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Xiao T, Feng S, Liu J, Wang Y, Shangguan X, Yu X, Shen Z, Hu Z, Xia Y. OsGLP8-7 interacts with OsPRX111 to detoxify excess copper in rice. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 210:108564. [PMID: 38555719 DOI: 10.1016/j.plaphy.2024.108564] [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: 02/29/2024] [Accepted: 03/23/2024] [Indexed: 04/02/2024]
Abstract
Lignin is a phenolic biopolymer generated from phenylpropanoid pathway in the secondary cell wall and is required for defense of plants against various stress. Although the fact of stress-induced lignin deposition has been clearly demonstrated, it remains largely elusive how the formation of lignin is promoted under Cu stress. The present study showed that OsGLP8-7, an extracellular glycoprotein of rice (Oryza sativa L.), plays an important function against Cu stress. The loss function of OsGLP8-7 results in Cu sensitivity whereas overexpression of OsGLP8-7 scavenges Cu-induced superoxide anion (O2•-). OsGLP8-7 interacts with apoplastic peroxidase111 (OsPRX111) and elevates OsPRX111 stability when exposed to excess Cu. In OsGLP8-7 overexpressing (OE) lines, the retention of Cu within cell wall limiting Cu uptake into cytoplasm is attributed to the enhanced lignification required for Cu tolerance. Exogenous application of a lignin inhibitor can impair the Cu tolerance of transgenic Arabidopsis lines overexpressing OsGLP8-7. In addition, co-expression of OsGLP8-7 and OsPRX111 genes in tobacco leaves leads to an improved lignin deposition compared to leaves expressing each gene individually or the empty vector. Taken together, our findings provided the convincing evidences that the interaction between OsGLP8-7 and OsPRX111 facilitates effectively lignin polymerization, thereby contributing to Cu tolerance in rice.
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Affiliation(s)
- Tengwei Xiao
- College of Life Sciences, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shuhua Feng
- Heilongjiang Vocational College of Agricultural Engineering, Harbin, 150088, China
| | - Jia Liu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing, 210014, China
| | - Yu Wang
- College of Life Sciences, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiangchao Shangguan
- College of Life Sciences, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaoyu Yu
- College of Life Sciences, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhenguo Shen
- College of Life Sciences, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Zhubing Hu
- Center for Multi-Omics Research, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, 475004, China.
| | - Yan Xia
- College of Life Sciences, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource, Nanjing Agricultural University, Nanjing, 210095, China.
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2
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Zhu Y, Li L. Wood of trees: Cellular structure, molecular formation, and genetic engineering. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:443-467. [PMID: 38032010 DOI: 10.1111/jipb.13589] [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: 08/30/2023] [Accepted: 11/28/2023] [Indexed: 12/01/2023]
Abstract
Wood is an invaluable asset to human society due to its renewable nature, making it suitable for both sustainable energy production and material manufacturing. Additionally, wood derived from forest trees plays a crucial role in sequestering a significant portion of the carbon dioxide fixed during photosynthesis by terrestrial plants. Nevertheless, with the expansion of the global population and ongoing industrialization, forest coverage has been substantially decreased, resulting in significant challenges for wood production and supply. Wood production practices have changed away from natural forests toward plantation forests. Thus, understanding the underlying genetic mechanisms of wood formation is the foundation for developing high-quality, fast-growing plantation trees. Breeding ideal forest trees for wood production using genetic technologies has attracted the interest of many. Tremendous studies have been carried out in recent years on the molecular, genetic, and cell-biological mechanisms of wood formation, and considerable progress and findings have been achieved. These studies and findings indicate enormous possibilities and prospects for tree improvement. This review will outline and assess the cellular and molecular mechanisms of wood formation, as well as studies on genetically improving forest trees, and address future development prospects.
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Affiliation(s)
- Yingying Zhu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems and College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Laigeng Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
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3
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Li W, Lin YCJ, Chen YL, Zhou C, Li S, De Ridder N, Oliveira DM, Zhang L, Zhang B, Wang JP, Xu C, Fu X, Luo K, Wu AM, Demura T, Lu MZ, Zhou Y, Li L, Umezawa T, Boerjan W, Chiang VL. Woody plant cell walls: Fundamentals and utilization. MOLECULAR PLANT 2024; 17:112-140. [PMID: 38102833 DOI: 10.1016/j.molp.2023.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/12/2023] [Accepted: 12/12/2023] [Indexed: 12/17/2023]
Abstract
Cell walls in plants, particularly forest trees, are the major carbon sink of the terrestrial ecosystem. Chemical and biosynthetic features of plant cell walls were revealed early on, focusing mostly on herbaceous model species. Recent developments in genomics, transcriptomics, epigenomics, transgenesis, and associated analytical techniques are enabling novel insights into formation of woody cell walls. Here, we review multilevel regulation of cell wall biosynthesis in forest tree species. We highlight current approaches to engineering cell walls as potential feedstock for materials and energy and survey reported field tests of such engineered transgenic trees. We outline opportunities and challenges in future research to better understand cell type biogenesis for more efficient wood cell wall modification and utilization for biomaterials or for enhanced carbon capture and storage.
