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da Fonseca-Pereira P, Monteiro-Batista RDC, Araújo WL, Nunes-Nesi A. Harnessing enzyme cofactors and plant metabolism: an essential partnership. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:1014-1036. [PMID: 36861364 DOI: 10.1111/tpj.16167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 02/18/2023] [Accepted: 02/25/2023] [Indexed: 05/31/2023]
Abstract
Cofactors are fundamental to the catalytic activity of enzymes. Additionally, because plants are a critical source of several cofactors (i.e., including their vitamin precursors) within the context of human nutrition, there have been several studies aiming to understand the metabolism of coenzymes and vitamins in plants in detail. For example, compelling evidence has been brought forth regarding the role of cofactors in plants; specifically, it is becoming increasingly clear that an adequate supply of cofactors in plants directly affects their development, metabolism, and stress responses. Here, we review the state-of-the-art knowledge on the significance of coenzymes and their precursors with regard to general plant physiology and discuss the emerging functions attributed to them. Furthermore, we discuss how our understanding of the complex relationship between cofactors and plant metabolism can be used for crop improvement.
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Affiliation(s)
- Paula da Fonseca-Pereira
- National Institute of Science and Technology on Plant Physiology under Stress Conditions, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Rita de Cássia Monteiro-Batista
- National Institute of Science and Technology on Plant Physiology under Stress Conditions, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Wagner L Araújo
- National Institute of Science and Technology on Plant Physiology under Stress Conditions, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Adriano Nunes-Nesi
- National Institute of Science and Technology on Plant Physiology under Stress Conditions, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
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Eggers R, Jammer A, Jha S, Kerschbaumer B, Lahham M, Strandback E, Toplak M, Wallner S, Winkler A, Macheroux P. The scope of flavin-dependent reactions and processes in the model plant Arabidopsis thaliana. PHYTOCHEMISTRY 2021; 189:112822. [PMID: 34118767 DOI: 10.1016/j.phytochem.2021.112822] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 05/23/2021] [Accepted: 05/24/2021] [Indexed: 06/12/2023]
Abstract
Flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD) are utilized as coenzymes in many biochemical reduction-oxidation reactions owing to the ability of the tricyclic isoalloxazine ring system to employ the oxidized, radical and reduced state. We have analyzed the genome of Arabidopsis thaliana to establish an inventory of genes encoding flavin-dependent enzymes (flavoenzymes) as a basis to explore the range of flavin-dependent biochemical reactions that occur in this model plant. Expectedly, flavoenzymes catalyze many pivotal reactions in primary catabolism, which are connected to the degradation of basic metabolites, such as fatty and amino acids as well as carbohydrates and purines. On the other hand, flavoenzymes play diverse roles in anabolic reactions most notably the biosynthesis of amino acids as well as the biosynthesis of pyrimidines and sterols. Importantly, the role of flavoenzymes goes much beyond these basic reactions and extends into pathways that are equally crucial for plant life, for example the production of natural products. In this context, we outline the participation of flavoenzymes in the biosynthesis and maintenance of cofactors, coenzymes and accessory plant pigments (e. g. carotenoids) as well as phytohormones. Moreover, several multigene families have emerged as important components of plant immunity, for example the family of berberine bridge enzyme-like enzymes, flavin-dependent monooxygenases and NADPH oxidases. Furthermore, the versatility of flavoenzymes is highlighted by their role in reactions leading to tRNA-modifications, chromatin regulation and cellular redox homeostasis. The favorable photochemical properties of the flavin chromophore are exploited by photoreceptors to govern crucial processes of plant adaptation and development. Finally, a sequence- and structure-based approach was undertaken to gain insight into the catalytic role of uncharacterized flavoenzymes indicating their involvement in unknown biochemical reactions and pathways in A. thaliana.
