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Jannat MAH, Park SH, Hwang S. Modeling interactions of Clostridium cadaveris and Clostridium sporogenes in anaerobic acidogenesis of glucose and peptone. BIORESOURCE TECHNOLOGY 2024; 393:130099. [PMID: 38013037 DOI: 10.1016/j.biortech.2023.130099] [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: 10/31/2023] [Revised: 11/22/2023] [Accepted: 11/22/2023] [Indexed: 11/29/2023]
Abstract
This study focuses on developing a mathematical model to assess interaction among acidogenic bacteria during the anaerobic degradation of two substrates. Clostridium cadaveris and Clostridium sporogenes were cultured in various combinations with glucose and peptone. Parameter estimates are given for both conventional Monod parameters from single substrate-single species cultures and sum kinetics with interaction parameters obtained from dual substrate-single species cultures. The presence of multiple substrates led to both inhibitory and enhancing effects on biodegradation rates for dual substrates compared to single substrate cultures. A new model of interspecies interaction was developed within the framework of Lotka-Volterra incorporating substrate interaction parameters, with a focus on accuracy, realism, simplicity, and biological significance. The model demonstrated competitive interaction for resource sharing and the additional non-linearity parameter eliminated the constraint of the linear relationship between growth rate and population density.
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Affiliation(s)
- Md Abu Hanifa Jannat
- Division of Environmental Science and Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, South Korea.
| | - Sang Hyeok Park
- Division of Environmental Science and Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, South Korea.
| | - Seokhwan Hwang
- Division of Environmental Science and Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, South Korea; Yonsei University Institute for Convergence Research and Education in Advanced Technology (I-CREATE), 85, Songdogwahak-ro, Yeonsu-gu, Incheon 21983, Republic of Korea.
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2
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Agrawal V, Singh V, Tripathi BN. Components and processes involved in retrograde signaling from chloroplast to nucleus. PHYSIOLOGIA PLANTARUM 2023; 175:e13987. [PMID: 37616006 DOI: 10.1111/ppl.13987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 07/01/2023] [Accepted: 07/23/2023] [Indexed: 08/25/2023]
Abstract
Retrograde signaling conceptually means the transfer of signals from semi-autonomous cell organelles to the nucleus to modulate nuclear gene expression. A generalized explanation is that chloroplasts are highly sensitive to environmental stimuli and quickly generate signaling molecules (retrograde signals) and transport them to the nucleus through the cytosol to reprogram nuclear gene expression for cellular/metabolic adjustments to cope with environmental fluctuations. During the past decade, substantial advancements have been made in the area of retrograde signaling, including information on putative retrograde signals. Researchers have also proposed possible mechanisms for generating retrograde signals and their transmission. However, the exact mechanisms and processes responsible for transmitting retrograde signaling from the chloroplast to the nucleus remain elusive, demanding substantial attention. This review highlights strategies employed to detect retrograde signals, their possible modes of signaling to the nucleus, and their implications for cellular processes during stress conditions. The present review also summarizes the role of ROS-mediated retrograde signaling in plastid-nucleus communication and its functional significance in co-coordinating the physiological profile of plant cells.
