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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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Kumbale CM, Zhang Q, Voit EO. Hepatic cholesterol biosynthesis and dioxin-induced dysregulation: A multiscale computational approach. Food Chem Toxicol 2023; 181:114086. [PMID: 37820785 PMCID: PMC10841405 DOI: 10.1016/j.fct.2023.114086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 09/18/2023] [Accepted: 10/03/2023] [Indexed: 10/13/2023]
Abstract
Humans are constantly exposed to lipophilic persistent organic pollutants (POPs) that accumulate in fatty foods. Among the numerous POPs, dioxins, in particular 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), can impact several organ systems. While the hazard is clearly recognized, it is still difficult to develop a comprehensive understanding of the overall health impacts of dioxins. As chemical toxicity testing is steadily adopting new approach methodologies (NAMs), it becomes imperative to develop computational models that can bridge the data gaps between in vitro testing and in vivo outcomes. As an effort to address this challenge, we propose a multiscale computational approach using a "template-and-anchor" (T&A) structure. A template is a high-level umbrella model that permits the integration of information from various, detailed anchor models. In the present study, we use this T&A approach to describe the effect of TCDD on cholesterol dynamics. Specifically, we represent hepatic cholesterol biosynthesis as an anchor model that is perturbed by TCDD, leading to steatosis, along with alterations of plasma cholesterol. In the future, incorporating pertinent information from all anchor models into the template model will allow the characterization of the global effects of dioxin, which can subsequently be translated into overall - and ultimately personalized - human health risk assessment.
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Affiliation(s)
- Carla M Kumbale
- Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA.
| | - Qiang Zhang
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA.
| | - Eberhard O Voit
- Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA.
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3
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Zhuo C, Wang X, Docampo-Palacios M, Sanders BC, Engle NL, Tschaplinski TJ, Hendry JI, Maranas CD, Chen F, Dixon RA. Developmental changes in lignin composition are driven by both monolignol supply and laccase specificity. SCIENCE ADVANCES 2022; 8:eabm8145. [PMID: 35263134 PMCID: PMC8906750 DOI: 10.1126/sciadv.abm8145] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 01/17/2022] [Indexed: 05/25/2023]
Abstract
The factors controlling lignin composition remain unclear. Catechyl (C)-lignin is a homopolymer of caffeyl alcohol with unique properties as a biomaterial and precursor of industrial chemicals. The lignin synthesized in the seed coat of Cleome hassleriana switches from guaiacyl (G)- to C-lignin at around 12 to 14 days after pollination (DAP), associated with a rerouting of the monolignol pathway. Lack of synthesis of caffeyl alcohol limits C-lignin formation before around 12 DAP, but coniferyl alcohol is still synthesized and highly accumulated after 14 DAP. We propose a model in which, during C-lignin biosynthesis, caffeyl alcohol noncompetitively inhibits oxidation of coniferyl alcohol by cell wall laccases, a process that might limit movement of coniferyl alcohol to the apoplast. Developmental changes in both substrate availability and laccase specificity together account for the metabolic fates of G- and C-monolignols in the Cleome seed coat.