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Affiliation(s)
- Wei Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | | | - Ying-Lan Chen
- Department of Biotechnology and Bioindustry Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan, Taiwan, China
| | - Chenguang Zhou
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Shuang Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Nette De Ridder
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Dyoni M Oliveira
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Lanjun Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Baocai Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jack P Wang
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695, USA
| | - Changzheng Xu
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Xiaokang Fu
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Keming Luo
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Ai-Min Wu
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University, Guangzhou 510642, China
| | - Taku Demura
- Center for Digital Green-innovation, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Meng-Zhu Lu
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A & F University, Hangzhou 311300, China
| | - Yihua Zhou
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Laigeng Li
- CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
| | - Toshiaki Umezawa
- Laboratory of Metabolic Science of Forest Plants and Microorganisms, Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Wout Boerjan
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - 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.
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4
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Colbert JB, Coleman HD. Functional Diversification and the Plant Secondary Cell Wall. J Mol Evol 2023; 91:761-772. [PMID: 37979044 DOI: 10.1007/s00239-023-10145-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 11/09/2023] [Indexed: 11/19/2023]
Abstract
Much evidence exists suggesting the presence of genetic functional diversification in plants, though literature associated with the role of functional diversification in the evolution of the plant secondary cell wall (SCW) has sparsely been compiled and reviewed in a recent context. This review aims to elucidate, through the examination of gene phylogenies associated with its biosynthesis and maintenance, the role of functional diversification in shaping the critical, dynamic, and characteristic organelle, the secondary cell wall. It will be asserted that gene families resulting from gene duplication and subsequent functional divergence are present and are heavily involved in SCW biosynthesis and maintenance. Furthermore, diversification will be presented as a significant driver behind the evolution of the many functional characteristics of the SCW. The structure and function of the plant cell wall and its constituents will first be explored, followed by a discussion on the phenomenon of gene duplication and the resulting genetic functional divergence that can emerge. Finally, the major constituents of the SCW and their individual relationships with duplication and divergence will be reviewed to the extent of current knowledge on the subject.
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Affiliation(s)
- Joseph B Colbert
- Biology Department, Syracuse University, 107 College Place, Syracuse, NY, 13244, USA
| | - Heather D Coleman
- Biology Department, Syracuse University, 107 College Place, Syracuse, NY, 13244, USA.
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5
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Zhou R, Jenkins JW, Zeng Y, Shu S, Jang H, Harding SA, Williams M, Plott C, Barry KW, Koriabine M, Amirebrahimi M, Talag J, Rajasekar S, Grimwood J, Schmitz RJ, Dawe RK, Schmutz J, Tsai CJ. Haplotype-resolved genome assembly of Populus tremula × P. alba reveals aspen-specific megabase satellite DNA. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1003-1017. [PMID: 37675609 DOI: 10.1111/tpj.16454] [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: 06/28/2023] [Revised: 08/23/2023] [Accepted: 08/25/2023] [Indexed: 09/08/2023]
Abstract
Populus species play a foundational role in diverse ecosystems and are important renewable feedstocks for bioenergy and bioproducts. Hybrid aspen Populus tremula × P. alba INRA 717-1B4 is a widely used transformation model in tree functional genomics and biotechnology research. As an outcrossing interspecific hybrid, its genome is riddled with sequence polymorphisms which present a challenge for sequence-sensitive analyses. Here we report a telomere-to-telomere genome for this hybrid aspen with two chromosome-scale, haplotype-resolved assemblies. We performed a comprehensive analysis of the repetitive landscape and identified both tandem repeat array-based and array-less centromeres. Unexpectedly, the most abundant satellite repeats in both haplotypes lie outside of the centromeres, consist of a 147 bp monomer PtaM147, frequently span >1 megabases, and form heterochromatic knobs. PtaM147 repeats are detected exclusively in aspens (section Populus) but PtaM147-like sequences occur in LTR-retrotransposons of closely related species, suggesting their origin from the retrotransposons. The genomic resource generated for this transformation model genotype has greatly improved the design and analysis of genome editing experiments that are highly sensitive to sequence polymorphisms. The work should motivate future hypothesis-driven research to probe into the function of the abundant and aspen-specific PtaM147 satellite DNA.
