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Rao X, Barros J. Modeling lignin biosynthesis: a pathway to renewable chemicals. TRENDS IN PLANT SCIENCE 2024; 29:546-559. [PMID: 37802691 DOI: 10.1016/j.tplants.2023.09.011] [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: 05/31/2023] [Revised: 09/01/2023] [Accepted: 09/18/2023] [Indexed: 10/08/2023]
Abstract
Plant biomass contains lignin that can be converted into high-value-added chemicals, fuels, and materials. The precise genetic manipulation of lignin content and composition in plant cells offers substantial environmental and economic benefits. However, the intricate regulatory mechanisms governing lignin formation challenge the development of crops with specific lignin profiles. Mathematical models and computational simulations have recently been employed to gain fundamental understanding of the metabolism of lignin and related phenolic compounds. This review article discusses the strategies used for modeling plant metabolic networks, focusing on the application of mathematical modeling for flux network analysis in monolignol biosynthesis. Furthermore, we highlight how current challenges might be overcome to optimize the use of metabolic modeling approaches for developing lignin-engineered plants.
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Affiliation(s)
- Xiaolan Rao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China.
| | - Jaime Barros
- Division of Plant Sciences and Interdisciplinary Plant Group, University of Missouri, Columbia, MO 65211, USA.
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2
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Kitashova A, Brodsky V, Chaturvedi P, Pierides I, Ghatak A, Weckwerth W, Nägele T. Quantifying the impact of dynamic plant-environment interactions on metabolic regulation. JOURNAL OF PLANT PHYSIOLOGY 2023; 290:154116. [PMID: 37839392 DOI: 10.1016/j.jplph.2023.154116] [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: 08/23/2023] [Revised: 10/03/2023] [Accepted: 10/06/2023] [Indexed: 10/17/2023]
Abstract
A plant's genome encodes enzymes, transporters and many other proteins which constitute metabolism. Interactions of plants with their environment shape their growth, development and resilience towards adverse conditions. Although genome sequencing technologies and applications have experienced triumphantly rapid development during the last decades, enabling nowadays a fast and cheap sequencing of full genomes, prediction of metabolic phenotypes from genotype × environment interactions remains, at best, very incomplete. The main reasons are a lack of understanding of how different levels of molecular organisation depend on each other, and how they are constituted and expressed within a setup of growth conditions. Phenotypic plasticity, e.g., of the genetic model plant Arabidopsis thaliana, has provided important insights into plant-environment interactions and the resulting genotype x phenotype relationships. Here, we summarize previous and current findings about plant development in a changing environment and how this might be shaped and reflected in metabolism and its regulation. We identify current challenges in the study of plant development and metabolic regulation and provide an outlook of how methodological workflows might support the application of findings made in model systems to crops and their cultivation.
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Affiliation(s)
- Anastasia Kitashova
- LMU Munich, Faculty of Biology, Plant Evolutionary Cell Biology, 82152, Planegg, Germany.
| | - Vladimir Brodsky
- LMU Munich, Faculty of Biology, Plant Evolutionary Cell Biology, 82152, Planegg, Germany.
| | - Palak Chaturvedi
- University of Vienna, Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, Djerassiplatz 1, 1030, Vienna, Austria.
| | - Iro Pierides
- University of Vienna, Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, Djerassiplatz 1, 1030, Vienna, Austria.
| | - Arindam Ghatak
- University of Vienna, Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, Djerassiplatz 1, 1030, Vienna, Austria; Vienna Metabolomics Center, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria.
| | - Wolfram Weckwerth
- University of Vienna, Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, Djerassiplatz 1, 1030, Vienna, Austria; Vienna Metabolomics Center, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria.
| | - Thomas Nägele
- LMU Munich, Faculty of Biology, Plant Evolutionary Cell Biology, 82152, Planegg, Germany.