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Affiliation(s)
- Chunliu Zhuo
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, 1155 Union Circle #311428, Denton, TX 76203, USA
- Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Xin Wang
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, 1155 Union Circle #311428, Denton, TX 76203, USA
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Maite Docampo-Palacios
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, 1155 Union Circle #311428, Denton, TX 76203, USA
| | - Brian C. Sanders
- Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Nancy L. Engle
- Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Timothy J. Tschaplinski
- Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - John I. Hendry
- Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Costas D. Maranas
- Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Fang Chen
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, 1155 Union Circle #311428, Denton, TX 76203, USA
- Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Richard A. Dixon
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, 1155 Union Circle #311428, Denton, TX 76203, USA
- Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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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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Voit EO. Metabolic Systems. SYSTEMS MEDICINE 2021. [DOI: 10.1016/b978-0-12-801238-3.11619-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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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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Matthews ML, Wang JP, Sederoff R, Chiang VL, Williams CM. Modeling cross-regulatory influences on monolignol transcripts and proteins under single and combinatorial gene knockdowns in Populus trichocarpa. PLoS Comput Biol 2020; 16:e1007197. [PMID: 32275650 PMCID: PMC7147730 DOI: 10.1371/journal.pcbi.1007197] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 02/27/2020] [Indexed: 11/18/2022] Open
Abstract
Accurate manipulation of metabolites in monolignol biosynthesis is a key step for controlling lignin content, structure, and other wood properties important to the bioenergy and biomaterial industries. A crucial component of this strategy is predicting how single and combinatorial knockdowns of monolignol specific gene transcripts influence the abundance of monolignol proteins, which are the driving mechanisms of monolignol biosynthesis. Computational models have been developed to estimate protein abundances from transcript perturbations of monolignol specific genes. The accuracy of these models, however, is hindered by their inability to capture indirect regulatory influences on other pathway genes. Here, we examine the manifestation of these indirect influences on transgenic transcript and protein abundances, identifying putative indirect regulatory influences that occur when one or more specific monolignol pathway genes are perturbed. We created a computational model using sparse maximum likelihood to estimate the resulting monolignol transcript and protein abundances in transgenic Populus trichocarpa based on targeted knockdowns of specific monolignol genes. Using in-silico simulations of this model and root mean square error, we showed that our model more accurately estimated transcript and protein abundances, in comparison to previous models, when individual and families of monolignol genes were perturbed. We leveraged insight from the inferred network structure obtained from our model to identify potential genes, including PtrHCT, PtrCAD, and Ptr4CL, involved in post-transcriptional and/or post-translational regulation. Our model provides a useful computational tool for exploring the cascaded impact of single and combinatorial modifications of monolignol specific genes on lignin and other wood properties.
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Affiliation(s)
- Megan L. Matthews
- Department of Electrical and Computer Engineering, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Jack P. Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- Department of Forestry and Environmental Resources, Forest Biotechnology Group, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Ronald Sederoff
- Department of Forestry and Environmental Resources, Forest Biotechnology Group, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Vincent L. Chiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- Department of Forestry and Environmental Resources, Forest Biotechnology Group, North Carolina State University, Raleigh, North Carolina, United States of America
- Department of Forest Biomaterials, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Cranos M. Williams
- Department of Electrical and Computer Engineering, North Carolina State University, Raleigh, North Carolina, United States of America
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Dixon RA, Barros J. Lignin biosynthesis: old roads revisited and new roads explored. Open Biol 2019; 9:190215. [PMID: 31795915 PMCID: PMC6936255 DOI: 10.1098/rsob.190215] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Accepted: 10/30/2019] [Indexed: 12/31/2022] Open
Abstract
Lignin is a major component of secondarily thickened plant cell walls and is considered to be the second most abundant biopolymer on the planet. At one point believed to be the product of a highly controlled polymerization procedure involving just three potential monomeric components (monolignols), it is becoming increasingly clear that the composition of lignin is quite flexible. Furthermore, the biosynthetic pathways to the major monolignols also appear to exhibit flexibility, particularly as regards the early reactions leading to the formation of caffeic acid from coumaric acid. The operation of parallel pathways to caffeic acid occurring at the level of shikimate esters or free acids may help provide robustness to the pathway under different physiological conditions. Several features of the pathway also appear to link monolignol biosynthesis to both generation and detoxification of hydrogen peroxide, one of the oxidants responsible for creating monolignol radicals for polymerization in the apoplast. Monolignol transport to the apoplast is not well understood. It may involve passive diffusion, although this may be targeted to sites of lignin initiation/polymerization by ordered complexes of both biosynthetic enzymes on the cytosolic side of the plasma membrane and structural anchoring of proteins for monolignol oxidation and polymerization on the apoplastic side. We present several hypothetical models to illustrate these ideas and stimulate further research. These are based primarily on studies in model systems, which may or may not reflect the major lignification process in forest trees.
