1
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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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Oliveira DM, Cesarino I. Genome editing of wood for sustainable pulping. TRENDS IN PLANT SCIENCE 2024; 29:111-113. [PMID: 37838517 DOI: 10.1016/j.tplants.2023.10.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 09/29/2023] [Accepted: 10/03/2023] [Indexed: 10/16/2023]
Abstract
Wood is an abundant and renewable feedstock for pulping and biorefining, but the aromatic polymer lignin greatly limits its efficient use. Sulis et al. recently reported a multiplex CRISPR editing strategy targeting multiple lignin biosynthetic genes to achieve combined lignin modifications, improve wood properties, and make pulping more sustainable.
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Affiliation(s)
- Dyoni M Oliveira
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Vlaams Instituut voor Biotechnologie (VIB) Center for Plant Systems Biology, 9052 Ghent, Belgium.
| | - Igor Cesarino
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão 277, 05508-090 São Paulo, Brazil; Synthetic and Systems Biology Center, InovaUSP, Avenida Professor Lucio Martins Rodrigues 370, 05508-020 São Paulo, Brazil.
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3
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Wang Y, Shang B, Génard M, Hilbert-Masson G, Delrot S, Gomès E, Poni S, Keller M, Renaud C, Kong J, Chen J, Liang Z, Dai Z. Model-assisted analysis for tuning anthocyanin composition in grape berries. ANNALS OF BOTANY 2023; 132:1033-1050. [PMID: 37850481 PMCID: PMC10808033 DOI: 10.1093/aob/mcad165] [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: 09/06/2023] [Accepted: 10/17/2023] [Indexed: 10/19/2023]
Abstract
Anthocyanin composition is responsible for the red colour of grape berries and wines, and contributes to their organoleptic quality. However, anthocyanin biosynthesis is under genetic, developmental and environmental regulation, making its targeted fine-tuning challenging. We constructed a mechanistic model to simulate the dynamics of anthocyanin composition throughout grape ripening in Vitis vinifera, employing a consensus anthocyanin biosynthesis pathway. The model was calibrated and validated using six datasets from eight cultivars and 37 growth conditions. Tuning the transformation and degradation parameters allowed us to accurately simulate the accumulation process of each individual anthocyanin under different environmental conditions. The model parameters were robust across environments for each genotype. The coefficients of determination (R2) for the simulated versus observed values for the six datasets ranged from 0.92 to 0.99, while the relative root mean square errors (RRMSEs) were between 16.8 and 42.1 %. The leave-one-out cross-validation for three datasets showed R2 values of 0.99, 0.96 and 0.91, and RRMSE values of 28.8, 32.9 and 26.4 %, respectively, suggesting a high prediction quality of the model. Model analysis showed that the anthocyanin profiles of diverse genotypes are relatively stable in response to parameter perturbations. Virtual experiments further suggested that targeted anthocyanin profiles may be reached by manipulating a minimum of three parameters, in a genotype-dependent manner. This model presents a promising methodology for characterizing the temporal progression of anthocyanin composition, while also offering a logical foundation for bioengineering endeavours focused on precisely adjusting the anthocyanin composition of grapes.