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Affiliation(s)
- Variyata Agrawal
- Department of Biotechnology, Indira Gandhi National Tribal University, Amarkantak, India
| | - Vijetna Singh
- Department of Biotechnology, Indira Gandhi National Tribal University, Amarkantak, India
| | - Bhumi Nath Tripathi
- Department of Biotechnology, Indira Gandhi National Tribal University, Amarkantak, India
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3
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Richter AS, Nägele T, Grimm B, Kaufmann K, Schroda M, Leister D, Kleine T. Retrograde signaling in plants: A critical review focusing on the GUN pathway and beyond. PLANT COMMUNICATIONS 2023; 4:100511. [PMID: 36575799 PMCID: PMC9860301 DOI: 10.1016/j.xplc.2022.100511] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 12/05/2022] [Accepted: 12/22/2022] [Indexed: 06/01/2023]
Abstract
Plastids communicate their developmental and physiological status to the nucleus via retrograde signaling, allowing nuclear gene expression to be adjusted appropriately. Signaling during plastid biogenesis and responses of mature chloroplasts to environmental changes are designated "biogenic" and "operational" controls, respectively. A prominent example of the investigation of biogenic signaling is the screen for gun (genomes uncoupled) mutants. Although the first five gun mutants were identified 30 years ago, the functions of GUN proteins in retrograde signaling remain controversial, and that of GUN1 is hotly disputed. Here, we provide background information and critically discuss recently proposed concepts that address GUN-related signaling and some novel gun mutants. Moreover, considering heme as a candidate in retrograde signaling, we revisit the spatial organization of heme biosynthesis and export from plastids. Although this review focuses on GUN pathways, we also highlight recent progress in the identification and elucidation of chloroplast-derived signals that regulate the acclimation response in green algae and plants. Here, stress-induced accumulation of unfolded/misassembled chloroplast proteins evokes a chloroplast-specific unfolded protein response, which leads to changes in the expression levels of nucleus-encoded chaperones and proteases to restore plastid protein homeostasis. We also address the importance of chloroplast-derived signals for activation of flavonoid biosynthesis leading to production of anthocyanins during stress acclimation through sucrose non-fermenting 1-related protein kinase 1. Finally, a framework for identification and quantification of intercompartmental signaling cascades at the proteomic and metabolomic levels is provided, and we discuss future directions of dissection of organelle-nucleus communication.
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Affiliation(s)
- Andreas S Richter
- Physiology of Plant Metabolism, Institute for Biosciences, University of Rostock, Albert-Einstein-Str. 3, 18059 Rostock, Germany
| | - Thomas Nägele
- Plant Evolutionary Cell Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Bernhard Grimm
- Institute of Biology/Plant Physiology, Humboldt-Universität zu Berlin, Philippstr. 13, 10115 Berlin, Germany
| | - Kerstin Kaufmann
- Plant Cell and Molecular Biology, Institute of Biology, Humboldt-Universität zu Berlin, Philippstr. 13, 10115 Berlin, Germany
| | - Michael Schroda
- Molecular Biotechnology and Systems Biology, TU Kaiserslautern, Kaiserslautern, Germany
| | - Dario Leister
- Plant Molecular Biology (Botany), Faculty of Biology, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Tatjana Kleine
- Plant Molecular Biology (Botany), Faculty of Biology, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany.
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Wijma M, Lembke CG, Diniz AL, Santini L, Zambotti-Villela L, Colepicolo P, Carneiro MS, Souza GM. Planting Season Impacts Sugarcane Stem Development, Secondary Metabolite Levels, and Natural Antisense Transcription. Cells 2021; 10:cells10123451. [PMID: 34943959 PMCID: PMC8700069 DOI: 10.3390/cells10123451] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 11/30/2021] [Accepted: 12/02/2021] [Indexed: 12/13/2022] Open
Abstract
To reduce the potentially irreversible environmental impacts caused by fossil fuels, the use of renewable energy sources must be increased on a global scale. One promising source of biomass and bioenergy is sugarcane. The study of this crop's development in different planting seasons can aid in successfully cultivating it in global climate change scenarios. The sugarcane variety SP80-3280 was field grown under two planting seasons with different climatic conditions. A systems biology approach was taken to study the changes on physiological, morphological, agrotechnological, transcriptomics, and metabolomics levels in the leaf +1, and immature, intermediate and mature internodes. Most of the variation found within the transcriptomics and metabolomics profiles is attributed to the differences among the distinct tissues. However, the integration of both transcriptomics and metabolomics data highlighted three main metabolic categories as the principal sources of variation across tissues: amino acid metabolism, biosynthesis of secondary metabolites, and xenobiotics biodegradation and metabolism. Differences in ripening and metabolite levels mainly in leaves and mature internodes may reflect the impact of contrasting environmental conditions on sugarcane development. In general, the same metabolites are found in mature internodes from both "one-year" and "one-and-a-half-year sugarcane", however, some metabolites (i.e., phenylpropanoids with economic value) and natural antisense transcript expression are only detected in the leaves of "one-year" sugarcane.