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Affiliation(s)
- Ran Zhou
- School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, USA
- Department of Genetics, University of Georgia, Athens, Georgia, USA
- Department of Plant Biology, University of Georgia, Athens, Georgia, USA
| | - Jerry W Jenkins
- HudsonAlpha Institute of Biotechnology, Huntsville, Alabama, USA
| | - Yibing Zeng
- Department of Genetics, University of Georgia, Athens, Georgia, USA
| | - Shengqiang Shu
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Hosung Jang
- Department of Genetics, University of Georgia, Athens, Georgia, USA
| | - Scott A Harding
- School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, USA
- Department of Genetics, University of Georgia, Athens, Georgia, USA
- Department of Plant Biology, University of Georgia, Athens, Georgia, USA
| | - Melissa Williams
- HudsonAlpha Institute of Biotechnology, Huntsville, Alabama, USA
| | | | - Kerrie W Barry
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Maxim Koriabine
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Mojgan Amirebrahimi
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Jayson Talag
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Shanmugam Rajasekar
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Jane Grimwood
- HudsonAlpha Institute of Biotechnology, Huntsville, Alabama, USA
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, Georgia, USA
| | - R Kelly Dawe
- Department of Genetics, University of Georgia, Athens, Georgia, USA
- Department of Plant Biology, University of Georgia, Athens, Georgia, USA
| | - Jeremy Schmutz
- HudsonAlpha Institute of Biotechnology, Huntsville, Alabama, USA
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Chung-Jui Tsai
- School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, USA
- Department of Genetics, University of Georgia, Athens, Georgia, USA
- Department of Plant Biology, University of Georgia, Athens, Georgia, USA
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6
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Buell CR, Dardick C, Parrott W, Schmitz RJ, Shih PM, Tsai CJ, Urbanowicz B. Engineering custom morpho- and chemotypes of Populus for sustainable production of biofuels, bioproducts, and biomaterials. FRONTIERS IN PLANT SCIENCE 2023; 14:1288826. [PMID: 37965014 PMCID: PMC10642751 DOI: 10.3389/fpls.2023.1288826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 10/16/2023] [Indexed: 11/16/2023]
Abstract
Humans have been modifying plant traits for thousands of years, first through selection (i.e., domestication) then modern breeding, and in the last 30 years, through biotechnology. These modifications have resulted in increased yield, more efficient agronomic practices, and enhanced quality traits. Precision knowledge of gene regulation and function through high-resolution single-cell omics technologies, coupled with the ability to engineer plant genomes at the DNA sequence, chromatin accessibility, and gene expression levels, can enable engineering of complex and complementary traits at the biosystem level. Populus spp., the primary genetic model system for woody perennials, are among the fastest growing trees in temperate zones and are important for both carbon sequestration and global carbon cycling. Ample genomic and transcriptomic resources for poplar are available including emerging single-cell omics datasets. To expand use of poplar outside of valorization of woody biomass, chassis with novel morphotypes in which stem branching and tree height are modified can be fabricated thereby leading to trees with altered leaf to wood ratios. These morphotypes can then be engineered into customized chemotypes that produce high value biofuels, bioproducts, and biomaterials not only in specific organs but also in a cell-type-specific manner. For example, the recent discovery of triterpene production in poplar leaf trichomes can be exploited using cell-type specific regulatory sequences to synthesize high value terpenes such as the jet fuel precursor bisabolene specifically in the trichomes. By spatially and temporally controlling expression, not only can pools of abundant precursors be exploited but engineered molecules can be sequestered in discrete cell structures in the leaf. The structural diversity of the hemicellulose xylan is a barrier to fully utilizing lignocellulose in biomaterial production and by leveraging cell-type-specific omics data, cell wall composition can be modified in a tailored and targeted specific manner to generate poplar wood with novel chemical features that are amenable for processing or advanced manufacturing. Precision engineering poplar as a multi-purpose sustainable feedstock highlights how genome engineering can be used to re-imagine a crop species.
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Affiliation(s)
- C. Robin Buell
- Center for Applied Genetic Technologies, Institute of Plant Breeding, Genetics, and Genomics, Department of Crop and Soil Sciences, University of Georgia, Athens, GA, United States
| | - Christopher Dardick
- Agricultural Research Service, U.S. Department of Agriculture, Kearneysville, WV, United States
| | - Wayne Parrott
- Center for Applied Genetic Technologies, Institute of Plant Breeding, Genetics, and Genomics, Department of Crop and Soil Sciences, University of Georgia, Athens, GA, United States
| | - Robert J. Schmitz
- Department of Genetics, University of Georgia, Athens, GA, United States
| | - Patrick M. Shih
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, United States
| | - Chung-Jui Tsai
- Department of Genetics, University of Georgia, Athens, GA, United States
- Department of Plant Biology, University of Georgia, Athens, GA, United States
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA, United States
| | - Breeanna Urbanowicz
- Center for Complex Carbohydrate Research, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
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Zhao J, Chao K, Wang A. Integrative analysis of metabolome, proteome, and transcriptome for identifying genes influencing total lignin content in Populus trichocarpa. FRONTIERS IN PLANT SCIENCE 2023; 14:1244020. [PMID: 37771490 PMCID: PMC10525687 DOI: 10.3389/fpls.2023.1244020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 08/22/2023] [Indexed: 09/30/2023]
Abstract
Lignin, a component of plant cell walls, possesses significant research potential as a renewable energy source to replace carbon-based products and as a notable pollutant in papermaking processes. The monolignol biosynthetic pathway has been elucidated and it is known that not all monolignol genes influence the total lignin content. However, it remains unclear which monolignol genes are more closely related to the total lignin content and which potential genes influence the total lignin content. In this study, we present a combination of t-test, differential gene expression analysis, correlation analysis, and weighted gene co-expression network analysis to identify genes that regulate the total lignin content by utilizing multi-omics data from transgenic knockdowns of the monolignol genes that includes data related to the transcriptome, proteome, and total lignin content. Firstly, it was discovered that enzymes from the PtrPAL, Ptr4CL, PtrC3H, and PtrC4H gene families are more strongly correlated with the total lignin content. Additionally, the co-downregulation of three genes, PtrC3H3, PtrC4H1, and PtrC4H2, had the greatest impact on the total lignin content. Secondly, GO and KEGG analysis of lignin-related modules revealed that the total lignin content is not only influenced by monolignol genes, but also closely related to genes involved in the "glutathione metabolic process", "cellular modified amino acid metabolic process" and "carbohydrate catabolic process" pathways. Finally, the cinnamyl alcohol dehydrogenase genes CAD1, CADL3, and CADL8 emerged as potential contributors to total lignin content. The genes HYR1 (UDP-glycosyltransferase superfamily protein) and UGT71B1 (UDP-glucosyltransferase), exhibiting a close relationship with coumarin, have the potential to influence total lignin content by regulating coumarin metabolism. Additionally, the monolignol genes PtrC3H3, PtrC4H1, and PtrC4H2, which belong to the cytochrome P450 genes, may have a significant impact on the total lignin content. Overall, this study establishes connections between gene expression levels and total lignin content, effectively identifying genes that have a significant impact on total lignin content and offering novel perspectives for future lignin research endeavours.