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Affiliation(s)
- Yongjian Wang
- State Key Laboratory of Plant Diversity and Specialty Crops and Beijing Key Laboratory of Grape Science and Enology, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Boxing Shang
- State Key Laboratory of Plant Diversity and Specialty Crops and Beijing Key Laboratory of Grape Science and Enology, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Michel Génard
- INRAE, UR1115, Unité Plantes et Systèmes de Culture Horticoles, Avignon, France
| | | | - Serge Delrot
- EGFV, University of Bordeaux, Bordeaux-Sciences Agro, INRAE, ISVV, Villenave d’Ornon, France
| | - Eric Gomès
- EGFV, University of Bordeaux, Bordeaux-Sciences Agro, INRAE, ISVV, Villenave d’Ornon, France
| | - Stefano Poni
- Department of Sustainable Crop Production, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy
| | - Markus Keller
- Department of Viticulture and Enology, Irrigated Agriculture Research and Extension Center, Washington State University, Prosser, WA, USA
| | - Christel Renaud
- EGFV, University of Bordeaux, Bordeaux-Sciences Agro, INRAE, ISVV, Villenave d’Ornon, France
| | - Junhua Kong
- State Key Laboratory of Plant Diversity and Specialty Crops and Beijing Key Laboratory of Grape Science and Enology, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Jinliang Chen
- Center for Agricultural Water Research in China, China Agricultural University, Beijing, 100083, China
| | - Zhenchang Liang
- State Key Laboratory of Plant Diversity and Specialty Crops and Beijing Key Laboratory of Grape Science and Enology, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhanwu Dai
- State Key Laboratory of Plant Diversity and Specialty Crops and Beijing Key Laboratory of Grape Science and Enology, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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4
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Wang Q, Hu Z, Li Z, Liu T, Bian G. Exploring the Application and Prospects of Synthetic Biology in Engineered Living Materials. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023:e2305828. [PMID: 37677048 DOI: 10.1002/adma.202305828] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 09/05/2023] [Indexed: 09/09/2023]
Abstract
At the intersection of synthetic biology and materials science, engineered living materials (ELMs) exhibit unprecedented potential. Possessing unique "living" attributes, ELMs represent a significant paradigm shift in material design, showcasing self-organization, self-repair, adaptability, and evolvability, surpassing conventional synthetic materials. This review focuses on reviewing the applications of ELMs derived from bacteria, fungi, and plants in environmental remediation, eco-friendly architecture, and sustainable energy. The review provides a comprehensive overview of the latest research progress and emerging design strategies for ELMs in various application fields from the perspectives of synthetic biology and materials science. In addition, the review provides valuable references for the design of novel ELMs, extending the potential applications of future ELMs. The investigation into the synergistic application possibilities amongst different species of ELMs offers beneficial reference information for researchers and practitioners in this field. Finally, future trends and development challenges of synthetic biology for ELMs in the coming years are discussed in detail.
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Affiliation(s)
- Qiwen Wang
- Department of Urology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
- Center of Materials Synthetic Biology, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Zhehui Hu
- Center of Materials Synthetic Biology, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan, 430071, China
| | - Zhixuan Li
- Center of Materials Synthetic Biology, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Tiangang Liu
- Department of Urology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Guangkai Bian
- Center of Materials Synthetic Biology, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
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5
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Sulis D, Jiang X, Yang C, Matthews ML, Marques B, Miller Z, Lan K, Cofre-Vega C, Liu B, Sun R, Sederoff H, Bing R, Sun X, Williams CM, Jameel H, Phillips R, Chang HM, Peszlen I, Huang YY, Li W, Kelly RM, Sederoff RR, Chiang VL, Barrangou R, Wang JP. Multiplex CRISPR editing of wood for sustainable fiber production. Science 2023; 381:216-221. [PMID: 37440632 PMCID: PMC10542590 DOI: 10.1126/science.add4514] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 05/16/2023] [Indexed: 07/15/2023]
Abstract
The domestication of forest trees for a more sustainable fiber bioeconomy has long been hindered by the complexity and plasticity of lignin, a biopolymer in wood that is recalcitrant to chemical and enzymatic degradation. Here, we show that multiplex CRISPR editing enables precise woody feedstock design for combinatorial improvement of lignin composition and wood properties. By assessing every possible combination of 69,123 multigenic editing strategies for 21 lignin biosynthesis genes, we deduced seven different genome editing strategies targeting the concurrent alteration of up to six genes and produced 174 edited poplar variants. CRISPR editing increased the wood carbohydrate-to-lignin ratio up to 228% that of wild type, leading to more-efficient fiber pulping. The edited wood alleviates a major fiber-production bottleneck regardless of changes in tree growth rate and could bring unprecedented operational efficiencies, bioeconomic opportunities, and environmental benefits.
