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Pfeffer T, Krug SM, Kracke T, Schürfeld R, Colbatzky F, Kirschner P, Medert R, Freichel M, Schumacher D, Bartosova M, Zarogiannis SG, Muckenthaler MU, Altamura S, Pezer S, Volk N, Schwab C, Duensing S, Fleming T, Heidenreich E, Zschocke J, Hell R, Poschet G, Schmitt CP, Peters V. Knock-out of dipeptidase CN2 in human proximal tubular cells disrupts dipeptide and amino acid homeostasis and para- and transcellular solute transport. Acta Physiol (Oxf) 2024; 240:e14126. [PMID: 38517248 DOI: 10.1111/apha.14126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 02/15/2024] [Accepted: 02/21/2024] [Indexed: 03/23/2024]
Abstract
AIM Although of potential biomedical relevance, dipeptide metabolism has hardly been studied. We found the dipeptidase carnosinase-2 (CN2) to be abundant in human proximal tubules, which regulate water and solute homeostasis. We therefore hypothesized, that CN2 has a key metabolic role, impacting proximal tubular transport function. METHODS A knockout of the CN2 gene (CNDP2-KO) was generated in human proximal tubule cells and characterized by metabolomics, RNA-seq analysis, paracellular permeability analysis and ion transport. RESULTS CNDP2-KO in human proximal tubule cells resulted in the accumulation of cellular dipeptides, reduction of amino acids and imbalance of related metabolic pathways, and of energy supply. RNA-seq analyses indicated altered protein metabolism and ion transport. Detailed functional studies demonstrated lower CNDP2-KO cell viability and proliferation, and altered ion and macromolecule transport via trans- and paracellular pathways. Regulatory and transport protein abundance was disturbed, either as a consequence of the metabolic imbalance or the resulting functional disequilibrium. CONCLUSION CN2 function has a major impact on intracellular amino acid and dipeptide metabolism and is essential for key metabolic and regulatory functions of proximal tubular cells. These findings deserve in vivo analysis of the relevance of CN2 for nephron function and regulation of body homeostasis.
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Affiliation(s)
- Tilman Pfeffer
- Medical Faculty Heidelberg, Center for Pediatric and Adolescent Medicine, Department I, Division of Pediatric Neurology and Metabolic Medicine, Heidelberg University, Heidelberg, Germany
- Tissue Bank of the German Center for Infection Research (DZIF), Partner Site Heidelberg, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Susanne M Krug
- Clinical Physiology/Nutritional Medicine, Charité-Universitätsmedizin Berlin, CBF, Berlin, Germany
| | - Tamara Kracke
- Medical Faculty Heidelberg, Center for Pediatric and Adolescent Medicine, Department I, Division of Pediatric Neurology and Metabolic Medicine, Heidelberg University, Heidelberg, Germany
| | - Robin Schürfeld
- Medical Faculty Heidelberg, Center for Pediatric and Adolescent Medicine, Department I, Division of Pediatric Neurology and Metabolic Medicine, Heidelberg University, Heidelberg, Germany
| | - Florian Colbatzky
- Medical Faculty Heidelberg, Center for Pediatric and Adolescent Medicine, Department I, Division of Pediatric Neurology and Metabolic Medicine, Heidelberg University, Heidelberg, Germany
| | - Philip Kirschner
- Medical Faculty Heidelberg, Center for Pediatric and Adolescent Medicine, Department I, Division of Pediatric Neurology and Metabolic Medicine, Heidelberg University, Heidelberg, Germany
| | - Rebekka Medert
- Institute of Pharmacology, Heidelberg University, Heidelberg, Germany
| | - Marc Freichel
- Institute of Pharmacology, Heidelberg University, Heidelberg, Germany
| | - Dagmar Schumacher
- Institute of Pharmacology, Heidelberg University, Heidelberg, Germany
| | - Maria Bartosova
- Medical Faculty Heidelberg, Center for Pediatric and Adolescent Medicine, Department I, Division of Pediatric Neurology and Metabolic Medicine, Heidelberg University, Heidelberg, Germany
| | - Sotiris G Zarogiannis
- Medical Faculty Heidelberg, Center for Pediatric and Adolescent Medicine, Department I, Division of Pediatric Neurology and Metabolic Medicine, Heidelberg University, Heidelberg, Germany
| | - Martina U Muckenthaler
- Department of Pediatric Oncology, Hematology and Immunology and Hopp Children Cancer Center (KiTZ), University Hospital Heidelberg, Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), EMBL and University of Heidelberg, Heidelberg, Germany
- Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), University of Heidelberg, Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Sandro Altamura
- Department of Pediatric Oncology, Hematology and Immunology and Hopp Children Cancer Center (KiTZ), University Hospital Heidelberg, Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), EMBL and University of Heidelberg, Heidelberg, Germany
| | - Silvia Pezer
- Medical Faculty Heidelberg, Center for Pediatric and Adolescent Medicine, Department I, Division of Pediatric Neurology and Metabolic Medicine, Heidelberg University, Heidelberg, Germany
| | - Nadine Volk
- Tissue Bank of the National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Constantin Schwab
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Stefan Duensing
- Department of Urology, University Hospital Heidelberg and National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany
| | - Thomas Fleming
- Internal Medicine I and Clinical Chemistry, University Hospital Heidelberg, Heidelberg, Germany
| | - Elena Heidenreich
- Centre for Organismal Studies (COS), University of Heidelberg, Heidelberg, Germany
| | - Johannes Zschocke
- Institute of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Rüdiger Hell
- Centre for Organismal Studies (COS), University of Heidelberg, Heidelberg, Germany
| | - Gernot Poschet
- Centre for Organismal Studies (COS), University of Heidelberg, Heidelberg, Germany
| | - Claus P Schmitt
- Medical Faculty Heidelberg, Center for Pediatric and Adolescent Medicine, Department I, Division of Pediatric Neurology and Metabolic Medicine, Heidelberg University, Heidelberg, Germany
| | - Verena Peters
- Medical Faculty Heidelberg, Center for Pediatric and Adolescent Medicine, Department I, Division of Pediatric Neurology and Metabolic Medicine, Heidelberg University, Heidelberg, Germany
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Boytsov D, Madej GM, Horn G, Blaha N, Köcher T, Sitte HH, Siekhaus D, Ziegler C, Sandtner W, Roblek M. Orphan lysosomal solute carrier MFSD1 facilitates highly selective dipeptide transport. Proc Natl Acad Sci U S A 2024; 121:e2319686121. [PMID: 38507452 PMCID: PMC10990142 DOI: 10.1073/pnas.2319686121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 02/27/2024] [Indexed: 03/22/2024] Open
Abstract
Orphan solute carrier (SLC) represents a group of membrane transporters whose exact functions and substrate specificities are not known. Elucidating the function and regulation of orphan SLC transporters is not only crucial for advancing our knowledge of cellular and molecular biology but can potentially lead to the development of new therapeutic strategies. Here, we provide evidence for the biological function of a ubiquitous orphan lysosomal SLC, the Major Facilitator Superfamily Domain-containing Protein 1 (MFSD1), which has remained phylogenetically unassigned. Targeted metabolomics revealed that dipeptides containing either lysine or arginine residues accumulate in lysosomes of cells lacking MFSD1. Whole-cell patch-clamp electrophysiological recordings of HEK293-cells expressing MFSD1 on the cell surface displayed transport affinities for positively charged dipeptides in the lower mM range, while dipeptides that carry a negative net charge were not transported. This was also true for single amino acids and tripeptides, which MFSD1 failed to transport. Our results identify MFSD1 as a highly selective lysosomal lysine/arginine/histidine-containing dipeptide exporter, which functions as a uniporter.