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Affiliation(s)
- Jia Zhao
- College of Computer and Control Engineering, Northeast Forestry University, Harbin, China
| | - Kairui Chao
- College of Forestry, Inner Mongolia Agricultural University, Hohhot, China
| | - Achuan Wang
- College of Computer and Control Engineering, Northeast Forestry University, Harbin, China
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8
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Chen YH, Sharma S, Bewg WP, Xue LJ, Gizelbach CR, Tsai CJ. Multiplex Editing of the Nucleoredoxin1 Tandem Array in Poplar: From Small Indels to Translocations and Complex Inversions. CRISPR J 2023; 6:339-349. [PMID: 37307061 PMCID: PMC10460964 DOI: 10.1089/crispr.2022.0096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 04/21/2023] [Indexed: 06/13/2023] Open
Abstract
The CRISPR-Cas9 system has been deployed for precision mutagenesis in an ever-growing number of species, including agricultural crops and forest trees. Its application to closely linked genes with extremely high sequence similarities has been less explored. In this study, we used CRISPR-Cas9 to mutagenize a tandem array of seven Nucleoredoxin1 (NRX1) genes spanning ∼100 kb in Populus tremula × Populus alba. We demonstrated efficient multiplex editing with one single guide RNA in 42 transgenic lines. The mutation profiles ranged from small insertions and deletions and local deletions in individual genes to large genomic dropouts and rearrangements spanning tandem genes. We also detected complex rearrangements including translocations and inversions resulting from multiple cleavage and repair events. Target capture sequencing was instrumental for unbiased assessments of repair outcomes to reconstruct unusual mutant alleles. The work highlights the power of CRISPR-Cas9 for multiplex editing of tandemly duplicated genes to generate diverse mutants with structural and copy number variations to aid future functional characterization.
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Affiliation(s)
- Yen-Ho Chen
- Department of Plant Biology, University of Georgia, Athens, Georgia, USA; College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Shakuntala Sharma
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, USA; College of Forestry, Nanjing Forestry University, Nanjing, China
| | - William P. Bewg
- Department of Plant Biology, University of Georgia, Athens, Georgia, USA; College of Forestry, Nanjing Forestry University, Nanjing, China
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, USA; College of Forestry, Nanjing Forestry University, Nanjing, China
- Department of Genetics, University of Georgia, Athens, Georgia, USA; and College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Liang-Jiao Xue
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, USA; College of Forestry, Nanjing Forestry University, Nanjing, China
- Department of Genetics, University of Georgia, Athens, Georgia, USA; and College of Forestry, Nanjing Forestry University, Nanjing, China
- State Key Laboratory of Tree Genetics and Breeding, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Cole R. Gizelbach
- Department of Genetics, University of Georgia, Athens, Georgia, USA; and College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Chung-Jui Tsai
- Department of Plant Biology, University of Georgia, Athens, Georgia, USA; College of Forestry, Nanjing Forestry University, Nanjing, China
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, USA; College of Forestry, Nanjing Forestry University, Nanjing, China
- Department of Genetics, University of Georgia, Athens, Georgia, USA; and College of Forestry, Nanjing Forestry University, Nanjing, China
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9
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Sun N, Bu Y, Wu X, Ma X, Yang H, Du L, Li X, Xiao J, Lin J, Jing Y. Comprehensive analysis of lncRNA-mRNA regulatory network in Populus associated with xylem development. JOURNAL OF PLANT PHYSIOLOGY 2023; 287:154055. [PMID: 37506405 DOI: 10.1016/j.jplph.2023.154055] [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: 04/19/2023] [Revised: 07/01/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023]
Abstract
Long noncoding RNAs (lncRNAs) play essential roles in numerous biological processes in plants, such as regulating the gene expression. However, only a few studies have looked into their potential functions in xylem development. High-throughput sequencing of P. euramericana 'Zhonglin46' developing and mature xylem was performed in this study. Through sequencing analysis, 14,028 putative lncRNA transcripts were identified, including 4525 differentially expressed lncRNAs (DELs). Additional research revealed that in mature xylem, a total of 2320 DELs were upregulated and 2205 were downregulated compared to developing xylem. Meanwhile, there were a total of 8122 differentially expressed mRNAs (DEMs) that were upregulated and 16,424 that were downregulated in mature xylem compared with developing xylem. The cis- and trans-target genes of DELs were analyzed for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, which indicated that these DELs participate in controlling the phenylpropanoid and lignin biosynthesis pathway as well as the starch and sucrose metabolism pathway. Among the cis-regulated DELs, LNC_006291, LNC_006292, and LNC_006532 all participate in regulating multiple HCT gene family membranes. As targets, POPTR_001G045900v3 (CCR2) and POPTR_018G063500v3 (SUS) both have only one cis-regulatory lncRNA, referred to as LNC_000057 and LNC_006212, respectively. Moreover, LNC_004484 and two DELs named LNC_008014 and LNC_010781 were revealed to be important nodes in the co-expression network of trans-lncRNAs and mRNAs associated to the lignin biosynthesis pathway and cellulose and xylan biosynthetic pathways, respectively. Finally, quantitative real-time PCR (qRT-PCR) was used to confirme 34 pairs of lncRNA-mRNA. Taken together, these findings may help to clarify the regulatory role that lncRNAs play in xylem development and wood formation.