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Affiliation(s)
- Richard A. Dixon
- Hagler Institute for Advanced Studies and Department of Biological Sciences, Texas A&M University, College Station, TX, USA
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, 1155 Union Circle #311428, Denton, TX 76203-5017, USA
| | - Jaime Barros
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, 1155 Union Circle #311428, Denton, TX 76203-5017, USA
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Low Lignin Mutants and Reduction of Lignin Content in Grasses for Increased Utilisation of Lignocellulose. AGRONOMY-BASEL 2019. [DOI: 10.3390/agronomy9050256] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Biomass rich in lignocellulose from grasses is a major source for biofuel production and animal feed. However, the presence of lignin in cell walls limits its efficient utilisation such as in its bioconversion to biofuel. Reduction of the lignin content or alteration of its structure in crop plants have been pursued, either by regulating genes encoding enzymes in the lignin biosynthetic pathway using biotechnological techniques or by breeding naturally-occurring low lignin mutant lines. The aim of this review is to provide a summary of these studies, focusing on lignin (monolignol) biosynthesis and composition in grasses and, where possible, the impact on recalcitrance to bioconversion. An overview of transgenic crops of the grass family with regulated gene expression in lignin biosynthesis is presented, including the effect on lignin content and changes in the ratio of p-hydroxyphenyl (H), guaiacyl (G) and syringyl (S) units. Furthermore, a survey is provided of low-lignin mutants in grasses, including cereals in particular, summarising their origin and phenotypic traits together with genetics and the molecular function of the various genes identified.
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Wang JP, Matthews ML, Naik PP, Williams CM, Ducoste JJ, Sederoff RR, Chiang VL. Flux modeling for monolignol biosynthesis. Curr Opin Biotechnol 2019; 56:187-192. [DOI: 10.1016/j.copbio.2018.12.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 10/30/2018] [Accepted: 12/02/2018] [Indexed: 10/27/2022]
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The regulatory role of shikimate in plant phenylalanine metabolism. J Theor Biol 2018; 462:158-170. [PMID: 30412698 DOI: 10.1016/j.jtbi.2018.11.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Revised: 10/31/2018] [Accepted: 11/06/2018] [Indexed: 01/19/2023]
Abstract
In higher plants, the amino acid phenylalanine is a substrate of both primary and secondary metabolic pathways. The primary pathway that consumes phenylalanine, protein biosynthesis, is essential for the viability of all cells. Meanwhile, the secondary pathways are not necessary for the survival of individual cells, but benefit of the plant as a whole. Here we focus on the monolignol pathway, a secondary metabolic pathway in the cytosol that rapidly consumes phenylalanine to produce the precursors of lignin during wood formation. In planta monolignol biosynthesis involves a series of seemingly redundant steps wherein shikimate, a precursor of phenylalanine synthesized in the plastid, is transiently ligated to the main substrate of the pathway. However, shikimate is not catalytically involved in the reactions of the monolignol pathway, and is only needed for pathway enzymes to recognize their main substrates. After some steps the shikimate moiety is removed unaltered, and the main substrate continues along the pathway. It has been suggested that this portion of the monolignol pathway fulfills a regulatory role in the following way. Low phenylalanine concentrations (viz. availability) correlate with low shikimate concentrations. When shikimate concentratios are low, flux into the monolignol pathway will be limited by means of the steps requiring shikimate. Thus, when the concentration of phenylalanine is low it will be reserved for protein biosynthesis. Here we employ a theoretical approach to test this hypothesis. Simplified versions of plant phenylalanine metabolism are modelled as systems of ordinary differential equations. Our analysis shows that the seemingly redundant steps can be sufficient for the prioritization of protein biosynthesis over the monolignol pathway when the availability of phenylalanine is low, depending on system parameters. Thus, the phenylalanine precursor shikimate may signal low phenylalanine availability to secondary pathways. Because our models have been abstracted from plant phenylalanine metabolism, this mechanism of metabolic signalling, which we call the Precursor Shutoff Valve (PSV), may also be present in other biochemical networks comprised of two pathways that share a common substrate.
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