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Affiliation(s)
- Danila Boytsov
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, ViennaAT-1090, Austria
| | - Gregor M. Madej
- Department of Biophysics II/Structural Biology, University of Regensburg, RegensburgDE-93053, Germany
| | - Georg Horn
- Department of Biophysics II/Structural Biology, University of Regensburg, RegensburgDE-93053, Germany
| | - Nadine Blaha
- Vienna BioCenter Core Facilities, Metabolomics, Vienna BioCenter, ViennaAT-1030, Austria
| | - Thomas Köcher
- Vienna BioCenter Core Facilities, Metabolomics, Vienna BioCenter, ViennaAT-1030, Austria
| | - Harald H. Sitte
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, ViennaAT-1090, Austria
- Hourani Center for Applied Scientific Research, Al-Ahliyya Amman University, AmmanJO-19328, Jordan
- Center for Addiction Research and Science, Medical University of Vienna, ViennaAT-1090, Austria
| | - Daria Siekhaus
- Institute of Science and Technology Austria, KlosterneuburgAT-3400, Austria
| | - Christine Ziegler
- Department of Biophysics II/Structural Biology, University of Regensburg, RegensburgDE-93053, Germany
| | - Walter Sandtner
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, ViennaAT-1090, Austria
| | - Marko Roblek
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, ViennaAT-1090, Austria
- Institute of Science and Technology Austria, KlosterneuburgAT-3400, Austria
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3
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Leporino M, Rouphael Y, Bonini P, Colla G, Cardarelli M. Protein hydrolysates enhance recovery from drought stress in tomato plants: phenomic and metabolomic insights. FRONTIERS IN PLANT SCIENCE 2024; 15:1357316. [PMID: 38533405 PMCID: PMC10963501 DOI: 10.3389/fpls.2024.1357316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 02/09/2024] [Indexed: 03/28/2024]
Abstract
Introduction High-throughput phenotyping technologies together with metabolomics analysis can speed up the development of highly efficient and effective biostimulants for enhancing crop tolerance to drought stress. The aim of this study was to examine the morphophysiological and metabolic changes in tomato plants foliarly treated with two protein hydrolysates obtained by enzymatic hydrolysis of vegetal proteins from Malvaceae (PH1) or Fabaceae (PH2) in comparison with a control treatment, as well as to investigate the mechanisms involved in the enhancement of plant resistance to repeated drought stress cycles. Methods A phenotyping device was used for daily monitoring morphophysiological traits while untargeted metabolomics analysis was carried out in leaves of the best performing treatment based on phenotypic results.Results: PH1 treatment was the most effective in enhancing plant resistance to water stress due to the better recovery of digital biomass and 3D leaf area after each water stress event while PH2 was effective in mitigating water stress only during the recovery period after the first drought stress event. Metabolomics data indicated that PH1 modified primary metabolism by increasing the concentration of dipeptides and fatty acids in comparison with untreated control, as well as secondary metabolism by regulating several compounds like phenols. In contrast, hormones and compounds involved in detoxification or signal molecules against reactive oxygen species were downregulated in comparison with untreated control. Conclusion The above findings demonstrated the advantages of a combined phenomics-metabolomics approach for elucidating the relationship between metabolic and morphophysiological changes associated with a biostimulant-mediated increase of crop resistance to repeated water stress events.
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Affiliation(s)
- Marzia Leporino
- Department of Agriculture and Forest Sciences, University of Tuscia, Viterbo, Italy
| | - Youssef Rouphael
- Department of Agricultural Sciences at the University of Naples, Portici, Italy
| | - Paolo Bonini
- oloBion SL, Barcelona, Spain
- Arcadia s.r.l., Rivoli Veronese, Italy
| | - Giuseppe Colla
- Department of Agriculture and Forest Sciences, University of Tuscia, Viterbo, Italy
- Arcadia s.r.l., Rivoli Veronese, Italy
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Tamizhselvan P, Madhavan S, Constan-Aguilar C, Elrefaay ER, Liu J, Pěnčík A, Novák O, Cairó A, Hrtyan M, Geisler M, Tognetti VB. Chloroplast Auxin Efflux Mediated by ABCB28 and ABCB29 Fine-Tunes Salt and Drought Stress Responses in Arabidopsis. PLANTS (BASEL, SWITZERLAND) 2023; 13:7. [PMID: 38202315 PMCID: PMC10780339 DOI: 10.3390/plants13010007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 11/26/2023] [Accepted: 12/13/2023] [Indexed: 01/12/2024]
Abstract
Photosynthesis is among the first processes negatively affected by environmental cues and its performance directly determines plant cell fitness and ultimately crop yield. Primarily sites of photosynthesis, chloroplasts are unique sites also for the biosynthesis of precursors of the growth regulator auxin and for sensing environmental stress, but their role in intracellular auxin homeostasis, vital for plant growth and survival in changing environments, remains poorly understood. Here, we identified two ATP-binding cassette (ABC) subfamily B transporters, ABCB28 and ABCB29, which export auxin across the chloroplast envelope to the cytosol in a concerted action in vivo. Moreover, we provide evidence for an auxin biosynthesis pathway in Arabidopsis thaliana chloroplasts. The overexpression of ABCB28 and ABCB29 influenced stomatal regulation and resulted in significantly improved water use efficiency and survival rates during salt and drought stresses. Our results suggest that chloroplast auxin production and transport contribute to stomata regulation for conserving water upon salt stress. ABCB28 and ABCB29 integrate photosynthesis and auxin signals and as such hold great potential to improve the adaptation potential of crops to environmental cues.