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Affiliation(s)
- Maryke Wijma
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508-900, Brazil; (M.W.); (C.G.L.); (A.L.D.); (L.S.); (L.Z.-V.); (P.C.)
| | - Carolina Gimiliani Lembke
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508-900, Brazil; (M.W.); (C.G.L.); (A.L.D.); (L.S.); (L.Z.-V.); (P.C.)
| | - Augusto Lima Diniz
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508-900, Brazil; (M.W.); (C.G.L.); (A.L.D.); (L.S.); (L.Z.-V.); (P.C.)
| | - Luciane Santini
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508-900, Brazil; (M.W.); (C.G.L.); (A.L.D.); (L.S.); (L.Z.-V.); (P.C.)
| | - Leonardo Zambotti-Villela
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508-900, Brazil; (M.W.); (C.G.L.); (A.L.D.); (L.S.); (L.Z.-V.); (P.C.)
| | - Pio Colepicolo
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508-900, Brazil; (M.W.); (C.G.L.); (A.L.D.); (L.S.); (L.Z.-V.); (P.C.)
| | - Monalisa Sampaio Carneiro
- Centro de Ciências Agrárias, Departamento de Biotecnologia e Produção Vegetal e Animal, Universidade Federal de São Carlos, São Paulo 13600-970, Brazil;
| | - Glaucia Mendes Souza
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508-900, Brazil; (M.W.); (C.G.L.); (A.L.D.); (L.S.); (L.Z.-V.); (P.C.)
- Correspondence:
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5
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Ascorbate and Thiamin: Metabolic Modulators in Plant Acclimation Responses. PLANTS 2020; 9:plants9010101. [PMID: 31941157 PMCID: PMC7020166 DOI: 10.3390/plants9010101] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 01/09/2020] [Accepted: 01/10/2020] [Indexed: 12/12/2022]
Abstract
Cell compartmentalization allows incompatible chemical reactions and localised responses to occur simultaneously, however, it also requires a complex system of communication between compartments in order to maintain the functionality of vital processes. It is clear that multiple such signals must exist, yet little is known about the identity of the key players orchestrating these interactions or about the role in the coordination of other processes. Mitochondria and chloroplasts have a considerable number of metabolites in common and are interdependent at multiple levels. Therefore, metabolites represent strong candidates as communicators between these organelles. In this context, vitamins and similar small molecules emerge as possible linkers to mediate metabolic crosstalk between compartments. This review focuses on two vitamins as potential metabolic signals within the plant cell, vitamin C (L-ascorbate) and vitamin B1 (thiamin). These two vitamins demonstrate the importance of metabolites in shaping cellular processes working as metabolic signals during acclimation processes. Inferences based on the combined studies of environment, genotype, and metabolite, in order to unravel signaling functions, are also highlighted.
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Yi J, Zhao D, Chu J, Yan J, Liu J, Wu M, Cheng J, Jiang H, Zeng Y, Liu D. AtDPG1 is involved in the salt stress response of Arabidopsis seedling through ABI4. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 287:110180. [PMID: 31481194 DOI: 10.1016/j.plantsci.2019.110180] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Revised: 06/20/2019] [Accepted: 06/25/2019] [Indexed: 05/08/2023]
Abstract
Although the genes controlling chloroplast development play important roles in plant responses to environmental stresses, the molecular mechanisms remain largely unclear. In this study, an Arabidopsis mutant dpg1 (delayed pale-greening1) with a chloroplast development defect was studied. By using quantitative RT-PCR and histochemical GUS assays, we demonstrated that AtDPG1 was mainly expressed in the green tissues of Arabidopsis seedlings and could be induced by salt stress. Phenotypic analysis showed that mutation in AtDPG1 lead to an enhanced sensitivity to salt stress in Arabidopsis seedlings. Further studies demonstrated that disruption of the AtDPG1 in Arabidopsis increases its sensitivity to salt stress in an ABA-dependent manner. Moreover, expression levels of various stress-responsive and ABA signal-related genes were remarkably altered in the dpg1 plants under NaCl treatment. Notably, the transcript levels of ABI4 in dpg1 mutant increased more significantly than that in wild type plants under salt conditions. The seedlings of dpg1/abi4 double mutant exhibited stronger resistance to salt stress after salt treatment compared with the dpg1 single mutant, suggesting that the salt-hypersensitive phenotype of dpg1 seedlings could be rescued via loss of ABI4 function. These results reveal that AtDPG1 is involved in the salt stress response of Arabidopsis seedling through ABI4.