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3
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Metabolites and Plant Hormones Related to the Resistance Response to Feeding Stimulation and Leaf Clipping Control in Chinese Pine ( Pinus tabuliformis Carr.). Curr Issues Mol Biol 2023; 45:1086-1099. [PMID: 36826017 PMCID: PMC9955327 DOI: 10.3390/cimb45020072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/25/2022] [Accepted: 12/28/2022] [Indexed: 02/03/2023] Open
Abstract
This experiment was conducted to define changes in metabolic pathways in response to mandibulate insect feeding and to provide a reference for further investigation of the molecular mechanisms underlying the development of conifer resistance. Chinese pine (Pinus tabuliformis Carr.) in good growth status in natural condition was chosen for stimulation by 10 pine caterpillars (Dendrolimus tabulaefomis Tsai et Liu) as feeding stimulation (FS), leaf clipping control (LCC) as mechanical damage, and CK group (with no treatment) (recorded as 0 h). The metabolome and total flavonoid content were measured in the needles at 0, 2, and 8 h after treatment. Plant hormones were measured with needles at 0, 0.5, 1, 1.5, 2, 4, 6, and 8 h after different treatments. The results show that a total of 30.8% flavonoids are identified by metabolomics analysis. Compared with leaf clipping control, feeding stimulation of Chinese pine caterpillars significantly induced the upregulation of metabolites in the flavonoid pathway in Chinese pine, and the plant hormones JA and IAA showed expression trends consistent with those of the metabolome. According to the biological processes of the four plant hormones involved, JA and SA are mostly involved in resistance formation, and in this study, both of them also have fluctuating expressions influenced by feeding stimulation, while the expressions of the growth-related hormones IAA and ABA have no significant changes at other time points except for 1 h after treatment. Thus, the flavonoid pathway is one of the main pathways involved in resistance formation in conifers, and JA and IAA are involved in the formation of resistance.
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Xiong JL, Ma N. Transcriptomic and Metabolomic Analyses Reveal That Fullerol Improves Drought Tolerance in Brassica napus L. Int J Mol Sci 2022; 23:ijms232315304. [PMID: 36499633 PMCID: PMC9740425 DOI: 10.3390/ijms232315304] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 11/22/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
Carbon nanoparticles have potential threats to plant growth and stress tolerance. The polyhydroxy fullerene-fullerol (one of the carbon nanoparticles) could increase biomass accumulation in several plants subjected to drought; however, the underlying molecular and metabolic mechanisms governed by fullerol in improving drought tolerance in Brassica napus remain unclear. In the present study, exogenous fullerol was applied to the leaves of B. napus seedlings under drought conditions. The results of transcriptomic and metabolomic analyses revealed changes in the molecular and metabolic profiles of B. napus. The differentially expressed genes and the differentially accumulated metabolites, induced by drought or fullerol treatment, were mainly enriched in the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways related to carbohydrate metabolism (e.g., "carbon metabolism" and "galactose metabolism"), amino acid metabolism (e.g., "biosynthesis of amino acids" and "arginine and proline metabolism"), and secondary metabolite metabolism (e.g., "biosynthesis of secondary metabolites"). For carbohydrate metabolism, the accumulation of oligosaccharides (e.g., sucrose) was decreased, whereas that of monosaccharides (e.g., mannose and myo-inositol) was increased by drought. With regard to amino acid metabolism, under drought stress, the accumulation of amino acids such as phenylalanine and tryptophan decreased, whereas that of glutamate and proline increased. Further, for secondary metabolite metabolism, B. napus subjected to soil drying showed a reduction in phenolics and flavonoids, such as hyperoside and trans-3-coumaric acid. However, the accumulation of carbohydrates was almost unchanged in fullerol-treated B. napus subjected to drought. When exposed to water shortage, the accumulation of amino acids, such as proline, was decreased upon fullerol treatment. However, that of phenolics and flavonoids, such as luteolin and trans-3-coumaric acid, was enhanced. Our findings suggest that fullerol can alleviate the inhibitory effects of drought on phenolics and flavonoids to enhance drought tolerance in B. napus.