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Affiliation(s)
- Prashanth Tamizhselvan
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic; (P.T.); (S.M.); (C.C.-A.); (E.R.E.); (A.C.); (M.H.)
| | - Sharmila Madhavan
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic; (P.T.); (S.M.); (C.C.-A.); (E.R.E.); (A.C.); (M.H.)
| | - Christian Constan-Aguilar
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic; (P.T.); (S.M.); (C.C.-A.); (E.R.E.); (A.C.); (M.H.)
| | - Eman Ryad Elrefaay
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic; (P.T.); (S.M.); (C.C.-A.); (E.R.E.); (A.C.); (M.H.)
| | - Jie Liu
- Department of Biology, University of Fribourg, CH-1700 Fribourg, Switzerland; (J.L.); (M.G.)
| | - Aleš Pěnčík
- Laboratory of Growth Regulators, Institute of Experimental Botany, The Czech Academy of Sciences, & Faculty of Science, Palacký University, Šlechtitelů 27, CZ-783 71 Olomouc, Czech Republic; (A.P.); (O.N.)
| | - Ondřej Novák
- Laboratory of Growth Regulators, Institute of Experimental Botany, The Czech Academy of Sciences, & Faculty of Science, Palacký University, Šlechtitelů 27, CZ-783 71 Olomouc, Czech Republic; (A.P.); (O.N.)
| | - Albert Cairó
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic; (P.T.); (S.M.); (C.C.-A.); (E.R.E.); (A.C.); (M.H.)
| | - Mónika Hrtyan
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic; (P.T.); (S.M.); (C.C.-A.); (E.R.E.); (A.C.); (M.H.)
| | - Markus Geisler
- Department of Biology, University of Fribourg, CH-1700 Fribourg, Switzerland; (J.L.); (M.G.)
| | - Vanesa Beatriz Tognetti
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic; (P.T.); (S.M.); (C.C.-A.); (E.R.E.); (A.C.); (M.H.)
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5
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Gyuzeleva D, Benina M, Ivanova V, Vatov E, Alseekh S, Mladenova T, Mladenov R, Todorov K, Bivolarska A, Stoyanov P. Metabolome Profiling of Marrubium peregrinum L. and Marrubium friwaldskyanum Boiss Reveals Their Potential as Sources of Plant-Based Pharmaceuticals. Int J Mol Sci 2023; 24:17035. [PMID: 38069358 PMCID: PMC10707198 DOI: 10.3390/ijms242317035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 11/22/2023] [Accepted: 11/25/2023] [Indexed: 12/18/2023] Open
Abstract
Marrubium species have been used since ancient times as food additives and curative treatments. Their phytochemical composition and various pharmacological activities were the focus of a number of scientific investigations but no comprehensive metabolome profiling to identify the numerous primary and secondary metabolites has been performed so far. This study aimed to generate a comprehensive picture of the total metabolite content of two Marrubium species-M. peregrinum and M. friwaldskyanum-to provide detailed information about the main primary and secondary metabolites. In addition, the elemental composition was also evaluated. For this purpose, non-targeted metabolomic analyses were conducted using GC-MS, UPLC-MS/MS and ICP-MS approaches. Nearly 500 compounds and 12 elements were detected and described. The results showed a strong presence of phenolic acids, flavonoids and their glucosides, which are generally of great interest due to their various pharmacological activities. Furthermore, tissue-specific analyses for M. friwaldskyanum stem, leaves and flowers were carried out in order to outline the sources of potentially important bioactive molecules. The results generated from this study depict the Marrubium metabolome and reveal its dual scientific importance-from one side, providing information about the metabolites that is fundamental and vital for the survival of these species, and from the other side, defining the large diversity of secondary substances that are a potential source of phytotherapeutic agents.
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Affiliation(s)
- Donika Gyuzeleva
- Department of Botany and Biological Education, Faculty of Biology, University of Plovdiv “Paisii Hilendarski”, 24 Tsar Assen Str., 4000 Plovdiv, Bulgaria; (D.G.); (T.M.)
| | - Maria Benina
- Center of Plant Systems Biology and Biotechnology, 14 Sveti Kniaz Boris I Pokrastitel Str., 4023 Plovdiv, Bulgaria
| | - Valentina Ivanova
- Center of Plant Systems Biology and Biotechnology, 14 Sveti Kniaz Boris I Pokrastitel Str., 4023 Plovdiv, Bulgaria
| | - Emil Vatov
- Center of Plant Systems Biology and Biotechnology, 14 Sveti Kniaz Boris I Pokrastitel Str., 4023 Plovdiv, Bulgaria
| | - Saleh Alseekh
- Center of Plant Systems Biology and Biotechnology, 14 Sveti Kniaz Boris I Pokrastitel Str., 4023 Plovdiv, Bulgaria
- Max Planck Institute for Molecular Plant Physiology, 1, Am Mühlenberg, 14476 Potsdam, Germany
| | - Tsvetelina Mladenova
- Department of Botany and Biological Education, Faculty of Biology, University of Plovdiv “Paisii Hilendarski”, 24 Tsar Assen Str., 4000 Plovdiv, Bulgaria; (D.G.); (T.M.)
| | - Rumen Mladenov
- Department of Botany and Biological Education, Faculty of Biology, University of Plovdiv “Paisii Hilendarski”, 24 Tsar Assen Str., 4000 Plovdiv, Bulgaria; (D.G.); (T.M.)
- Department of Bioorganic Chemistry, Faculty of Pharmacy, Medical University of Plovdiv, 15A Vasil Aprilov Blvd., 4002 Plovdiv, Bulgaria
| | - Krasimir Todorov
- Department of Botany and Biological Education, Faculty of Biology, University of Plovdiv “Paisii Hilendarski”, 24 Tsar Assen Str., 4000 Plovdiv, Bulgaria; (D.G.); (T.M.)
| | - Anelia Bivolarska
- Department of Medical Biochemistry, Faculty of Pharmacy, Medical University of Plovdiv, 15A Vasil Aprilov Blvd., 4002 Plovdiv, Bulgaria
| | - Plamen Stoyanov
- Department of Botany and Biological Education, Faculty of Biology, University of Plovdiv “Paisii Hilendarski”, 24 Tsar Assen Str., 4000 Plovdiv, Bulgaria; (D.G.); (T.M.)
- Department of Bioorganic Chemistry, Faculty of Pharmacy, Medical University of Plovdiv, 15A Vasil Aprilov Blvd., 4002 Plovdiv, Bulgaria
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Xu Z. A Specific Protective Mechanism Against Chloroplast Photo-Reactive Oxygen Species in Phosphate-Starved Rice Plants. Adv Biol (Weinh) 2023; 7:e2300106. [PMID: 37409401 DOI: 10.1002/adbi.202300106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 05/22/2023] [Indexed: 07/07/2023]
Abstract
Phosphorus (Pi) starvation prevents a good match between light energy absorption and photosynthetic carbon metabolism, generating photo-reactive oxygen species (photo-ROS) in chloroplasts. Plants have evolved to withstand photo-oxidative stress, but the key regulatory mechanism underlying it remains unclear. In rice (Oryza sativa), DEEP GREEN PANICLE1 (DGP1) is robustly up-regulated in response to Pi deficiency. DGP1 decreases the DNA-binding capacities of the transcriptional activators GLK1/2 on the photosynthetic genes involved in chlorophyll biosynthesis, light harvesting, and electron transport. This Pi-starvation-induced mechanism dampens both electron transport rates through photosystem I and II (ETRI and ETRII) and thus mitigates the electron-excessive stress in mesophyll cells. Meanwhile, DGP1 hijacks glycolytic enzymes GAPC1/2/3, redirecting glucose metabolism toward the pentose phosphate pathway with superfluous NADPH production. Phenotypically, light irradiation induces O2 - production in Pi-starved WT leaves but is observably accelerated in dgp1 mutant and impaired in GAPCsRNAi and glk1glk2 lines. Interestingly, overexpressed DGP1 in rice caused hyposensitivity to ROS-inducers (catechin and methyl viologen), but the dgp1 mutant shows a similar inhibitory phenotype with the WT seedlings. Overall, the DGP1 gene serves as a specific antagonizer against photo-ROS in Pi-starved rice plants, which coordinates light-absorbing and anti-oxidative systems by orchestrating transcriptional and metabolic regulations, respectively.