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Affiliation(s)
- Daniel Sulis
- TreeCo, Raleigh, NC 27695
- Forest Biotechnology Group, North Carolina State University, Raleigh, NC 27695
| | - Xiao Jiang
- Department of Forest Biomaterials, North Carolina State University, Raleigh, NC 27695
| | - Chenmin Yang
- TreeCo, Raleigh, NC 27695
- Forest Biotechnology Group, North Carolina State University, Raleigh, NC 27695
| | - Megan L. Matthews
- Department of Electrical and Computer Engineering, North Carolina State University, Raleigh, NC 27695
| | - Barbara Marques
- Forest Biotechnology Group, North Carolina State University, Raleigh, NC 27695
| | - Zachary Miller
- Department of Forest Biomaterials, North Carolina State University, Raleigh, NC 27695
| | - Kai Lan
- Department of Forest Biomaterials, North Carolina State University, Raleigh, NC 27695
| | - Carlos Cofre-Vega
- Forest Biotechnology Group, North Carolina State University, Raleigh, NC 27695
| | - Baoguang Liu
- TreeCo, Raleigh, NC 27695
- Forest Biotechnology Group, North Carolina State University, Raleigh, NC 27695
| | - Runkun Sun
- Department of Forest Biomaterials, North Carolina State University, Raleigh, NC 27695
| | - Henry Sederoff
- Forest Biotechnology Group, North Carolina State University, Raleigh, NC 27695
| | - Ryan Bing
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695
| | - Xiaoyan Sun
- Molecular Education, Technology and Research Innovation Center (METRIC), North Carolina State University, Raleigh, NC 27695
| | - Cranos M. Williams
- Department of Electrical and Computer Engineering, North Carolina State University, Raleigh, NC 27695
| | - Hasan Jameel
- Department of Forest Biomaterials, North Carolina State University, Raleigh, NC 27695
| | - Richard Phillips
- Department of Forest Biomaterials, North Carolina State University, Raleigh, NC 27695
| | - Hou-min Chang
- Department of Forest Biomaterials, North Carolina State University, Raleigh, NC 27695
| | - Ilona Peszlen
- Department of Forest Biomaterials, North Carolina State University, Raleigh, NC 27695
| | - Yung-Yun Huang
- Department of Operations Research, North Carolina State University, Raleigh, NC 27695
| | - Wei Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China 10040
| | - Robert M. Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695
| | - Ronald R. Sederoff
- TreeCo, Raleigh, NC 27695
- Forest Biotechnology Group, North Carolina State University, Raleigh, NC 27695
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China 10040
| | - Vincent L. Chiang
- TreeCo, Raleigh, NC 27695
- Forest Biotechnology Group, North Carolina State University, Raleigh, NC 27695
- Department of Forest Biomaterials, North Carolina State University, Raleigh, NC 27695
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China 10040
| | - Rodolphe Barrangou
- TreeCo, Raleigh, NC 27695
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC 27695
| | - Jack P. Wang
- TreeCo, Raleigh, NC 27695
- Forest Biotechnology Group, North Carolina State University, Raleigh, NC 27695
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China 10040
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6
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Hong J, Gunasekara C, He C, Liu S, Huang J, Wei H. Identification of biological pathway and process regulators using sparse partial least squares and triple-gene mutual interaction. Sci Rep 2021; 11:13174. [PMID: 34162988 PMCID: PMC8222328 DOI: 10.1038/s41598-021-92610-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 06/03/2021] [Indexed: 11/09/2022] Open
Abstract
Identification of biological process- and pathway-specific regulators is essential for advancing our understanding of regulation and formation of various phenotypic and complex traits. In this study, we applied two methods, triple-gene mutual interaction (TGMI) and Sparse Partial Least Squares (SPLS), to identify the regulators of multiple metabolic pathways in Arabidopsis thaliana and Populus trichocarpa using high-throughput gene expression data. We analyzed four pathways: (1) lignin biosynthesis pathway in A. thaliana and P. trichocarpa; (2) flavanones, flavonol and anthocyannin biosynthesis in A. thaliana; (3) light reaction pathway and Calvin cycle in A. thaliana. (4) light reaction pathway alone in A. thaliana. The efficiencies of two methods were evaluated by examining the positive known regulators captured, the receiver operating characteristic (ROC) curves and the area under ROC curves (AUROC). Our results showed that TGMI is in general more efficient than SPLS in identifying true pathway regulators and ranks them to the top of candidate regulatory gene lists, but the two methods are to some degree complementary because they could identify some different pathway regulators. This study identified many regulators that potentially regulate the above pathways in plants and are valuable for genetic engineering of these pathways.
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Affiliation(s)
- Junyan Hong
- School of Forestry and Biotechnology, Zhejiang Agricultural and Forestry University, Linan, Zhejiang, 311300, People's Republic of China.,State Key Laboratory of Subtropical Silviculture, Zhejiang Agricultural and Forestry University, Linan, Zhejiang, 311300, People's Republic of China
| | - Chathura Gunasekara
- Department of Pediatrics, Baylor College of Medicine, USDA/ARS Children's Nutrition Research Center, Houston, TX, 77030, USA
| | - Cheng He
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Sanzhen Liu
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Jianqin Huang
- School of Forestry and Biotechnology, Zhejiang Agricultural and Forestry University, Linan, Zhejiang, 311300, People's Republic of China.,State Key Laboratory of Subtropical Silviculture, Zhejiang Agricultural and Forestry University, Linan, Zhejiang, 311300, People's Republic of China
| | - Hairong Wei
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931, USA.