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Affiliation(s)
- Jian Yi
- College of Agronomy/Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Dongming Zhao
- College of Agronomy/Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Jinfang Chu
- National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Jijun Yan
- National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Jinsong Liu
- College of Agronomy/Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Meijia Wu
- College of Agronomy/Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Jianfeng Cheng
- College of Agronomy/Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Haiyan Jiang
- College of Agronomy/Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Yongjun Zeng
- College of Agronomy/Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Dong Liu
- College of Agronomy/Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045, China.
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7
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Qin J, Yan B, Hu Y, Wang P, Wang J. Applications of integrative OMICs approaches to gene regulation studies. QUANTITATIVE BIOLOGY 2016. [DOI: 10.1007/s40484-016-0085-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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8
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Frédérich M, Pirotte B, Fillet M, de Tullio P. Metabolomics as a Challenging Approach for Medicinal Chemistry and Personalized Medicine. J Med Chem 2016; 59:8649-8666. [PMID: 27295417 DOI: 10.1021/acs.jmedchem.5b01335] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
"Omics" sciences have been developed to provide a holistic point of view of biology and to better understand the complexity of an organism as a whole. These systems biology approaches can be examined at different levels, starting from the most fundamental, i.e., the genome, and finishing with the most functional, i.e., the metabolome. Similar to how genomics is applied to the exploration of DNA, metabolomics is the qualitative and quantitative study of metabolites. This emerging field is clearly linked to genomics, transcriptomics, and proteomics. In addition, metabolomics provides a unique and direct vision of the functional outcome of an organism's activities that are required for it to survive, grow, and respond to internal and external stimuli or stress, e.g., pathologies and drugs. The links between metabolic changes, patient phenotype, physiological and/or pathological status, and treatment are now well established and have opened a new area for the application of metabolomics in the drug discovery process and in personalized medicine.
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Affiliation(s)
- Michel Frédérich
- Laboratory of Pharmacognosy, Center for Interdisciplinary Research on Medicines (CIRM), University of Liege , Quartier Hôpital, Avenue Hippocrate 15, B-4000 Liege, Belgium
| | - Bernard Pirotte
- Laboratory of Medicinal Chemistry, Center for Interdisciplinary Research on Medicines (CIRM), University of Liege , Quartier Hôpital, Avenue Hippocrate 15, B-4000 Liege, Belgium
| | - Marianne Fillet
- Laboratory for the Analysis of Medicines, Center for Interdisciplinary Research on Medicines (CIRM), University of Liege , Quartier Hôpital, Avenue Hippocrate 15, B-4000 Liege, Belgium
| | - Pascal de Tullio
- Laboratory of Medicinal Chemistry, Center for Interdisciplinary Research on Medicines (CIRM), University of Liege , Quartier Hôpital, Avenue Hippocrate 15, B-4000 Liege, Belgium
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Aretz I, Meierhofer D. Advantages and Pitfalls of Mass Spectrometry Based Metabolome Profiling in Systems Biology. Int J Mol Sci 2016; 17:ijms17050632. [PMID: 27128910 PMCID: PMC4881458 DOI: 10.3390/ijms17050632] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 04/19/2016] [Accepted: 04/21/2016] [Indexed: 12/22/2022] Open
Abstract
Mass spectrometry-based metabolome profiling became the method of choice in systems biology approaches and aims to enhance biological understanding of complex biological systems. Genomics, transcriptomics, and proteomics are well established technologies and are commonly used by many scientists. In comparison, metabolomics is an emerging field and has not reached such high-throughput, routine and coverage than other omics technologies. Nevertheless, substantial improvements were achieved during the last years. Integrated data derived from multi-omics approaches will provide a deeper understanding of entire biological systems. Metabolome profiling is mainly hampered by its diversity, variation of metabolite concentration by several orders of magnitude and biological data interpretation. Thus, multiple approaches are required to cover most of the metabolites. No software tool is capable of comprehensively translating all the data into a biologically meaningful context yet. In this review, we discuss the advantages of metabolome profiling and main obstacles limiting progress in systems biology.
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Affiliation(s)
- Ina Aretz
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany.
| | - David Meierhofer
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany.