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Affiliation(s)
- Zhan Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- Guangzhou City Academy of Agricultural Sciences, Key Laboratory of Biology, Genetics and Breeding, Guangzhou, 510000, China
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Pan T, Liu Y, Hu X, Li P, Lin C, Tang Y, Tang W, Liu Y, Guo L, Kim C, Fang J, Lin H, Wu Z, Blumwald E, Wang S. Stress-induced endocytosis from chloroplast inner envelope membrane is mediated by CHLOROPLAST VESICULATION but inhibited by GAPC. Cell Rep 2023; 42:113208. [PMID: 37792531 DOI: 10.1016/j.celrep.2023.113208] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 06/16/2023] [Accepted: 09/18/2023] [Indexed: 10/06/2023] Open
Abstract
Clathrin-mediated vesicular formation and trafficking are responsible for molecular cargo transport and signal transduction among organelles. Our previous study shows that CHLOROPLAST VESICULATION (CV)-containing vesicles (CVVs) are generated from chloroplasts for chloroplast degradation under abiotic stress. Here, we show that CV interacts with the clathrin heavy chain (CHC) and induces vesicle budding toward the cytosol from the chloroplast inner envelope membrane. In the defective mutants of CHC2 and the dynamin-encoding DRP1A, CVV budding and releasing from chloroplast are impeded. The mutations of CHC2 inhibit CV-induced chloroplast degradation and hypersensitivity to water stress. Moreover, CV-CHC2 interaction is impaired by the oxidized GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE (GAPC). GAPC1 overexpression suppresses CV-mediated chloroplast degradation and hypersensitivity to water stress, while CV silencing alleviates the hypersensitivity of the gapc1gapc2 plant to water stress. Together, our work identifies a pathway of clathrin-assisted CVV budding outward from chloroplast, which is involved in chloroplast degradation and stress response.
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Affiliation(s)
- Ting Pan
- Anhui Province Key Laboratory of Horticultural Crop Quality Biology, School of Horticulture, Anhui Agricultural University, Hefei 230036, China; Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yangxuan Liu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Xufan Hu
- Anhui Province Key Laboratory of Horticultural Crop Quality Biology, School of Horticulture, Anhui Agricultural University, Hefei 230036, China
| | - Pengwei Li
- Anhui Province Key Laboratory of Horticultural Crop Quality Biology, School of Horticulture, Anhui Agricultural University, Hefei 230036, China
| | - Chengcheng Lin
- Anhui Province Key Laboratory of Horticultural Crop Quality Biology, School of Horticulture, Anhui Agricultural University, Hefei 230036, China
| | - Yuying Tang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Wei Tang
- Anhui Province Key Laboratory of Horticultural Crop Quality Biology, School of Horticulture, Anhui Agricultural University, Hefei 230036, China
| | - Yongsheng Liu
- Anhui Province Key Laboratory of Horticultural Crop Quality Biology, School of Horticulture, Anhui Agricultural University, Hefei 230036, China
| | - Liang Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Chanhong Kim
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jun Fang
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Honghui Lin
- Ministry of Education, Key Laboratory for Bio-Resource and Eco-Environment, College of Life Science, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610064, China
| | - Zhihua Wu
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Eduardo Blumwald
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Songhu Wang
- Anhui Province Key Laboratory of Horticultural Crop Quality Biology, School of Horticulture, Anhui Agricultural University, Hefei 230036, China; Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China.
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Minen RI, Thirumalaikumar VP, Skirycz A. Proteinogenic dipeptides, an emerging class of small-molecule regulators. CURRENT OPINION IN PLANT BIOLOGY 2023; 75:102395. [PMID: 37311365 DOI: 10.1016/j.pbi.2023.102395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 05/07/2023] [Accepted: 05/10/2023] [Indexed: 06/15/2023]
Abstract
Proteinogenic dipeptides, with few known exceptions, are products of protein degradation. Dipeptide levels respond to the changes in the environment, often in a dipeptide-specific manner. What drives this specificity is currently unknown; what likely contributes is the activity of the different peptidases that cleave off the terminal dipeptide from the longer peptides. Dipeptidases that degrade dipeptides to amino acids, and the turnover rates of the "substrate" proteins/peptides. Plants can both uptake dipeptides from the soil, but dipeptides are also found in root exudates. Dipeptide transporters, members of the proton-coupled peptide transporters NTR1/PTR family, contribute to nitrogen reallocation between the sink and source tissues. Besides their role in nitrogen distribution, it becomes increasingly clear that dipeptides may also serve regulatory, dipeptide-specific functions. Dipeptides are found in protein complexes affecting the activity of their protein partners. Moreover, dipeptide supplementation leads to cellular phenotypes reflected in changes in plant growth and stress tolerance. Herein we will review the current understanding of dipeptides' metabolism, transport, and functions and discuss significant challenges and future directions for the comprehensive characterization of this fascinating but underrated group of small-molecule compounds.
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Affiliation(s)
| | | | - Aleksandra Skirycz
- Boyce Thompson Institute, 14853, Ithaca, NY, USA; Cornell University, 14853, Ithaca, NY, USA.
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Cheng WH, Huang PJ, Lee CC, Yeh YM, Ong SC, Lin R, Ku FM, Chiu CH, Tang P. Metabolomics analysis reveals changes related to pseudocyst formation induced by iron depletion in Trichomonas vaginalis. Parasit Vectors 2023; 16:226. [PMID: 37415204 DOI: 10.1186/s13071-023-05842-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 06/18/2023] [Indexed: 07/08/2023] Open
Abstract
BACKGROUND Iron is an essential element for cellular functions, such as energy metabolism. Trichomonas vaginalis, a human urogenital tract pathogen, is capable of surviving in the environment without sufficient iron supplementation. Pseudocysts (cyst-like structures) are an environmentally tolerated stage of this parasite while encountering undesired conditions, including iron deficiency. We previously demonstrated that iron deficiency induces more active glycolysis but a drastic downregulation of hydrogenosomal energy metabolic enzymes. Therefore, the metabolic direction of the end product of glycolysis is still controversial. METHODS In the present work, we conducted an LC‒MS-based metabolomics analysis to obtain accurate insights into the enzymatic events of T. vaginalis under iron-depleted (ID) conditions. RESULTS First, we showed the possible digestion of glycogen, cellulose polymerization, and accumulation of raffinose family oligosaccharides (RFOs). Second, a medium-chain fatty acid (MCFA), capric acid, was elevated, whereas most detected C18 fatty acids were reduced significantly. Third, amino acids were mostly reduced, especially alanine, glutamate, and serine. Thirty-three dipeptides showed significant accumulation in ID cells, which was probably associated with the decrease in amino acids. Our results indicated that glycogen was metabolized as the carbon source, and the structural component cellulose was synthesized at same time. The decrease in C18 fatty acids implied possible incorporation in the membranous compartment for pseudocyst formation. The decrease in amino acids accompanied by an increase in dipeptides implied incomplete proteolysis. These enzymatic reactions (alanine dehydrogenase, glutamate dehydrogenase, and threonine dehydratase) were likely involved in ammonia release. CONCLUSION These findings highlighted the possible glycogen utilization, cellulose biosynthesis, and fatty acid incorporation in pseudocyst formation as well as NO precursor ammonia production induced by iron-depleted stress.