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7
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Bing RG, Sulis DB, Wang JP, Adams MW, Kelly RM. Thermophilic microbial deconstruction and conversion of natural and transgenic lignocellulose. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:272-293. [PMID: 33684253 PMCID: PMC10519370 DOI: 10.1111/1758-2229.12943] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 02/25/2021] [Accepted: 02/28/2021] [Indexed: 06/12/2023]
Abstract
The potential to convert renewable plant biomasses into fuels and chemicals by microbial processes presents an attractive, less environmentally intense alternative to conventional routes based on fossil fuels. This would best be done with microbes that natively deconstruct lignocellulose and concomitantly form industrially relevant products, but these two physiological and metabolic features are rarely and simultaneously observed in nature. Genetic modification of both plant feedstocks and microbes can be used to increase lignocellulose deconstruction capability and generate industrially relevant products. Separate efforts on plants and microbes are ongoing, but these studies lack a focus on optimal, complementary combinations of these disparate biological systems to obtain a convergent technology. Improving genetic tools for plants have given rise to the generation of low-lignin lines that are more readily solubilized by microorganisms. Most focus on the microbiological front has involved thermophilic bacteria from the genera Caldicellulosiruptor and Clostridium, given their capacity to degrade lignocellulose and to form bio-products through metabolic engineering strategies enabled by ever-improving molecular genetics tools. Bioengineering plant properties to better fit the deconstruction capabilities of candidate consolidated bioprocessing microorganisms has potential to achieve the efficient lignocellulose deconstruction needed for industrial relevance.
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Affiliation(s)
- Ryan G. Bing
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695
| | - Daniel B. Sulis
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695
| | - Jack P. Wang
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695
| | - Michael W.W. Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602
| | - Robert M. Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695
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8
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Matthews ML, Marshall-Colón A. Multiscale plant modeling: from genome to phenome and beyond. Emerg Top Life Sci 2021; 5:231-237. [PMID: 33543231 PMCID: PMC8166335 DOI: 10.1042/etls20200276] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 01/18/2021] [Accepted: 01/20/2021] [Indexed: 01/08/2023]
Abstract
Plants are complex organisms that adapt to changes in their environment using an array of regulatory mechanisms that span across multiple levels of biological organization. Due to this complexity, it is difficult to predict emergent properties using conventional approaches that focus on single levels of biology such as the genome, transcriptome, or metabolome. Mathematical models of biological systems have emerged as useful tools for exploring pathways and identifying gaps in our current knowledge of biological processes. Identification of emergent properties, however, requires their vertical integration across biological scales through multiscale modeling. Multiscale models that capture and predict these emergent properties will allow us to predict how plants will respond to a changing climate and explore strategies for plant engineering. In this review, we (1) summarize the recent developments in plant multiscale modeling; (2) examine multiscale models of microbial systems that offer insight to potential future directions for the modeling of plant systems; (3) discuss computational tools and resources for developing multiscale models; and (4) examine future directions of the field.
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Affiliation(s)
- Megan L Matthews
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
- Institute for Sustainability, Energy, and Environment, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
| | - Amy Marshall-Colón
- Institute for Sustainability, Energy, and Environment, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
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9
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Matthews ML, Williams CM. Multiscale Modeling of Cross-Regulatory Transcript and Protein Influences. Methods Mol Biol 2021; 2328:115-138. [PMID: 34251622 DOI: 10.1007/978-1-0716-1534-8_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
With the popularity of high-throughput transcriptomic techniques like RNAseq, models of gene regulatory networks have been important tools for understanding how genes are regulated. These transcriptomic datasets are usually assumed to reflect their associated proteins. This assumption, however, ignores post-transcriptional, translational, and post-translational regulatory mechanisms that regulate protein abundance but not transcript abundance. Here we describe a method to model cross-regulatory influences between the transcripts and proteins of a set of genes using abundance data collected from a series of transgenic experiments. The developed model can capture the effects of regulation that impacts transcription as well as regulatory mechanisms occurring after transcription. This approach uses a sparse maximum likelihood algorithm to determine relationships that influence transcript and protein abundance. An example of how to explore the network topology of this type of model is also presented. This model can be used to predict how the transcript and protein abundances will change in novel transgenic modification strategies.