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10
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Chi W, Feng P, Ma J, Zhang L. Metabolites and chloroplast retrograde signaling. CURRENT OPINION IN PLANT BIOLOGY 2015; 25:32-8. [PMID: 25912815 DOI: 10.1016/j.pbi.2015.04.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Revised: 04/10/2015] [Accepted: 04/13/2015] [Indexed: 05/23/2023]
Abstract
Intracellular signaling from chloroplast to nucleus followed by a subsequent response in the chloroplast is called retrograde signaling. It not only coordinates the expression of nuclear and chloroplast genes, which is essential for chloroplast biogenesis, but also maintains chloroplast function at optimal levels in response to fluxes in metabolites and changes in environmental conditions. In recent years several putative retrograde signals have been identified and signaling pathways have been proposed. Here we review retrograde signals derived from tetrapyrroles, carotenoids, nucleotides and isoprene precursors in response to abiotic stresses, including oxidative stress. We discuss the responses that these signals elicit and show that they not only modify chloroplast function but also influence other aspects of plant development and adaptation.
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Affiliation(s)
- Wei Chi
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Peiqiang Feng
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Jinfang Ma
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Lixin Zhang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
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Krasensky J, Broyart C, Rabanal FA, Jonak C. The redox-sensitive chloroplast trehalose-6-phosphate phosphatase AtTPPD regulates salt stress tolerance. Antioxid Redox Signal 2014; 21:1289-304. [PMID: 24800789 PMCID: PMC4158992 DOI: 10.1089/ars.2013.5693] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
AIMS High salinity stress impairs plant growth and development. Trehalose metabolism has been implicated in sugar signaling, and enhanced trehalose metabolism can positively regulate abiotic stress tolerance. However, the molecular mechanism(s) of the stress-related trehalose pathway and the role of individual trehalose biosynthetic enzymes for stress tolerance remain unclear. RESULTS Trehalose-6-phosphate phosphatase (TPP) catalyzes the final step of trehalose metabolism. Investigating the subcellular localization of the Arabidopsis thaliana TPP family members, we identified AtTPPD as a chloroplast-localized enzyme. Plants deficient in AtTPPD were hypersensitive, whereas plants overexpressing AtTPPD were more tolerant to high salinity stress. Elevated stress tolerance of AtTPPD overexpressors correlated with high starch levels and increased accumulation of soluble sugars, suggesting a role for AtTPPD in regulating sugar metabolism under salinity conditions. Biochemical analyses indicate that AtTPPD is a target of post-translational redox regulation and can be reversibly inactivated by oxidizing conditions. Two cysteine residues were identified as the redox-sensitive sites. Structural and mutation analyses suggest that the formation of an intramolecular disulfide bridge regulates AtTPPD activity. INNOVATION The activity of different AtTPP isoforms, located in the cytosol, nucleus, and chloroplasts, can be redox regulated, suggesting that the trehalose metabolism might relay the redox status of different cellular compartments to regulate diverse biological processes such as stress responses. CONCLUSION The evolutionary conservation of the two redox regulatory cysteine residues of TPPs in spermatophytes indicates that redox regulation of TPPs might be a common mechanism enabling plants to rapidly adjust trehalose metabolism to the prevailing environmental and developmental conditions.
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Affiliation(s)
- Julia Krasensky
- GMI-Gregor Mendel Institute of Molecular Plant Biology , Austrian Academy of Sciences, Vienna, Austria
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12
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Geigenberger P, Fernie AR. Metabolic control of redox and redox control of metabolism in plants. Antioxid Redox Signal 2014; 21:1389-421. [PMID: 24960279 PMCID: PMC4158967 DOI: 10.1089/ars.2014.6018] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
SIGNIFICANCE Reduction-oxidation (Redox) status operates as a major integrator of subcellular and extracellular metabolism and is simultaneously itself regulated by metabolic processes. Redox status not only dominates cellular metabolism due to the prominence of NAD(H) and NADP(H) couples in myriad metabolic reactions but also acts as an effective signal that informs the cell of the prevailing environmental conditions. After relay of this information, the cell is able to appropriately respond via a range of mechanisms, including directly affecting cellular functioning and reprogramming nuclear gene expression. RECENT ADVANCES The facile accession of Arabidopsis knockout mutants alongside the adoption of broad-scale post-genomic approaches, which are able to provide transcriptomic-, proteomic-, and metabolomic-level information alongside traditional biochemical and emerging cell biological techniques, has dramatically advanced our understanding of redox status control. This review summarizes redox status control of metabolism and the metabolic control of redox status at both cellular and subcellular levels. CRITICAL ISSUES It is becoming apparent that plastid, mitochondria, and peroxisome functions influence a wide range of processes outside of the organelles themselves. While knowledge of the network of metabolic pathways and their intraorganellar redox status regulation has increased in the last years, little is known about the interorganellar redox signals coordinating these networks. A current challenge is, therefore, synthesizing our knowledge and planning experiments that tackle redox status regulation at both inter- and intracellular levels. FUTURE DIRECTIONS Emerging tools are enabling ever-increasing spatiotemporal resolution of metabolism and imaging of redox status components. Broader application of these tools will likely greatly enhance our understanding of the interplay of redox status and metabolism as well as elucidating and characterizing signaling features thereof. We propose that such information will enable us to dissect the regulatory hierarchies that mediate the strict coupling of metabolism and redox status which, ultimately, determine plant growth and development.