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Affiliation(s)
- Na Sun
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.
| | - Yufen Bu
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.
| | - Xinyuan Wu
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.
| | - Xiaocen Ma
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.
| | - Haobo Yang
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.
| | - Liang Du
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.
| | - Xiaojuan Li
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.
| | - Jianwei Xiao
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.
| | - Jinxing Lin
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.
| | - Yanping Jing
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.
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10
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Verma V, Kumar A, Partap M, Thakur M, Bhargava B. CRISPR-Cas: A robust technology for enhancing consumer-preferred commercial traits in crops. FRONTIERS IN PLANT SCIENCE 2023; 14:1122940. [PMID: 36824195 PMCID: PMC9941649 DOI: 10.3389/fpls.2023.1122940] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
The acceptance of new crop varieties by consumers is contingent on the presence of consumer-preferred traits, which include sensory attributes, nutritional value, industrial products and bioactive compounds production. Recent developments in genome editing technologies provide novel insight to identify gene functions and improve the various qualitative and quantitative traits of commercial importance in plants. Various conventional as well as advanced gene-mutagenesis techniques such as physical and chemical mutagenesis, CRISPR-Cas9, Cas12 and base editors are used for the trait improvement in crops. To meet consumer demand, breakthrough biotechnologies, especially CRISPR-Cas have received a fair share of scientific and industrial interest, particularly in plant genome editing. CRISPR-Cas is a versatile tool that can be used to knock out, replace and knock-in the desired gene fragments at targeted locations in the genome, resulting in heritable mutations of interest. This review highlights the existing literature and recent developments in CRISPR-Cas technologies (base editing, prime editing, multiplex gene editing, epigenome editing, gene delivery methods) for reliable and precise gene editing in plants. This review also discusses the potential of gene editing exhibited in crops for the improvement of consumer-demanded traits such as higher nutritional value, colour, texture, aroma/flavour, and production of industrial products such as biofuel, fibre, rubber and pharmaceuticals. In addition, the bottlenecks and challenges associated with gene editing system, such as off targeting, ploidy level and the ability to edit organelle genome have also been discussed.
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Affiliation(s)
- Vipasha Verma
- Floriculture Laboratory, Agrotechnology Division, Council of Scientific and Industrial Research (CSIR) –Institute of Himalayan Bioresource Technology (IHBT), Palampur, India
| | - Akhil Kumar
- Floriculture Laboratory, Agrotechnology Division, Council of Scientific and Industrial Research (CSIR) –Institute of Himalayan Bioresource Technology (IHBT), Palampur, India
| | - Mahinder Partap
- Floriculture Laboratory, Agrotechnology Division, Council of Scientific and Industrial Research (CSIR) –Institute of Himalayan Bioresource Technology (IHBT), Palampur, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Meenakshi Thakur
- Floriculture Laboratory, Agrotechnology Division, Council of Scientific and Industrial Research (CSIR) –Institute of Himalayan Bioresource Technology (IHBT), Palampur, India
| | - Bhavya Bhargava
- Floriculture Laboratory, Agrotechnology Division, Council of Scientific and Industrial Research (CSIR) –Institute of Himalayan Bioresource Technology (IHBT), Palampur, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
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11
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Mottiar Y, Karlen SD, Goacher RE, Ralph J, Mansfield SD. Metabolic engineering of p-hydroxybenzoate in poplar lignin. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:176-188. [PMID: 36161690 PMCID: PMC9829402 DOI: 10.1111/pbi.13935] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 08/10/2022] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
Ester-linked p-hydroxybenzoate occurs naturally in poplar lignin as pendent groups that can be released by mild alkaline hydrolysis. These 'clip-off' phenolics can be separated from biomass and upgraded into diverse high-value bioproducts. We introduced a bacterial chorismate pyruvate lyase gene into transgenic poplar trees with the aim of producing more p-hydroxybenzoate from chorismate, itself a metabolic precursor to lignin. By driving heterologous expression specifically in the plastids of cells undergoing secondary wall formation, this strategy achieved a 50% increase in cell-wall-bound p-hydroxybenzoate in mature wood and nearly 10 times more in developing xylem relative to control trees. Comparable amounts also remained as soluble p-hydroxybenzoate-containing xylem metabolites, pointing to even greater engineering potential. Mass spectrometry imaging showed that the elevated p-hydroxybenzoylation was largely restricted to the cell walls of fibres. Finally, transgenic lines outperformed control trees in assays of saccharification potential. This study highlights the biotech potential of cell-wall-bound phenolate esters and demonstrates the importance of substrate supply in lignin engineering.