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Affiliation(s)
- Megan L Matthews
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Institute for Sustainability, Energy, and Environment, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Cranos M Williams
- Department of Electrical and Computer Engineering, North Carolina State University, Raleigh, NC, USA.
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10
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Matthews ML, Wang JP, Sederoff R, Chiang VL, Williams CM. A multiscale model of lignin biosynthesis for predicting bioenergy traits in Populus trichocarpa. Comput Struct Biotechnol J 2020; 19:168-182. [PMID: 33425249 PMCID: PMC7773863 DOI: 10.1016/j.csbj.2020.11.046] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 11/22/2020] [Accepted: 11/23/2020] [Indexed: 11/15/2022] Open
Abstract
Understanding the mechanisms behind lignin formation is an important research area with significant implications for the bioenergy and biomaterial industries. Computational models are indispensable tools for understanding this complex process. Models of the monolignol pathway in Populus trichocarpa and other plants have been developed to explore how transgenic modifications affect important bioenergy traits. Many of these models, however, only capture one level of biological organization and are unable to capture regulation across multiple biological scales. This limits their ability to predict how gene modification strategies will impact lignin and other wood properties. While the first multiscale model of lignin biosynthesis in P. trichocarpa spanned the transcript, protein, metabolic, and phenotypic layers, it did not account for cross-regulatory influences that could impact abundances of untargeted monolignol transcripts and proteins. Here, we present a multiscale model incorporating these cross-regulatory influences for predicting lignin and wood traits from transgenic knockdowns of the monolignol genes. The three main components of this multiscale model are (1) a transcript-protein model capturing cross-regulatory influences, (2) a kinetic-based metabolic model, and (3) random forest models relating the steady state metabolic fluxes to 25 physical traits. We demonstrate that including the cross-regulatory behavior results in smaller predictive error for 23 of the 25 traits. We use this multiscale model to explore the predicted impact of novel combinatorial knockdowns on key bioenergy traits, and identify the perturbation of PtrC3H3 and PtrCAld5H1&2 monolignol genes as a candidate strategy for increasing saccharification efficiencies while reducing negative impacts on wood density and height.
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Affiliation(s)
- Megan L Matthews
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.,Institute for Sustainability, Energy, and Environment, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Jack P Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China.,Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695, USA
| | - Ronald Sederoff
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695, USA
| | - Vincent L Chiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China.,Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695, USA
| | - Cranos M Williams
- Department of Electrical and Computer Engineering, North Carolina State University, Raleigh, NC 27695, USA
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11
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Tong H, Madison I, Long TA, Williams CM. Computational solutions for modeling and controlling plant response to abiotic stresses: a review with focus on iron deficiency. CURRENT OPINION IN PLANT BIOLOGY 2020; 57:8-15. [PMID: 32619968 DOI: 10.1016/j.pbi.2020.05.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 05/15/2020] [Accepted: 05/23/2020] [Indexed: 06/11/2023]
Abstract
Computational solutions enable plant scientists to model protein-mediated stress responses and characterize novel gene functions that coordinate responses to a variety of abiotic stress conditions. Recently, density functional theory was used to study proteins active sites and elucidate enzyme conversion mechanisms involved in iron deficiency responsive signaling pathways. Computational approaches for protein homology modeling and the kinetic modeling of signaling pathways have also resolved the identity and function in proteins involved in iron deficiency signaling pathways. Significant changes in gene relationships under other stress conditions, such as heat or drought stress, have been recently identified using differential network analysis, suggesting that stress tolerance is achieved through asynchronous control. Moreover, the increasing development and use of statistical modeling and systematic modeling of transcriptomic data have provided significant insight into the gene regulatory mechanisms associated with abiotic stress responses. These types of in silico approaches have facilitated the plant science community's future goals of developing multi-scale models of responses to iron deficiency stress and other abiotic stress conditions.
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Affiliation(s)
- Haonan Tong
- Electrical and Computer Engineering, North Carolina State University, Raleigh, USA
| | - Imani Madison
- Plant and Microbial Biology, North Carolina State University, Raleigh, USA
| | - Terri A Long
- Plant and Microbial Biology, North Carolina State University, Raleigh, USA.
| | - Cranos M Williams
- Electrical and Computer Engineering, North Carolina State University, Raleigh, USA.
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