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Affiliation(s)
- Reinmar Eggers
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/2, 8010, Graz, Austria
| | - Alexandra Jammer
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/2, 8010, Graz, Austria
| | - Shalinee Jha
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/2, 8010, Graz, Austria
| | - Bianca Kerschbaumer
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/2, 8010, Graz, Austria
| | - Majd Lahham
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/2, 8010, Graz, Austria
| | - Emilia Strandback
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/2, 8010, Graz, Austria
| | - Marina Toplak
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/2, 8010, Graz, Austria
| | - Silvia Wallner
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/2, 8010, Graz, Austria
| | - Andreas Winkler
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/2, 8010, Graz, Austria
| | - Peter Macheroux
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/2, 8010, Graz, Austria.
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Kiontke S, Göbel T, Brych A, Batschauer A. DASH-type cryptochromes - solved and open questions. Biol Chem 2021; 401:1487-1493. [PMID: 32663167 DOI: 10.1515/hsz-2020-0182] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 07/09/2020] [Indexed: 01/04/2023]
Abstract
Drosophila, Arabidopsis, Synechocystis, human (DASH)-type cryptochromes (cry-DASHs) form one subclade of the cryptochrome/photolyase family (CPF). CPF members are flavoproteins that act as DNA-repair enzymes (DNA-photolyases), or as ultraviolet(UV)-A/blue light photoreceptors (cryptochromes). In mammals, cryptochromes are essential components of the circadian clock feed-back loop. Cry-DASHs are present in almost all major taxa and were initially considered as photoreceptors. Later studies demonstrated DNA-repair activity that was, however, restricted to UV-lesions in single-stranded DNA. Very recent studies, particularly on microbial organisms, substantiated photoreceptor functions of cry-DASHs suggesting that they could be transitions between photolyases and cryptochromes.
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Affiliation(s)
- Stephan Kiontke
- University of Marburg, Department of Biology, Molecular Plant Physiology and Photobiology, D-35032 Marburg, Germany
| | - Tanja Göbel
- University of Marburg, Department of Biology, Molecular Plant Physiology and Photobiology, D-35032 Marburg, Germany
| | - Annika Brych
- University of Marburg, Department of Biology, Molecular Plant Physiology and Photobiology, D-35032 Marburg, Germany
| | - Alfred Batschauer
- University of Marburg, Department of Biology, Molecular Plant Physiology and Photobiology, D-35032 Marburg, Germany
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Banaś AK, Zgłobicki P, Kowalska E, Bażant A, Dziga D, Strzałka W. All You Need Is Light. Photorepair of UV-Induced Pyrimidine Dimers. Genes (Basel) 2020; 11:E1304. [PMID: 33158066 PMCID: PMC7694213 DOI: 10.3390/genes11111304] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 10/27/2020] [Accepted: 10/27/2020] [Indexed: 12/18/2022] Open
Abstract
Although solar light is indispensable for the functioning of plants, this environmental factor may also cause damage to living cells. Apart from the visible range, including wavelengths used in photosynthesis, the ultraviolet (UV) light present in solar irradiation reaches the Earth's surface. The high energy of UV causes damage to many cellular components, with DNA as one of the targets. Putting together the puzzle-like elements responsible for the repair of UV-induced DNA damage is of special importance in understanding how plants ensure the stability of their genomes between generations. In this review, we have presented the information on DNA damage produced under UV with a special focus on the pyrimidine dimers formed between the neighboring pyrimidines in a DNA strand. These dimers are highly mutagenic and cytotoxic, thus their repair is essential for the maintenance of suitable genetic information. In prokaryotic and eukaryotic cells, with the exception of placental mammals, this is achieved by means of highly efficient photorepair, dependent on blue/UVA light, which is performed by specialized enzymes known as photolyases. Photolyase properties, as well as their structure, specificity and action mechanism, have been briefly discussed in this paper. Additionally, the main gaps in our knowledge on the functioning of light repair in plant organelles, its regulation and its interaction between different DNA repair systems in plants have been highlighted.