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Affiliation(s)
- Wei-Hung Cheng
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Department of Parasitology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Po-Jung Huang
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Guishan Dist., Taoyuan City, Taiwan
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Chi-Ching Lee
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan
- Department of Computer Science and Information Engineering, College of Engineering, Chang Gung University, Guishan Dist., Taoyuan City, Taiwan
| | - Yuan-Ming Yeh
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan
- Graduate Institute of Health Industry Technology, Chang Gung University of Science and Technology, Taoyuan, Taiwan
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Seow-Chin Ong
- Department of Parasitology, College of Medicine, Chang Gung University, Guishan Dist., Taoyuan City, Taiwan
| | - Rose Lin
- Department of Parasitology, College of Medicine, Chang Gung University, Guishan Dist., Taoyuan City, Taiwan
| | - Fu-Man Ku
- Department of Parasitology, College of Medicine, Chang Gung University, Guishan Dist., Taoyuan City, Taiwan
| | - Cheng-Hsun Chiu
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Petrus Tang
- Department of Parasitology, College of Medicine, Chang Gung University, Guishan Dist., Taoyuan City, Taiwan.
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Linkou, Taiwan.
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10
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Rojas BE, Iglesias AA. Integrating multiple regulations on enzyme activity: the case of phospho enolpyruvate carboxykinases. AOB PLANTS 2023; 15:plad053. [PMID: 37608926 PMCID: PMC10441589 DOI: 10.1093/aobpla/plad053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 07/27/2023] [Indexed: 08/24/2023]
Abstract
Data on protein post-translational modifications (PTMs) increased exponentially in the last years due to the refinement of mass spectrometry techniques and the development of databases to store and share datasets. Nevertheless, these data per se do not create comprehensive biochemical knowledge. Complementary studies on protein biochemistry are necessary to fully understand the function of these PTMs at the molecular level and beyond, for example, designing rational metabolic engineering strategies to improve crops. Phosphoenolpyruvate carboxykinases (PEPCKs) are critical enzymes for plant metabolism with diverse roles in plant development and growth. Multiple lines of evidence showed the complex regulation of PEPCKs, including PTMs. Herein, we present PEPCKs as an example of the integration of combined mechanisms modulating enzyme activity and metabolic pathways. PEPCK studies strongly advanced after the production of the recombinant enzyme and the establishment of standardized biochemical assays. Finally, we discuss emerging open questions for future research and the challenges in integrating all available data into functional biochemical models.
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Affiliation(s)
- Bruno E Rojas
- Instituto de Agrobiotecnología del Litoral, UNL, CONICET, FBCB, Santa Fe, Argentina
| | - Alberto A Iglesias
- Instituto de Agrobiotecnología del Litoral, UNL, CONICET, FBCB, Santa Fe, Argentina
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11
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Rojas BE, Tonetti T, Figueroa CM. Trehalose 6-phosphate metabolism in C 4 species. CURRENT OPINION IN PLANT BIOLOGY 2023; 72:102347. [PMID: 36806837 DOI: 10.1016/j.pbi.2023.102347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 01/09/2023] [Accepted: 01/19/2023] [Indexed: 06/18/2023]
Abstract
Trehalose 6-phosphate (Tre6P), the intermediate of trehalose biosynthesis, is an essential signal metabolite in plants, linking growth and development to carbon status. Our current understanding of Tre6P metabolism and signaling pathways in plants is based almost entirely on studies performed with Arabidopsis thaliana, a model plant that performs C3 photosynthesis. Conversely, our knowledge on the molecular mechanisms involved in Tre6P regulation of carbon partitioning and metabolism in C4 plants is scarce. This topic is especially relevant due to the agronomic importance of crops performing C4 photosynthesis, such as maize, sorghum and sugarcane. In this review, we focused our attention on recent developments related to Tre6P metabolism in C4 species and raised some open questions that should be addressed in the near future to improve the yield of economically important crops.
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Affiliation(s)
- Bruno E Rojas
- Instituto de Agrobiotecnología del Litoral, UNL, CONICET, FBCB, Santa Fe, Argentina
| | - Tomás Tonetti
- Instituto de Agrobiotecnología del Litoral, UNL, CONICET, FBCB, Santa Fe, Argentina
| | - Carlos M Figueroa
- Instituto de Agrobiotecnología del Litoral, UNL, CONICET, FBCB, Santa Fe, Argentina.
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12
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Schlossarek D, Zhang Y, Sokolowska EM, Fernie AR, Luzarowski M, Skirycz A. Don't let go: co-fractionation mass spectrometry for untargeted mapping of protein-metabolite interactomes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 113:904-914. [PMID: 36575913 DOI: 10.1111/tpj.16084] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 12/20/2022] [Accepted: 12/23/2022] [Indexed: 06/17/2023]
Abstract
The chemical complexity of metabolomes goes hand in hand with their functional diversity. Small molecules have many essential roles, many of which are executed by binding and modulating the function of a protein partner. The complex and dynamic protein-metabolite interaction (PMI) network underlies most if not all biological processes, but remains under-characterized. Herein, we highlight how co-fractionation mass spectrometry (CF-MS), a well-established approach to map protein assemblies, can be used for proteome and metabolome identification of the PMIs. We will review recent CF-MS studies, discuss the main advantages and limitations, summarize the available CF-MS guidelines, and outline future challenges and opportunities.
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Affiliation(s)
- Dennis Schlossarek
- Depeartment One, Max-Planck-Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
| | - Youjun Zhang
- Depeartment One, Max-Planck-Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
| | - Ewelina M Sokolowska
- Depeartment One, Max-Planck-Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
| | - Alisdair R Fernie
- Depeartment One, Max-Planck-Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
| | - Marcin Luzarowski
- Center for Molecular Biology Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Aleksandra Skirycz
- Depeartment One, Max-Planck-Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
- Boyce Thompson Institute, Ithaca, NY, 14850, USA
- School of Integrative Plant Science, Cornell University, Ithaca, NY, 14850, USA
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13
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Figueroa NE, Hernandez-Sanchez IE, Maruri-Lopez I, Chodasiewicz M. Affinity Purification Protocol Starting with a Small Molecule as Bait. Methods Mol Biol 2023; 2554:11-19. [PMID: 36178617 DOI: 10.1007/978-1-0716-2624-5_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Protein-metabolite interactions (PMIs) are fundamental for several biological processes. Even though PMI studies have increased in recent years, our knowledge is still limited. The screening of PMIs using small molecules as bait will broaden our ability to uncover novel PMIs, setting the basis for establishing their biological relevance. Here, we describe a protocol that allows the identification of multiple protein partners for one ligand. This protocol describes a straightforward methodology that can be adapted to a wide variety of organisms.