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Affiliation(s)
- Yaseen Mottiar
- Department of Wood ScienceUniversity of British ColumbiaVancouverBCCanada
- Department of Energy Great Lakes Bioenergy Research CenterMadisonWIUSA
| | - Steven D. Karlen
- Department of Energy Great Lakes Bioenergy Research CenterMadisonWIUSA
| | - Robyn E. Goacher
- Department of Biochemistry, Chemistry, and PhysicsNiagara UniversityNorth TonawandaNYUSA
| | - John Ralph
- Department of Energy Great Lakes Bioenergy Research CenterMadisonWIUSA
- Department of BiochemistryUniversity of WisconsinMadisonWIUSA
| | - Shawn D. Mansfield
- Department of Wood ScienceUniversity of British ColumbiaVancouverBCCanada
- Department of Energy Great Lakes Bioenergy Research CenterMadisonWIUSA
- Department of BotanyUniversity of British ColumbiaVancouverBCCanada
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12
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Afifi OA, Tobimatsu Y, Lam PY, Martin AF, Miyamoto T, Osakabe Y, Osakabe K, Umezawa T. Genome-edited rice deficient in two 4-COUMARATE:COENZYME A LIGASE genes displays diverse lignin alterations. PLANT PHYSIOLOGY 2022; 190:2155-2172. [PMID: 36149320 PMCID: PMC9706450 DOI: 10.1093/plphys/kiac450] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 09/01/2022] [Indexed: 06/16/2023]
Abstract
The 4-coumarate:coenzyme A ligase (4CL) is a key enzyme that contributes to channeling metabolic flux in the cinnamate/monolignol pathway, leading to the production of monolignols, p-hydroxycinnamates, and a flavonoid tricin, the major building blocks of lignin polymer in grass cell walls. Vascular plants often contain multiple 4CL genes; however, the contribution of each 4CL isoform to lignin biosynthesis remains unclear, especially in grasses. In this study, we characterized the functions of two rice (Oryza sativa L.) 4CL isoforms (Os4CL3 and Os4CL4) primarily by analyzing the cell wall chemical structures of rice mutants generated by CRISPR/Cas9-mediated targeted mutagenesis. A series of chemical and nuclear magnetic resonance analyses revealed that loss-of-function of Os4CL3 and Os4CL4 differently altered the composition of lignin polymer units. Loss of function of Os4CL3 induced marked reductions in the major guaiacyl and syringyl lignin units derived from both the conserved non-γ-p-coumaroylated and the grass-specific γ-p-coumaroylated monolignols, with more prominent reductions in guaiacyl units than in syringyl units. In contrast, the loss-of-function mutation to Os4CL4 primarily decreased the abundance of the non-γ-p-coumaroylated guaiacyl units. Loss-of-function of Os4CL4, but not of Os4CL3, reduced the grass-specific lignin-bound tricin units, indicating that Os4CL4 plays a key role not only in monolignol biosynthesis but also in the biosynthesis of tricin used for lignification. Further, the loss-of-function of Os4CL3 and Os4CL4 notably reduced cell-wall-bound ferulates, indicating their roles in cell wall feruloylation. Overall, this study demonstrates the overlapping but divergent roles of 4CL isoforms during the coordinated production of various lignin monomers.
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Affiliation(s)
- Osama Ahmed Afifi
- Research Institute for Sustainable Humanosphere (RISH), Kyoto University, Kyoto 611-0011, Japan
- Faculty of Science, Al-Azhar University, Cairo 11884, Egypt
| | - Yuki Tobimatsu
- Research Institute for Sustainable Humanosphere (RISH), Kyoto University, Kyoto 611-0011, Japan
| | - Pui Ying Lam
- Center for Crossover Education, Graduate School of Engineering Science, Akita University, Akita 010-8502, Japan
| | - Andri Fadillah Martin
- Research Center for Genetic Engineering, National Research and Innovation Agency (BRIN), Bogor 16911, Indonesia
| | - Takuji Miyamoto
- Sakeology Center, Niigata University, Niigata 950-2181, Japan
| | - Yuriko Osakabe
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | - Keishi Osakabe
- Faculty of Bioscience and Bioindustry, Tokushima University, Tokushima 770-8506, Japan
| | - Toshiaki Umezawa
- Research Institute for Sustainable Humanosphere (RISH), Kyoto University, Kyoto 611-0011, Japan
- Research Unit for Realization of Sustainable Society (RURSS), Kyoto University, Kyoto 611-0011, Japan
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13
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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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14
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Ferreira SS, Goeminne G, Simões MS, Pina AVDA, Lima LGAD, Pezard J, Gutiérrez A, Rencoret J, Mortimer JC, Del Río JC, Boerjan W, Cesarino I. Transcriptional and metabolic changes associated with internode development and reduced cinnamyl alcohol dehydrogenase activity in sorghum. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:6307-6333. [PMID: 35788296 DOI: 10.1093/jxb/erac300] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 07/04/2022] [Indexed: 06/15/2023]
Abstract
The molecular mechanisms associated with secondary cell wall (SCW) deposition in sorghum remain largely uncharacterized. Here, we employed untargeted metabolomics and large-scale transcriptomics to correlate changes in SCW deposition with variation in global gene expression profiles and metabolite abundance along an elongating internode of sorghum, with a major focus on lignin and phenolic metabolism. To gain deeper insight into the metabolic and transcriptional changes associated with pathway perturbations, a bmr6 mutant [with reduced cinnamyl alcohol dehydrogenase (CAD) activity] was analyzed. In the wild type, internode development was accompanied by an increase in the content of oligolignols, p-hydroxybenzaldehyde, hydroxycinnamate esters, and flavonoid glucosides, including tricin derivatives. We further identified modules of genes whose expression pattern correlated with SCW deposition and the accumulation of these target metabolites. Reduced CAD activity resulted in the accumulation of hexosylated forms of hydroxycinnamates (and their derivatives), hydroxycinnamaldehydes, and benzenoids. The expression of genes belonging to one specific module in our co-expression analysis correlated with the differential accumulation of these compounds and contributed to explaining this metabolic phenotype. Metabolomics and transcriptomics data further suggested that CAD perturbation activates distinct detoxification routes in sorghum internodes. Our systems biology approach provides a landscape of the metabolic and transcriptional changes associated with internode development and with reduced CAD activity in sorghum.