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Affiliation(s)
- Jun-Lan Xiong
- Oil Crops Research Institute, Chinese Academy of Agricultural Science, Wuhan 430062, China
- School of Life Science, Lanzhou University, Lanzhou 730000, China
- Correspondence:
| | - Ni Ma
- Oil Crops Research Institute, Chinese Academy of Agricultural Science, Wuhan 430062, China
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Wang P, Guo L, Morgan J, Dudareva N, Chapple C. Transcript and metabolite network perturbations in lignin biosynthetic mutants of Arabidopsis. PLANT PHYSIOLOGY 2022; 190:2828-2846. [PMID: 35880844 PMCID: PMC9706439 DOI: 10.1093/plphys/kiac344] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 06/24/2022] [Indexed: 06/01/2023]
Abstract
Lignin, one of the most abundant polymers in plants, is derived from the phenylpropanoid pathway, which also gives rise to an array of metabolites that are essential for plant fitness. Genetic engineering of lignification can cause drastic changes in transcription and metabolite accumulation with or without an accompanying development phenotype. To understand the impact of lignin perturbation, we analyzed transcriptome and metabolite data from the rapidly lignifying stem tissue in 13 selected phenylpropanoid mutants and wild-type Arabidopsis (Arabidopsis thaliana). Our dataset contains 20,974 expressed genes, of which over 26% had altered transcript levels in at least one mutant, and 18 targeted metabolites, all of which displayed altered accumulation in at least one mutant. We found that lignin biosynthesis and phenylalanine supply via the shikimate pathway are tightly co-regulated at the transcriptional level. The hierarchical clustering analysis of differentially expressed genes (DEGs) grouped the 13 mutants into 5 subgroups with similar profiles of mis-regulated genes. Functional analysis of the DEGs in these mutants and correlation between gene expression and metabolite accumulation revealed system-wide effects on transcripts involved in multiple biological processes.
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Affiliation(s)
- Peng Wang
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Longyun Guo
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - John Morgan
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, Indiana 47907, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907, USA
| | - Natalia Dudareva
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907, USA
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De Meester B, Vanholme R, Mota T, Boerjan W. Lignin engineering in forest trees: From gene discovery to field trials. PLANT COMMUNICATIONS 2022; 3:100465. [PMID: 36307984 PMCID: PMC9700206 DOI: 10.1016/j.xplc.2022.100465] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/10/2022] [Accepted: 10/21/2022] [Indexed: 06/16/2023]
Abstract
Wood is an abundant and renewable feedstock for the production of pulp, fuels, and biobased materials. However, wood is recalcitrant toward deconstruction into cellulose and simple sugars, mainly because of the presence of lignin, an aromatic polymer that shields cell-wall polysaccharides. Hence, numerous research efforts have focused on engineering lignin amount and composition to improve wood processability. Here, we focus on results that have been obtained by engineering the lignin biosynthesis and branching pathways in forest trees to reduce cell-wall recalcitrance, including the introduction of exotic lignin monomers. In addition, we draw general conclusions from over 20 years of field trial research with trees engineered to produce less or altered lignin. We discuss possible causes and solutions for the yield penalty that is often associated with lignin engineering in trees. Finally, we discuss how conventional and new breeding strategies can be combined to develop elite clones with desired lignin properties. We conclude this review with priorities for the development of commercially relevant lignin-engineered trees.
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Affiliation(s)
- Barbara De Meester
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Ruben Vanholme
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Thatiane Mota
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Wout Boerjan
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium.