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Affiliation(s)
- Nicolás E Figueroa
- Center for Desert Agriculture, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Itzell E Hernandez-Sanchez
- Center for Desert Agriculture, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Israel Maruri-Lopez
- Center for Desert Agriculture, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Monika Chodasiewicz
- Center for Desert Agriculture, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.
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14
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Vaughan-Hirsch J, Li D, Roig Martinez A, Roden S, Pattyn J, Taira S, Shikano H, Miyama Y, Okano Y, Voet A, Van de Poel B. A 1-aminocyclopropane-1-carboxylic-acid (ACC) dipeptide elicits ethylene responses through ACC-oxidase mediated substrate promiscuity. FRONTIERS IN PLANT SCIENCE 2022; 13:995073. [PMID: 36172554 PMCID: PMC9510837 DOI: 10.3389/fpls.2022.995073] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 08/26/2022] [Indexed: 06/16/2023]
Abstract
Plants produce the volatile hormone ethylene to regulate many developmental processes and to deal with (a)biotic stressors. In seed plants, ethylene is synthesized from 1-aminocyclopropane-1-carboxylic acid (ACC) by the dedicated enzyme ACC oxidase (ACO). Ethylene biosynthesis is tightly regulated at the level of ACC through ACC synthesis, conjugation and transport. ACC is a non-proteinogenic amino acid, which also has signaling roles independent from ethylene. In this work, we investigated the biological function of an uncharacterized ACC dipeptide. The custom-synthesized di-ACC molecule can be taken up by Arabidopsis in a similar way as ACC, in part via Lysine Histidine Transporters (e.g., LHT1). Using Nano-Particle Assisted Laser Desoprtion/Ionization (Nano-PALDI) mass-spectrometry imaging, we revealed that externally fed di-ACC predominantly localizes to the vasculature tissue, despite it not being detectable in control hypocotyl segments. Once taken up, the ACC dimer can evoke a triple response phenotype in dark-grown seedlings, reminiscent of ethylene responses induced by ACC itself, albeit less efficiently compared to ACC. Di-ACC does not act via ACC-signaling, but operates via the known ethylene signaling pathway. In vitro ACO activity and molecular docking showed that di-ACC can be used as an alternative substrate by ACO to form ethylene. The promiscuous nature of ACO for the ACC dimer also explains the higher ethylene production rates observed in planta, although this reaction occurred less efficiently compared to ACC. Overall, the ACC dipeptide seems to be transported and converted into ethylene in a similar way as ACC, and is able to augment ethylene production levels and induce subsequent ethylene responses in Arabidopsis.
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Affiliation(s)
- John Vaughan-Hirsch
- Division of Crop Biotechnics, Department of Biosystems, University of Leuven, Leuven, Belgium
| | - Dongdong Li
- Division of Crop Biotechnics, Department of Biosystems, University of Leuven, Leuven, Belgium
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Albert Roig Martinez
- Division of Biochemistry, Molecular and Structural Biology, Department of Chemistry, University of Leuven, Leuven, Belgium
| | - Stijn Roden
- Division of Crop Biotechnics, Department of Biosystems, University of Leuven, Leuven, Belgium
| | - Jolien Pattyn
- Division of Crop Biotechnics, Department of Biosystems, University of Leuven, Leuven, Belgium
| | - Shu Taira
- Department of Agriculture, Fukushima University, Fukushima, Japan
| | - Hitomi Shikano
- Department of Agriculture, Fukushima University, Fukushima, Japan
| | - Yoko Miyama
- Department of Agriculture, Fukushima University, Fukushima, Japan
| | - Yukari Okano
- Department of Agriculture, Fukushima University, Fukushima, Japan
| | - Arnout Voet
- Division of Biochemistry, Molecular and Structural Biology, Department of Chemistry, University of Leuven, Leuven, Belgium
| | - Bram Van de Poel
- Division of Crop Biotechnics, Department of Biosystems, University of Leuven, Leuven, Belgium
- KU Leuven Plant Institute, University of Leuven, Leuven, Belgium
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15
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Alseekh S, Zhu F, Vallarino JG, Sokolowska EM, Yoshida T, Bergmann S, Wendenburg R, Bolze A, Skirycz A, Avin-Wittenberg T, Fernie AR. Autophagy modulates the metabolism and growth of tomato fruit during development. HORTICULTURE RESEARCH 2022; 9:uhac129. [PMID: 35928403 PMCID: PMC9343920 DOI: 10.1093/hr/uhac129] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 05/29/2022] [Indexed: 06/15/2023]
Abstract
Although autophagy is a conserved mechanism operating across eukaryotes, its effects on crops and especially their metabolism has received relatively little attention. Indeed, whilst a few recent studies have used systems biology tools to look at the consequences of lack of autophagy in maize these focused on leaf tissues rather than the kernels. Here we utilized RNA interference (RNAi) to generate tomato plants that were deficient in the autophagy-regulating protease ATG4. Plants displayed an early senescence phenotype yet relatively mild changes in the foliar metabolome and were characterized by a reduced fruit yield phenotype. Metabolite profiling indicated that metabolites of ATG4-RNAi tomato leaves just exhibited minor alterations while that of fruit displayed bigger difference compared to the WT. In detail, many primary metabolites exhibited decreases in the ATG4-RNAi lines, such as proline, tryptophan and phenylalanine, while the representative secondary metabolites (quinic acid and 3-trans-caffeoylquinic acid) were present at substantially higher levels in ATG4-RNAi green fruits than in WT. Moreover, transcriptome analysis indicated that the most prominent differences were in the significant upregulation of organelle degradation genes involved in the proteasome or chloroplast vesiculation pathways, which was further confirmed by the reduced levels of chloroplastic proteins in the proteomics data. Furthermore, integration analysis of the metabolome, transcriptome and proteome data indicated that ATG4 significantly affected the lipid metabolism, chlorophyll binding proteins and chloroplast biosynthesis. These data collectively lead us to propose a more sophisticated model to explain the cellular co-ordination of the process of autophagy.
