for metabolic compatibility of Arabidopsis with the adapted powdery mildew fungus Erysiphe cruciferarum. New Phytol 2014; 202:1310-1319. [PMID: 24602105 DOI: 10.1111/nph.12759] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 02/07/2014] [Indexed: 05/08/2023]
Abstract
Aliphatic glucosinolates function in the chemical defense of Capparales. The cytochrome P450 83A1 monooxygenase (CYP83A1) catalyzes the initial conversion of methionine-derived aldoximes to thiohydroximates in the biosynthesis of glucosinolates, and thus cyp83a1 mutants have reduced levels of aliphatic glucosinolates. Loss of CYP83A1 function leads to dramatically reduced parasitic growth of the biotrophic powdery mildew fungus Erysiphe cruciferarum on Arabidopsis thaliana. The cyp83a1 mutants support less well the germination and appressorium formation of E. cruciferarum on the leaf surface and post-penetration conidiophore formation by the fungus. By contrast, a myb28-1 myb29-1 double mutant, which totally lacks aliphatic glucosinolates, shows a wild-type level of susceptibility to E. cruciferarum. The cyp83a1 mutants also lack very-long-chain aldehydes on their leaf surface. Such aldehydes support appressorium formation by E. cruciferarum in vitro. In addition, when chemically complemented with the C26 aldehyde n-hexacosanal, cyp83a1 mutants can again support appressorium formation. The mutants further accumulate 5-methylthiopentanaldoxime, the potentially toxic substrate of CYP83A1. Loss of powdery mildew susceptibility by cyp83a1 may be explained by a reduced supply of the fungus with inductive signals from the host and an accumulation of potentially fungitoxic metabolites.
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Affiliation(s)
- Corina Weis
- Lehrstuhl für Phytopathologie, Technische Universität München, Emil-Ramann-Straße 2, 85354, Freising, Germany
| | - Ulrich Hildebrandt
- Julius-von-Sachs-Institut für Biowissenschaften, Lehrstuhl für Botanik II, Universität Würzburg, Julius-von-Sachs-Platz 3, 97082, Würzburg, Germany
| | - Thomas Hoffmann
- Biotechnologie der Naturstoffe, Technische Universität München, Liesel-Beckmann-Str. 1, 85354, Freising, Germany
| | - Christoph Hemetsberger
- Lehrstuhl für Phytopathologie, Technische Universität München, Emil-Ramann-Straße 2, 85354, Freising, Germany
| | - Sebastian Pfeilmeier
- Lehrstuhl für Phytopathologie, Technische Universität München, Emil-Ramann-Straße 2, 85354, Freising, Germany
| | - Constanze König
- Lehrstuhl für Phytopathologie, Technische Universität München, Emil-Ramann-Straße 2, 85354, Freising, Germany
| | - Wilfried Schwab
- Biotechnologie der Naturstoffe, Technische Universität München, Liesel-Beckmann-Str. 1, 85354, Freising, Germany
| | - Ruth Eichmann
- Lehrstuhl für Phytopathologie, Technische Universität München, Emil-Ramann-Straße 2, 85354, Freising, Germany
| | - Ralph Hückelhoven
- Lehrstuhl für Phytopathologie, Technische Universität München, Emil-Ramann-Straße 2, 85354, Freising, Germany
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