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7
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Miller TA, Hudson DA, Johnson RD, Singh JS, Mace WJ, Forester NT, Maclean PH, Voisey CR, Johnson LJ. Dissection of the epoxyjanthitrem pathway in Epichloë sp. LpTG-3 strain AR37 by CRISPR gene editing. FRONTIERS IN FUNGAL BIOLOGY 2022; 3:944234. [PMID: 37746172 PMCID: PMC10512260 DOI: 10.3389/ffunb.2022.944234] [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: 05/14/2022] [Accepted: 07/18/2022] [Indexed: 09/26/2023]
Abstract
Epichloë festucae var. lolii and Epichloë sp. LpTG-3 are filamentous fungal endophytes of perennial ryegrass (Lolium perenne) that have a substantial impact on New Zealand's agricultural economy by conferring biotic advantages to the host grass. Overall, Epichloë endophytes contribute NZ$200 million to the economy annually, with strain AR37 estimated to contribute NZ$3.6 billion to the New Zealand economy over a 20-year period. This strain produces secondary metabolites, including epoxyjanthitrems, which are a class of indole diterpenes, associated with the observed effects of AR37 on livestock and insect pests. Until very recently, AR37 was intractable to genetic modification but this has changed with the application of CRISPR-Cas9 based gene editing techniques. In this paper, gene inactivation by CRISPR-Cas9 was used to deconvolute the genetic basis for epoxyjanthitrem biosynthesis, including creating an AR37 strain that has been edited to remove the biosynthesis of all indole diterpenes. We show that gene editing of Epichloë can be achieved without off-target events or introduction of foreign DNA (footprint-less) through an AMA1-based plasmid that simultaneously expresses the CRISPR-Cas9 system and selectable marker. Genetic modification events in these transformants were investigated through genome sequencing and in planta chemistry.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Linda J. Johnson
- Grasslands Research Centre, AgResearch, Palmerston North, New Zealand
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8
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Computational Metabolomics Tools Reveal Metabolic Reconfigurations Underlying the Effects of Biostimulant Seaweed Extracts on Maize Plants under Drought Stress Conditions. Metabolites 2022; 12:metabo12060487. [PMID: 35736420 PMCID: PMC9231236 DOI: 10.3390/metabo12060487] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 05/12/2022] [Accepted: 05/23/2022] [Indexed: 12/19/2022] Open
Abstract
Drought is one of the major abiotic stresses causing severe damage and losses in economically important crops worldwide. Drought decreases the plant water status, leading to a disruptive metabolic reprogramming that negatively affects plant growth and yield. Seaweed extract-based biostimulants show potential as a sustainable strategy for improved crop health and stress resilience. However, cellular, biochemical, and molecular mechanisms governing the agronomically observed benefits of the seaweed extracts on plants are still poorly understood. In this study, a liquid chromatography–mass spectrometry-based untargeted metabolomics approach combined with computational metabolomics strategies was applied to unravel the molecular ‘stamps’ that define the effects of seaweed extracts on greenhouse-grown maize (Zea mays) under drought conditions. We applied mass spectral networking, substructure discovery, chemometrics, and metabolic pathway analyses to mine and interpret the generated mass spectral data. The results showed that the application of seaweed extracts induced alterations in the different pathways of primary and secondary metabolism, such as phenylpropanoid, flavonoid biosynthesis, fatty acid metabolism, and amino acids pathways. These metabolic changes involved increasing levels of phenylalanine, tryptophan, coumaroylquinic acid, and linolenic acid metabolites. These metabolic alterations are known to define some of the various biochemical and physiological events that lead to enhanced drought resistance traits. The latter include root growth, alleviation of oxidative stress, improved water, and nutrient uptake. Moreover, this study demonstrates the use of molecular networking in annotating maize metabolome. Furthermore, the results reveal that seaweed extract-based biostimulants induced a remodeling of maize metabolism, subsequently readjusting the plant towards stress alleviation, for example, by increasing the plant height and diameter through foliar application. Such insights add to ongoing efforts in elucidating the modes of action of biostimulants, such as seaweed extracts. Altogether, our study contributes to the fundamental scientific knowledge that is necessary for the development of a biostimulants industry aiming for a sustainable food security.
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El-Azaz J, Cánovas FM, Barcelona B, Ávila C, de la Torre F. Deregulation of phenylalanine biosynthesis evolved with the emergence of vascular plants. PLANT PHYSIOLOGY 2022; 188:134-150. [PMID: 34633048 PMCID: PMC8774845 DOI: 10.1093/plphys/kiab454] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 08/24/2021] [Indexed: 06/01/2023]
Abstract
Phenylalanine (Phe) is the precursor of essential secondary products in plants. Here we show that a key, rate-limiting step in Phe biosynthesis, which is catalyzed by arogenate dehydratase, experienced feedback de-regulation during evolution. Enzymes from microorganisms and type-I ADTs from plants are strongly feedback-inhibited by Phe, while type-II isoforms remain active at high levels of Phe. We have found that type-II ADTs are widespread across seed plants and their overproduction resulted in a dramatic accumulation of Phe in planta, reaching levels up to 40 times higher than those observed following the expression of type-I enzymes. Punctual changes in the allosteric binding site of Phe and adjacent region are responsible for the observed relaxed regulation. The phylogeny of plant ADTs evidences that the emergence of type-II isoforms with relaxed regulation occurred at some point in the transition between nonvascular plants and tracheophytes, enabling the massive production of Phe-derived compounds, primarily lignin, a hallmark of vascular plants.