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Affiliation(s)
| | | | - José G Vallarino
- Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | | | - Takuya Yoshida
- Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Susan Bergmann
- Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Regina Wendenburg
- Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Antje Bolze
- Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Aleksandra Skirycz
- Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
- Boyce Thompson Institute, 14850, Ithaca, US
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16
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Chodasiewicz M, Kerber O, Gorka M, Moreno JC, Maruri-Lopez I, Minen RI, Sampathkumar A, Nelson ADL, Skirycz A. 2',3'-cAMP treatment mimics the stress molecular response in Arabidopsis thaliana. PLANT PHYSIOLOGY 2022; 188:1966-1978. [PMID: 35043968 PMCID: PMC8968299 DOI: 10.1093/plphys/kiac013] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 12/01/2021] [Indexed: 05/12/2023]
Abstract
The role of the RNA degradation product 2',3'-cyclic adenosine monophosphate (2',3'-cAMP) is poorly understood. Recent studies have identified 2',3'-cAMP in plant material and determined its role in stress signaling. The level of 2',3'-cAMP increases upon wounding, in the dark, and under heat, and 2',3'-cAMP binding to an RNA-binding protein, Rbp47b, promotes stress granule (SG) assembly. To gain further mechanistic insights into the function of 2',3'-cAMP, we used a multi-omics approach by combining transcriptomics, metabolomics, and proteomics to dissect the response of Arabidopsis (Arabidopsis thaliana) to 2',3'-cAMP treatment. We demonstrated that 2',3'-cAMP is metabolized into adenosine, suggesting that the well-known cyclic nucleotide-adenosine pathway of human cells might also exist in plants. Transcriptomics analysis revealed only minor overlap between 2',3'-cAMP- and adenosine-treated plants, suggesting that these molecules act through independent mechanisms. Treatment with 2',3'-cAMP changed the levels of hundreds of transcripts, proteins, and metabolites, many previously associated with plant stress responses, including protein and RNA degradation products, glucosinolates, chaperones, and SG components. Finally, we demonstrated that 2',3'-cAMP treatment influences the movement of processing bodies, confirming the role of 2',3'-cAMP in the formation and motility of membraneless organelles.
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Affiliation(s)
| | - Olga Kerber
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Michal Gorka
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Juan C Moreno
- Center for Desert Agriculture, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Israel Maruri-Lopez
- Center for Desert Agriculture, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Romina I Minen
- Boyce Thompson Institute, Cornell University, Ithaca, New York 14853, USA
| | - Arun Sampathkumar
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Andrew D L Nelson
- Boyce Thompson Institute, Cornell University, Ithaca, New York 14853, USA
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17
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Calderan-Rodrigues MJ, Luzarowski M, Monte-Bello CC, Minen RI, Zühlke BM, Nikoloski Z, Skirycz A, Caldana C. Proteogenic Dipeptides Are Characterized by Diel Fluctuations and Target of Rapamycin Complex-Signaling Dependency in the Model Plant Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2021; 12:758933. [PMID: 35003157 PMCID: PMC8727597 DOI: 10.3389/fpls.2021.758933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 11/11/2021] [Indexed: 06/14/2023]
Abstract
As autotrophic organisms, plants capture light energy to convert carbon dioxide into ATP, nicotinamide adenine dinucleotide phosphate (NADPH), and sugars, which are essential for the biosynthesis of building blocks, storage, and growth. At night, metabolism and growth can be sustained by mobilizing carbon (C) reserves. In response to changing environmental conditions, such as light-dark cycles, the small-molecule regulation of enzymatic activities is critical for reprogramming cellular metabolism. We have recently demonstrated that proteogenic dipeptides, protein degradation products, act as metabolic switches at the interface of proteostasis and central metabolism in both plants and yeast. Dipeptides accumulate in response to the environmental changes and act via direct binding and regulation of critical enzymatic activities, enabling C flux distribution. Here, we provide evidence pointing to the involvement of dipeptides in the metabolic rewiring characteristics for the day-night cycle in plants. Specifically, we measured the abundance of 13 amino acids and 179 dipeptides over short- (SD) and long-day (LD) diel cycles, each with different light intensities. Of the measured dipeptides, 38 and eight were characterized by day-night oscillation in SD and LD, respectively, reaching maximum accumulation at the end of the day and then gradually falling in the night. Not only the number of dipeptides, but also the amplitude of the oscillation was higher in SD compared with LD conditions. Notably, rhythmic dipeptides were enriched in the glucogenic amino acids that can be converted into glucose. Considering the known role of Target of Rapamycin (TOR) signaling in regulating both autophagy and metabolism, we subsequently investigated whether diurnal fluctuations of dipeptides levels are dependent on the TOR Complex (TORC). The Raptor1b mutant (raptor1b), known for the substantial reduction of TOR kinase activity, was characterized by the augmented accumulation of dipeptides, which is especially pronounced under LD conditions. We were particularly intrigued by the group of 16 dipeptides, which, based on their oscillation under SD conditions and accumulation in raptor1b, can be associated with limited C availability or photoperiod. By mining existing protein-metabolite interaction data, we delineated putative protein interactors for a representative dipeptide Pro-Gln. The obtained list included enzymes of C and amino acid metabolism, which are also linked to the TORC-mediated metabolic network. Based on the obtained results, we speculate that the diurnal accumulation of dipeptides contributes to its metabolic adaptation in response to changes in C availability. We hypothesize that dipeptides would act as alternative respiratory substrates and by directly modulating the activity of the focal enzymes.
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Affiliation(s)
| | - Marcin Luzarowski
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | | | | | - Boris M. Zühlke
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Zoran Nikoloski
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Aleksandra Skirycz
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
- Boyce Thompson Institute, Ithaca, NY, United States
| | - Camila Caldana
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
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18
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Heidenreich E, Pfeffer T, Kracke T, Mechtel N, Nawroth P, Hoffmann GF, Schmitt CP, Hell R, Poschet G, Peters V. A Novel UPLC-MS/MS Method Identifies Organ-Specific Dipeptide Profiles. Int J Mol Sci 2021; 22:9979. [PMID: 34576148 PMCID: PMC8465603 DOI: 10.3390/ijms22189979] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/10/2021] [Accepted: 09/13/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Amino acids have a central role in cell metabolism, and intracellular changes contribute to the pathogenesis of various diseases, while the role and specific organ distribution of dipeptides is largely unknown. METHOD We established a sensitive, rapid and reliable UPLC-MS/MS method for quantification of 36 dipeptides. Dipeptide patterns were analyzed in brown and white adipose tissues, brain, eye, heart, kidney, liver, lung, muscle, sciatic nerve, pancreas, spleen and thymus, serum and urine of C57BL/6N wildtype mice and related to the corresponding amino acid profiles. RESULTS A total of 30 out of the 36 investigated dipeptides were detected with organ-specific distribution patterns. Carnosine and anserine were most abundant in all organs, with the highest concentrations in muscles. In liver, Asp-Gln and Ala-Gln concentrations were high, in the spleen and thymus, Glu-Ser and Gly-Asp. In serum, dipeptide concentrations were several magnitudes lower than in organ tissues. In all organs, dipeptides with C-terminal proline (Gly-Pro and Leu-Pro) were present at higher concentrations than dipeptides with N-terminal proline (Pro-Gly and Pro-Leu). Organ-specific amino acid profiles were related to the dipeptide profile with several amino acid concentrations being related to the isomeric form of the dipeptides. Aspartate, histidine, proline and serine tissue concentrations correlated with dipeptide concentrations, when the amino acids were present at the C- but not at the N-terminus. CONCLUSION Our multi-dipeptide quantification approach demonstrates organ-specific dipeptide distribution. This method allows us to understand more about the dipeptide metabolism in disease or in healthy state.