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Affiliation(s)
- Sávio Siqueira Ferreira
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, São Paulo, Brazil
| | - Geert Goeminne
- VIB Center for Plant Systems Biology, Ghent, Belgium
- VIB Metabolomics Core, Ghent, Belgium
| | - Marcella Siqueira Simões
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, São Paulo, Brazil
| | | | | | - Jade Pezard
- Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ana Gutiérrez
- Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Avenida de la Reina Mercedes, Seville, Spain
| | - Jorge Rencoret
- Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Avenida de la Reina Mercedes, Seville, Spain
| | - Jenny C Mortimer
- Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - José C Del Río
- Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Avenida de la Reina Mercedes, Seville, Spain
| | - Wout Boerjan
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Igor Cesarino
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, São Paulo, Brazil
- Synthetic and Systems Biology Center, InovaUSP, Avenida Professor Lucio Martins Rodrigues, São Paulo, Brazil
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15
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Li M, Wang L, Zhang J, Zhan R, An N, Sun Y, Wu F, Yang J, Su H. Single-walled carbon nanotubes promotes wood formation in Populus davidiana × P.bolleana. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 184:137-143. [PMID: 35653939 DOI: 10.1016/j.plaphy.2022.05.015] [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: 02/25/2022] [Revised: 04/27/2022] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
Abundant studies have revealed that single-walled carbon nanotubes (SWCNTs) regulate plant growth. However, whether or how SWCNTs influence plant wood formation remains largely unknown. In this report, we found that SWCNTs had positive effects on poplar growth, as reflected by significantly increased plant height, leaf size, and fresh and dry weight. Transmission electron microscopy (TEM) images showed that the SWCNTs were absorbed in the exposed poplar root cells. A relatively higher content of cellulose and lignin was observed in the SWCNTs-treated poplar stems than in those of the control plants. It also showed darker phloroglucinol staining in the stems of exposed plants than that in control plants. Further analysis showed that the activities of key enzymes related to cellulose synthesis (cellulose synthase, CesA) and lignin biosynthesis (phenylalanine ammonia-lyase, PAL; cinnamate 4-hydroxylase, C4H; 4-coumarate:CoA ligase, 4CL; cinnamyl alcohol dehydrogenase, CAD) increased significantly after SWCNTs treatment. Consistent with the change trend of enzyme activity, the relative expression levels of a few lignin- and cellulose-related genes were activated by SWCNTs. Taken together, we proposed that SWCNTs have positive effects on poplar wood formation by modifying the expression of enzymes involved in the cellulose and lignin synthesis pathways. Our data suggest the modifications of wood formation through SWCNTs application could be a useful strategy for improvement of wood bioengineering.
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Affiliation(s)
- Mengjie Li
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong/College of Agriculture, Ludong Universtiy, Yantai, 264025, PR China; The Institute of Ecological Garden, Ludong University, Yantai, 264025, PR China
| | - Lei Wang
- College of Life Sciences, Ludong Universtiy, Yantai, 264025, PR China
| | - Jin Zhang
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong/College of Agriculture, Ludong Universtiy, Yantai, 264025, PR China
| | - Ruiling Zhan
- Key Laboratory of Fruit Tree Research in Ganzi Academy of Agricultural Sciences, Sichuan, 626000, PR China
| | - Ningning An
- Yantai Laishan Garden Construction and Maintenance Center, PR China
| | - Yadong Sun
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong/College of Agriculture, Ludong Universtiy, Yantai, 264025, PR China
| | - Fanlin Wu
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong/College of Agriculture, Ludong Universtiy, Yantai, 264025, PR China
| | - Jingjing Yang
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong/College of Agriculture, Ludong Universtiy, Yantai, 264025, PR China.
| | - Hongyan Su
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong/College of Agriculture, Ludong Universtiy, Yantai, 264025, PR China; The Institute of Ecological Garden, Ludong University, Yantai, 264025, PR China.
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16
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Bewg WP, Harding SA, Engle NL, Vaidya BN, Zhou R, Reeves J, Horn TW, Joshee N, Jenkins JW, Shu S, Barry KW, Yoshinaga Y, Grimwood J, Schmitz RJ, Schmutz J, Tschaplinski TJ, Tsai CJ. Multiplex knockout of trichome-regulating MYB duplicates in hybrid poplar using a single gRNA. PLANT PHYSIOLOGY 2022; 189:516-526. [PMID: 35298644 PMCID: PMC9157173 DOI: 10.1093/plphys/kiac128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 02/24/2022] [Indexed: 05/13/2023]
Abstract
As the focus for CRISPR/Cas-edited plants moves from proof-of-concept to real-world applications, precise gene manipulation will increasingly require concurrent multiplex editing for polygenic traits. A common approach for editing across multiple sites is to design one guide RNA (gRNA) per target; however, this complicates construct assembly and increases the possibility of off-target mutations. In this study, we utilized one gRNA to target MYB186, a known positive trichome regulator, as well as its paralogs MYB138 and MYB38 at a consensus site for mutagenesis in hybrid poplar (Populus tremula × P. alba INRA 717-1B4). Unexpected duplications of MYB186 and MYB138 resulted in eight alleles for the three targeted genes in the hybrid poplar. Deep sequencing and polymerase chain reaction analyses confirmed editing across all eight targets in nearly all of the resultant glabrous mutants, ranging from small indels to large genomic dropouts, with no off-target activity detected at four potential sites. This highlights the effectiveness of a single gRNA targeting conserved exonic regions for multiplex editing. Additionally, cuticular wax and whole-leaf analyses showed a complete absence of triterpenes in the trichomeless mutants, hinting at a previously undescribed role for the nonglandular trichomes of poplar.