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Affiliation(s)
- Jorge El-Azaz
- Departamento de Biología Molecular y Bioquímica, Universidad de Málaga. Edificio I+D, Málaga 29071, Spain
| | - Francisco M Cánovas
- Departamento de Biología Molecular y Bioquímica, Universidad de Málaga. Edificio I+D, Málaga 29071, Spain
| | - Belén Barcelona
- Departamento de Genómica y Proteómica, Instituto de Biomedicina de Valencia, CSIC, Unidad de Enzimopatología Estructural, Valencia 46010, Spain
| | - Concepción Ávila
- Departamento de Biología Molecular y Bioquímica, Universidad de Málaga. Edificio I+D, Málaga 29071, Spain
| | - Fernando de la Torre
- Departamento de Biología Molecular y Bioquímica, Universidad de Málaga. Edificio I+D, Málaga 29071, Spain
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10
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Wang X, Chao N, Zhang A, Kang J, Jiang X, Gai Y. Systematic Analysis and Biochemical Characterization of the Caffeoyl Shikimate Esterase Gene Family in Poplar. Int J Mol Sci 2021; 22:ijms222413366. [PMID: 34948162 PMCID: PMC8704367 DOI: 10.3390/ijms222413366] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/09/2021] [Accepted: 12/10/2021] [Indexed: 02/07/2023] Open
Abstract
Caffeoyl shikimate esterase (CSE) hydrolyzes caffeoyl shikimate into caffeate and shikimate in the phenylpropanoid pathway. In this study, we performed a systematic analysis of the CSE gene family and investigated the possible roles of CSE and CSE-like genes in Populus. We conducted a genome-wide analysis of the CSE gene family, including functional and phylogenetic analyses of CSE and CSE-like genes, using the poplar (Populus trichocarpa) genome. Eighteen CSE and CSE-like genes were identified in the Populus genome, and five phylogenetic groups were identified from phylogenetic analysis. CSEs in Group Ia, which were proposed as bona fide CSEs, have probably been lost in most monocots except Oryza sativa. Primary functional classification showed that PoptrCSE1 and PoptrCSE2 had putative function in lignin biosynthesis. In addition, PoptrCSE2, along with PoptrCSE12, might also respond to stress with a function in cell wall biosynthesis. Enzymatic assay of PoptoCSE1 (Populus tomentosa), -2 and -12 showed that PoptoCSE1 and -2 maintained CSE activity. PoptoCSE1 and 2 had similar biochemical properties, tissue expression patterns and subcellular localization. Most of the PoptrCSE-like genes are homologs of AtMAGL (monoacylglycerol lipase) genes in Arabidopsis and may function as MAG lipase in poplar. Our study provides a systematic understanding of this novel gene family and suggests the function of CSE in monolignol biosynthesis in Populus.
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Affiliation(s)
- Xuechun Wang
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; (X.W.); (N.C.); (A.Z.); (J.K.); (X.J.)
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory, National Forestry and Grassland Administration, Beijing 100083, China
- National Engineering Laboratory for Tree Breeding, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing 100083, China
| | - Nan Chao
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; (X.W.); (N.C.); (A.Z.); (J.K.); (X.J.)
- Jiangsu Key Laboratory of Sericutural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212018, China
| | - Aijing Zhang
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; (X.W.); (N.C.); (A.Z.); (J.K.); (X.J.)
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory, National Forestry and Grassland Administration, Beijing 100083, China
- National Engineering Laboratory for Tree Breeding, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing 100083, China
| | - Jiaqi Kang
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; (X.W.); (N.C.); (A.Z.); (J.K.); (X.J.)