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Affiliation(s)
- Peter Geigenberger
- 1 Department of Biology I, Ludwig Maximilian University Munich , Planegg-Martinsried, Germany
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13
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Schmitz J, Heinrichs L, Scossa F, Fernie AR, Oelze ML, Dietz KJ, Rothbart M, Grimm B, Flügge UI, Häusler RE. The essential role of sugar metabolism in the acclimation response of Arabidopsis thaliana to high light intensities. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:1619-36. [PMID: 24523502 PMCID: PMC3967092 DOI: 10.1093/jxb/eru027] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Retrograde signals from chloroplasts are thought to control the expression of nuclear genes associated with plastidial processes such as acclimation to varying light conditions. Arabidopsis mutants altered in the day and night path of photoassimilate export from the chloroplasts served as tools to study the involvement of carbohydrates in high light (HL) acclimation. A double mutant impaired in the triose phosphate/phosphate translocator (TPT) and ADP-glucose pyrophosphorylase (AGPase) (adg1-1/tpt-2) exhibits a HL-dependent depletion in endogenous carbohydrates combined with a severe growth and photosynthesis phenotype. The acclimation response of mutant and wild-type plants has been assessed in time series after transfer from low light (LL) to HL by analysing photosynthetic performance, carbohydrates, MgProtoIX (a chlorophyll precursor), and the ascorbate/glutathione redox system, combined with microarray-based transcriptomic and GC-MS-based metabolomic approaches. The data indicate that the accumulation of soluble carbohydrates (predominantly glucose) acts as a short-term response to HL exposure in both mutant and wild-type plants. Only if carbohydrates are depleted in the long term (e.g. after 2 d) is the acclimation response impaired, as observed in the adg1-1/tpt-2 double mutant. Furthermore, meta-analyses conducted with in-house and publicly available microarray data suggest that, in the long term, reactive oxygen species such as H₂O₂ can replace carbohydrates as signals. Moreover, a cross-talk exists between genes associated with the regulation of starch and lipid metabolism. The involvement of genes responding to phytohormones in HL acclimation appears to be less likely. Various candidate genes involved in retrograde control of nuclear gene expression emerged from the analyses of global gene expression.