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Affiliation(s)
- Elena Heidenreich
- Centre for Organismal Studies (COS), Metabolomics Core Technology Platform, Heidelberg University, 69120 Heidelberg, Germany; (E.H.); (N.M.); (R.H.)
| | - Tilman Pfeffer
- Centre for Paediatric and Adolescent Medicine, University Hospital Heidelberg, 69120 Heidelberg, Germany; (T.P.); (T.K.); (G.F.H.); (C.P.S.)
| | - Tamara Kracke
- Centre for Paediatric and Adolescent Medicine, University Hospital Heidelberg, 69120 Heidelberg, Germany; (T.P.); (T.K.); (G.F.H.); (C.P.S.)
| | - Nils Mechtel
- Centre for Organismal Studies (COS), Metabolomics Core Technology Platform, Heidelberg University, 69120 Heidelberg, Germany; (E.H.); (N.M.); (R.H.)
| | - Peter Nawroth
- Department of Internal Medicine I and Clinical Chemistry, University Hospital of Heidelberg, 69120 Heidelberg, Germany;
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
- Institute for Diabetes and Cancer (IDC) Helmholtz Center Munich, 85764 Neuherberg, Germany
- Joint Heidelberg-Institute for Diabetes and Cancer (IDC) Translational Diabetes Program, 85764 Neuherberg, Germany
| | - Georg F Hoffmann
- Centre for Paediatric and Adolescent Medicine, University Hospital Heidelberg, 69120 Heidelberg, Germany; (T.P.); (T.K.); (G.F.H.); (C.P.S.)
| | - Claus Peter Schmitt
- Centre for Paediatric and Adolescent Medicine, University Hospital Heidelberg, 69120 Heidelberg, Germany; (T.P.); (T.K.); (G.F.H.); (C.P.S.)
| | - Rüdiger Hell
- Centre for Organismal Studies (COS), Metabolomics Core Technology Platform, Heidelberg University, 69120 Heidelberg, Germany; (E.H.); (N.M.); (R.H.)
| | - Gernot Poschet
- Centre for Organismal Studies (COS), Metabolomics Core Technology Platform, Heidelberg University, 69120 Heidelberg, Germany; (E.H.); (N.M.); (R.H.)
| | - Verena Peters
- Centre for Paediatric and Adolescent Medicine, University Hospital Heidelberg, 69120 Heidelberg, Germany; (T.P.); (T.K.); (G.F.H.); (C.P.S.)
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Moreno JC, Rojas BE, Vicente R, Gorka M, Matz T, Chodasiewicz M, Peralta‐Ariza JS, Zhang Y, Alseekh S, Childs D, Luzarowski M, Nikoloski Z, Zarivach R, Walther D, Hartman MD, Figueroa CM, Iglesias AA, Fernie AR, Skirycz A. Tyr-Asp inhibition of glyceraldehyde 3-phosphate dehydrogenase affects plant redox metabolism. EMBO J 2021; 40:e106800. [PMID: 34156108 PMCID: PMC8327957 DOI: 10.15252/embj.2020106800] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 05/13/2021] [Indexed: 12/28/2022] Open
Abstract
How organisms integrate metabolism with the external environment is a central question in biology. Here, we describe a novel regulatory small molecule, a proteogenic dipeptide Tyr-Asp, which improves plant tolerance to oxidative stress by directly interfering with glucose metabolism. Specifically, Tyr-Asp inhibits the activity of a key glycolytic enzyme, glyceraldehyde 3-phosphate dehydrogenase (GAPC), and redirects glucose toward pentose phosphate pathway (PPP) and NADPH production. In line with the metabolic data, Tyr-Asp supplementation improved the growth performance of both Arabidopsis and tobacco seedlings subjected to oxidative stress conditions. Moreover, inhibition of Arabidopsis phosphoenolpyruvate carboxykinase (PEPCK) activity by a group of branched-chain amino acid-containing dipeptides, but not by Tyr-Asp, points to a multisite regulation of glycolytic/gluconeogenic pathway by dipeptides. In summary, our results open the intriguing possibility that proteogenic dipeptides act as evolutionarily conserved small-molecule regulators at the nexus of stress, protein degradation, and metabolism.
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Affiliation(s)
- Juan C Moreno
- Max Planck Institute of Molecular Plant PhysiologyPotsdamGermany
- Center for Desert Agriculture, Biological and Environmental Science and Engineering Division (BESE)King Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
| | - Bruno E Rojas
- Instituto de Agrobiotecnología del LitoralUNLCONICET, FBCBSanta FeArgentina
| | - Rubén Vicente
- Max Planck Institute of Molecular Plant PhysiologyPotsdamGermany
| | - Michal Gorka
- Max Planck Institute of Molecular Plant PhysiologyPotsdamGermany
| | - Timon Matz
- Max Planck Institute of Molecular Plant PhysiologyPotsdamGermany
- BioinformaticsInstitute of Biochemistry and BiologyUniversity of PotsdamPotsdamGermany
| | | | | | - Youjun Zhang
- Max Planck Institute of Molecular Plant PhysiologyPotsdamGermany
- Center of Plant Systems Biology and Biotechnology (CPSBB)PlovdivBulgaria
| | - Saleh Alseekh
- Max Planck Institute of Molecular Plant PhysiologyPotsdamGermany
- Center of Plant Systems Biology and Biotechnology (CPSBB)PlovdivBulgaria
| | - Dorothee Childs
- European Molecular Biology Laboratory (EMBL) HeidelbergHeidelbergGermany
| | | | - Zoran Nikoloski
- Max Planck Institute of Molecular Plant PhysiologyPotsdamGermany
- BioinformaticsInstitute of Biochemistry and BiologyUniversity of PotsdamPotsdamGermany
- Center of Plant Systems Biology and Biotechnology (CPSBB)PlovdivBulgaria
| | - Raz Zarivach
- Faculty of Natural SciencesThe Ben Gurion University of the NegevBeer ShevaIsrael
| | - Dirk Walther
- Max Planck Institute of Molecular Plant PhysiologyPotsdamGermany
| | - Matías D Hartman
- Instituto de Agrobiotecnología del LitoralUNLCONICET, FBCBSanta FeArgentina
| | - Carlos M Figueroa
- Instituto de Agrobiotecnología del LitoralUNLCONICET, FBCBSanta FeArgentina
| | - Alberto A Iglesias
- Instituto de Agrobiotecnología del LitoralUNLCONICET, FBCBSanta FeArgentina
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant PhysiologyPotsdamGermany
- Center of Plant Systems Biology and Biotechnology (CPSBB)PlovdivBulgaria
| | - Aleksandra Skirycz
- Max Planck Institute of Molecular Plant PhysiologyPotsdamGermany
- Boyce Thompson InstituteIthacaUSA
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