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory, National Forestry and Grassland Administration, Beijing 100083, China
- National Engineering Laboratory for Tree Breeding, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing 100083, China
| | - Xiangning Jiang
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; (X.W.); (N.C.); (A.Z.); (J.K.); (X.J.)
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory, National Forestry and Grassland Administration, Beijing 100083, China
- National Engineering Laboratory for Tree Breeding, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing 100083, China
| | - Ying Gai
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; (X.W.); (N.C.); (A.Z.); (J.K.); (X.J.)
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory, National Forestry and Grassland Administration, Beijing 100083, China
- National Engineering Laboratory for Tree Breeding, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing 100083, China
- Correspondence: ; Tel.: +86-10-6233-8063
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12
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Foster CJ, Wang L, Dinh HV, Suthers PF, Maranas CD. Building kinetic models for metabolic engineering. Curr Opin Biotechnol 2020; 67:35-41. [PMID: 33360621 DOI: 10.1016/j.copbio.2020.11.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 11/09/2020] [Accepted: 11/22/2020] [Indexed: 12/16/2022]
Abstract
Kinetic formalisms of metabolism link metabolic fluxes to enzyme levels, metabolite concentrations and their allosteric regulatory interactions. Though they require the identification of physiologically relevant values for numerous parameters, kinetic formalisms uniquely establish a mechanistic link across heterogeneous omics datasets and provide an overarching vantage point to effectively inform metabolic engineering strategies. Advances in computational power, gene annotation coverage, and formalism standardization have led to significant progress over the past few years. However, careful interpretation of model predictions, limited metabolic flux datasets, and assessment of parameter sensitivity remain as challenges. In this review we highlight fundamental considerations which influence model quality and prediction, advances in methodologies, and success stories of deploying kinetic models to guide metabolic engineering.
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Affiliation(s)
- Charles J Foster
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA
| | - Lin Wang
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA
| | - Hoang V Dinh
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA; DOE Center for Advanced Bioenergy and Bioproducts Innovation, The Pennsylvania State University, Univesity Park, PA, USA
| | - Patrick F Suthers
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA; DOE Center for Advanced Bioenergy and Bioproducts Innovation, The Pennsylvania State University, Univesity Park, PA, USA
| | - Costas D Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA.
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Clark TJ, Guo L, Morgan J, Schwender J. Modeling Plant Metabolism: From Network Reconstruction to Mechanistic Models. ANNUAL REVIEW OF PLANT BIOLOGY 2020; 71:303-326. [PMID: 32017600 DOI: 10.1146/annurev-arplant-050718-100221] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Mathematical modeling of plant metabolism enables the plant science community to understand the organization of plant metabolism, obtain quantitative insights into metabolic functions, and derive engineering strategies for manipulation of metabolism. Among the various modeling approaches, metabolic pathway analysis can dissect the basic functional modes of subsections of core metabolism, such as photorespiration, and reveal how classical definitions of metabolic pathways have overlapping functionality. In the many studies using constraint-based modeling in plants, numerous computational tools are currently available to analyze large-scale and genome-scale metabolic networks. For 13C-metabolic flux analysis, principles of isotopic steady state have been used to study heterotrophic plant tissues, while nonstationary isotope labeling approaches are amenable to the study of photoautotrophic and secondary metabolism. Enzyme kinetic models explore pathways in mechanistic detail, and we discuss different approaches to determine or estimate kinetic parameters. In this review, we describe recent advances and challenges in modeling plant metabolism.