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Affiliation(s)
- Jessica Schmitz
- Department of Botany II, Cologne Biocenter, University of Cologne, Zülpicher Straße 47b, D-50674 Cologne, Germany
- * Present address: Plant Molecular Physiology and Biotechnology, Heinrich-Heine-University, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
| | - Luisa Heinrichs
- Department of Botany II, Cologne Biocenter, University of Cologne, Zülpicher Straße 47b, D-50674 Cologne, Germany
| | - Federico Scossa
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam OT Golm, Germany
- Agriculture Research Council, Research Center for Vegetable Crops, Via Cavalleggeri 25, 84098 Pontecagnano (Salerno), Italy
| | - Alisdair R. Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam OT Golm, Germany
| | - Marie-Luise Oelze
- Biochemistry and Physiology of Plants, University of Bielefeld, Universitätsstraße 25, D-33615 Bielefeld, Germany
| | - Karl-Josef Dietz
- Biochemistry and Physiology of Plants, University of Bielefeld, Universitätsstraße 25, D-33615 Bielefeld, Germany
| | - Maxi Rothbart
- Institute of Biology, Plant Physiology, Humboldt-University Berlin, Philippstraße 13, D-10115 Berlin, Germany
| | - Bernhard Grimm
- Institute of Biology, Plant Physiology, Humboldt-University Berlin, Philippstraße 13, D-10115 Berlin, Germany
| | - Ulf-Ingo Flügge
- Department of Botany II, Cologne Biocenter, University of Cologne, Zülpicher Straße 47b, D-50674 Cologne, Germany
| | - Rainer E. Häusler
- Department of Botany II, Cologne Biocenter, University of Cologne, Zülpicher Straße 47b, D-50674 Cologne, Germany
- To whom correspondence should be addressed. E-mail:
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14
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Coordinating metabolite changes with our perception of plant abiotic stress responses: emerging views revealed by integrative-omic analyses. Metabolites 2013; 3:761-86. [PMID: 24958149 PMCID: PMC3901284 DOI: 10.3390/metabo3030761] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Revised: 08/21/2013] [Accepted: 08/28/2013] [Indexed: 11/17/2022] Open
Abstract
Metabolic configuration and adaptation under a range of abiotic stresses, including drought, heat, salinity, cold, and nutrient deprivation, are subjected to an intricate span of molecular pathways that work in parallel in order to enhance plant fitness and increase stress tolerance. In recent years, unprecedented advances have been made in identifying and linking different abiotic stresses, and the current challenge in plant molecular biology is deciphering how the signaling responses are integrated and transduced throughout metabolism. Metabolomics have often played a fundamental role in elucidating the distinct and overlapping biochemical changes that occur in plants. However, a far greater understanding and appreciation of the complexity in plant metabolism under specific stress conditions have become apparent when combining metabolomics with other—omic platforms. This review focuses on recent advances made in understanding the global changes occurring in plant metabolism under abiotic stress conditions using metabolite profiling as an integrated discovery platform.
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15
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Kleine T, Leister D. Retrograde signals galore. FRONTIERS IN PLANT SCIENCE 2013; 4:45. [PMID: 23487593 PMCID: PMC3594843 DOI: 10.3389/fpls.2013.00045] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Accepted: 02/22/2013] [Indexed: 05/20/2023]
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16
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Osorio S, Scossa F, Fernie AR. Molecular regulation of fruit ripening. FRONTIERS IN PLANT SCIENCE 2013; 4:198. [PMID: 23785378 PMCID: PMC3682129 DOI: 10.3389/fpls.2013.00198] [Citation(s) in RCA: 115] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Accepted: 05/28/2013] [Indexed: 05/18/2023]
Abstract
Fruit ripening is a highly coordinated developmental process that coincides with seed maturation. The ripening process is regulated by thousands of genes that control progressive softening and/or lignification of pericarp layers, accumulation of sugars, acids, pigments, and release of volatiles. Key to crop improvement is a deeper understanding of the processes underlying fruit ripening. In tomato, mutations blocking the transition to ripe fruits have provided insights into the role of ethylene and its associated molecular networks involved in the control of ripening. However, the role of other plant hormones is still poorly understood. In this review, we describe how plant hormones, transcription factors, and epigenetic changes are intimately related to provide a tight control of the ripening process. Recent findings from comparative genomics and system biology approaches are discussed.
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Affiliation(s)
- Sonia Osorio
- Max-Planck-Institut für Molekulare PflanzenphysiologiePotsdam-Golm, Germany
- Departamento de Biología Molecular y Bioquímica, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Consejo Superior de Investigaciones Científicas, Universidad de MálagaMálaga, Spain
- *Correspondence: Sonia Osorio, Departamento de Biologïa Molecular y Bioquímica, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Consejo Superior de Investigaciones Científicas, Universidad de Málaga, Edificio I+D, 3 Planta, Campus Teatinos, 29071 Málaga, Spain e-mail:
| | - Federico Scossa
- Max-Planck-Institut für Molekulare PflanzenphysiologiePotsdam-Golm, Germany
- Consiglio per la ricerca e la sperimentazione in agricoltura, Centro di ricerca per l’OrticolturaPontecagnano (Salerno), Italy
| | - Alisdair R. Fernie
- Max-Planck-Institut für Molekulare PflanzenphysiologiePotsdam-Golm, Germany
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