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Affiliation(s)
- Agnieszka Katarzyna Banaś
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland; (A.K.B.); (P.Z.); (E.K.); (A.B.)
| | - Piotr Zgłobicki
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland; (A.K.B.); (P.Z.); (E.K.); (A.B.)
| | - Ewa Kowalska
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland; (A.K.B.); (P.Z.); (E.K.); (A.B.)
| | - Aneta Bażant
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland; (A.K.B.); (P.Z.); (E.K.); (A.B.)
| | - Dariusz Dziga
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland;
| | - Wojciech Strzałka
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland; (A.K.B.); (P.Z.); (E.K.); (A.B.)
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Mombaerts L, Carignano A, Robertson FC, Hearn TJ, Junyang J, Hayden D, Rutterford Z, Hotta CT, Hubbard KE, Maria MRC, Yuan Y, Hannah MA, Goncalves J, Webb AAR. Dynamical differential expression (DyDE) reveals the period control mechanisms of the Arabidopsis circadian oscillator. PLoS Comput Biol 2019; 15:e1006674. [PMID: 30703082 PMCID: PMC6377142 DOI: 10.1371/journal.pcbi.1006674] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 02/15/2019] [Accepted: 11/26/2018] [Indexed: 12/12/2022] Open
Abstract
The circadian oscillator, an internal time-keeping device found in most organisms, enables timely regulation of daily biological activities by maintaining synchrony with the external environment. The mechanistic basis underlying the adjustment of circadian rhythms to changing external conditions, however, has yet to be clearly elucidated. We explored the mechanism of action of nicotinamide in Arabidopsis thaliana, a metabolite that lengthens the period of circadian rhythms, to understand the regulation of circadian period. To identify the key mechanisms involved in the circadian response to nicotinamide, we developed a systematic and practical modeling framework based on the identification and comparison of gene regulatory dynamics. Our mathematical predictions, confirmed by experimentation, identified key transcriptional regulatory mechanisms of circadian period and uncovered the role of blue light in the response of the circadian oscillator to nicotinamide. We suggest that our methodology could be adapted to predict mechanisms of drug action in complex biological systems.
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Affiliation(s)
- Laurent Mombaerts
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Alberto Carignano
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Fiona C. Robertson
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Timothy J. Hearn
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Jin Junyang
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - David Hayden
- Department of Engineering, University of Cambridge, Cambridge, United Kingdom
| | - Zoe Rutterford
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Carlos T. Hotta
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Katherine E. Hubbard
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Marti Ruiz C. Maria
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Ye Yuan
- Department of Engineering, University of Cambridge, Cambridge, United Kingdom
| | | | - Jorge Goncalves
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
- Department of Engineering, University of Cambridge, Cambridge, United Kingdom
| | - Alex A. R. Webb
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
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Gärtner W. In-Planta Expression: Searching for the Genuine Chromophores of Cryptochrome-3 from Arabidopsis thaliana. Photochem Photobiol 2018; 93:382-384. [PMID: 28211124 DOI: 10.1111/php.12693] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 11/15/2016] [Indexed: 11/30/2022]
Abstract
Göbel et al. present in this issue an exemplary study of identification of chromophores from Arabidopsis thaliana cryptochrome-3. Usually taken for granted, proteins and cofactors, respective chromophores, from heterologous expression are considered identical to material isolated from their genuine host. Cryptochromes carry two chromophores, an antenna cofactor and a functional flavin chromophore, both noncovalently embedded into the protein. In particular the antenna chromophore is loosely bound and often lost during protein purification. The authors identify from plant-extracted Cry3 unambiguously N5 ,N10 -methenyltetrahydrofolate as antenna chromophore and flavin adenine dinucleotide as the functional chromophore.
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Affiliation(s)
- Wolfgang Gärtner
- Max-Planck-Institute for Chemical Energy Conversion, Mülheim, Germany
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