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Affiliation(s)
- Teresa J Clark
- Biology Department, Brookhaven National Laboratory, Upton, New York 11973, USA; ,
| | - Longyun Guo
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, Indiana 47907, USA; ,
| | - John Morgan
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, Indiana 47907, USA; ,
| | - Jorg Schwender
- Biology Department, Brookhaven National Laboratory, Upton, New York 11973, USA; ,
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14
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Shih ML, Morgan JA. Metabolic flux analysis of secondary metabolism in plants. Metab Eng Commun 2020; 10:e00123. [PMID: 32099803 PMCID: PMC7031320 DOI: 10.1016/j.mec.2020.e00123] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 01/13/2020] [Accepted: 01/27/2020] [Indexed: 11/30/2022] Open
Abstract
Numerous secondary metabolites from plants are important for their medicinal, nutraceutical or sensory properties. Recently, significant progress has been made in the identification of the genes and enzymes of plant secondary metabolic pathways. Hence, there is interest in using synthetic biology to enhance the production of targeted valuable metabolites in plants. In this article, we examine the contribution that metabolic flux analysis will have on informing the rational selection of metabolic engineering targets as well as analysis of carbon and energy efficiency. Compared to microbes, plants have more complex tissue, cellular and subcellular organization, making precise metabolite concentration measurements more challenging. We review different techniques involved in quantifying flux and provide examples illustrating the application of the techniques. For linear and branched pathways that lead to end products with low turnover, flux quantification is straightforward and doesn’t require isotopic labeling. However, for metabolites synthesized via parallel pathways, there is a requirement for isotopic labeling experiments. If the fed isotopically labeled carbons don’t scramble, one needs to apply transient label balancing methods. In the transient case, it is also necessary to measure metabolite concentrations. While flux analysis is not able to directly identify mechanisms of regulation, it is a powerful tool to examine flux distribution at key metabolic nodes in intermediary metabolism, detect flux to wasteful side pathways, and show how parallel pathways handle flux in wild-type and engineered plants under a variety of physiological conditions. Plant secondary metabolites have high economic value to human health and pleasure. Plant secondary metabolites are synthesized by pathways in subcellular compartments. Metabolic flux analysis can guide the selection of metabolic engineering targets.
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Key Words
- 13C MFA, Steady state isotopically labeled metabolic flux analysis
- BA, Benzoic acid
- DMAPP, Dimethylallyl diphosphate
- GC, Gas chromatography
- INST-MFA, Isotopically non-steady state metabolic flux analysis
- IP, Isopentenyl phosphate
- IPP, Isopentenyl diphosphate
- LC, Liquid chromatography
- MEP, Methylerythritol 4-phosphate
- MFA, Metabolic flux analysis
- MS, Mass spectrometry
- MVA, Mevalonic acid
- MVAP, Mevalonate 5-phosphate
- MVAPP, Mevalonate 5-diphosphate
- Metabolic channeling
- Metabolic flux analysis
- NMR, Nuclear magnetic resonance
- Phe, Phenylalanine
- Plant secondary metabolites
- Stable isotopic labeling
- Subcellular compartmentation
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Affiliation(s)
- Meng-Ling Shih
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN, 47907, USA
| | - John A Morgan
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN, 47907, USA
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Vanholme R, De Meester B, Ralph J, Boerjan W. Lignin biosynthesis and its integration into metabolism. Curr Opin Biotechnol 2019; 56:230-239. [PMID: 30913460 DOI: 10.1016/j.copbio.2019.02.018] [Citation(s) in RCA: 322] [Impact Index Per Article: 64.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 02/05/2019] [Accepted: 02/22/2019] [Indexed: 11/25/2022]
Abstract
Lignin is a principal structural component of cell walls in higher terrestrial plants. It reinforces the cell walls, facilitates water transport, and acts as a physical barrier to pathogens. Lignin is typically described as being composed of p-hydroxyphenyl (H), guaiacyl (G), and syringyl (S) units that derive from the polymerization of the hydroxycinnamyl alcohols, p-coumaryl, coniferyl, and sinapyl alcohol, respectively. However, lignin also derives from various other aromatic monomers. Here, we review the biosynthetic pathway to the lignin monomers, and how flux through the pathway is regulated. Upon perturbation of the phenylpropanoid pathway, pathway intermediates may successfully incorporate into the lignin polymer, thereby affecting its physicochemical properties, or may remain soluble as such or as derivatized molecules that might interfere with physiological processes.
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Affiliation(s)
- Ruben Vanholme
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Barbara De Meester
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - John Ralph
- Department of Energy, Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, WI 53726, USA; Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Wout Boerjan
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium.
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