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Affiliation(s)
- William P Bewg
- School of Forestry and Natural Resources, University of Georgia, Athens, Georgia 30602, USA
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602, USA
| | - Scott A Harding
- School of Forestry and Natural Resources, University of Georgia, Athens, Georgia 30602, USA
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602, USA
| | - Nancy L Engle
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
| | - Brajesh N Vaidya
- Department of Plant Science, Fort Valley State University, Georgia, 31030, USA
| | - Ran Zhou
- School of Forestry and Natural Resources, University of Georgia, Athens, Georgia 30602, USA
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602, USA
| | - Jacob Reeves
- Department of Computer Science, University of Georgia, Athens, Georgia 30602, USA
| | - Thomas W Horn
- Department of Computer Science, University of Georgia, Athens, Georgia 30602, USA
| | - Nirmal Joshee
- Department of Plant Science, Fort Valley State University, Georgia, 31030, USA
| | - Jerry W Jenkins
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
- U.S. Department of Energy Joint Genome Institute, Berkeley, California 94720, USA
| | - Shengqiang Shu
- U.S. Department of Energy Joint Genome Institute, Berkeley, California 94720, USA
| | - Kerrie W Barry
- U.S. Department of Energy Joint Genome Institute, Berkeley, California 94720, USA
| | - Yuko Yoshinaga
- U.S. Department of Energy Joint Genome Institute, Berkeley, California 94720, USA
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
- U.S. Department of Energy Joint Genome Institute, Berkeley, California 94720, USA
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
- U.S. Department of Energy Joint Genome Institute, Berkeley, California 94720, USA
| | | | - Chung-Jui Tsai
- School of Forestry and Natural Resources, University of Georgia, Athens, Georgia 30602, USA
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602, USA
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17
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Mendes GGM, Mota TR, Bossoni GEB, Marchiosi R, Oliveira DMD, Constantin RP, Dos Santos WD, Ferrarese-Filho O. Inhibiting tricin biosynthesis improves maize lignocellulose saccharification. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 178:12-19. [PMID: 35247693 DOI: 10.1016/j.plaphy.2022.02.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 02/14/2022] [Accepted: 02/19/2022] [Indexed: 06/14/2023]
Abstract
Lignin is a technological bottleneck to convert polysaccharides into fermentable sugars, and different strategies of genetic-based metabolic engineering have been applied to improve biomass saccharification. Using maize seedlings grown hydroponically for 24 h, we conducted a quick non-transgenic approach with five enzyme inhibitors of the lignin and tricin pathways. Two compounds [3,4-(methylenedioxy)cinnamic acid: MDCA and 2,4-pyridinedicarboxylic acid: PDCA] revealed interesting findings on root growth, lignin composition, and saccharification. By inhibiting hydroxycinnamoyl-CoA ligase, a key enzyme of phenylpropanoid pathway, MDCA decreased the lignin content and improved saccharification, but it decreased root growth. By inhibiting flavone synthase, a key enzyme of tricin biosynthesis, PDCA decreased total lignin content and improved saccharification without affecting root growth. PDCA was three-fold more effective than MDCA, suggesting that controlling lignin biosynthesis with enzymatic inhibitors may be an attractive strategy to improve biomass saccharification.
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Affiliation(s)
| | - Thatiane Rodrigues Mota
- Ghent University, Department of Plant Biotechnology and Bioinformatics and VIB Center for Plant Systems Biology, Ghent, Belgium
| | | | - Rogério Marchiosi
- Laboratory of Plant Biochemistry, State University of Maringá, Av. Colombo, 5790, 87020-900, Maringá, PR, Brazil
| | - Dyoni Matias de Oliveira
- Ghent University, Department of Plant Biotechnology and Bioinformatics and VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Rodrigo Polimeni Constantin
- Laboratory of Plant Biochemistry, State University of Maringá, Av. Colombo, 5790, 87020-900, Maringá, PR, Brazil
| | - Wanderley Dantas Dos Santos
- Laboratory of Plant Biochemistry, State University of Maringá, Av. Colombo, 5790, 87020-900, Maringá, PR, Brazil
| | - Osvaldo Ferrarese-Filho
- Laboratory of Plant Biochemistry, State University of Maringá, Av. Colombo, 5790, 87020-900, Maringá, PR, Brazil.
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18
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Joshi A, Verma KK, D Rajput V, Minkina T, Arora J. Recent advances in metabolic engineering of microorganisms for advancing lignocellulose-derived biofuels. Bioengineered 2022; 13:8135-8163. [PMID: 35297313 PMCID: PMC9161965 DOI: 10.1080/21655979.2022.2051856] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Combating climate change and ensuring energy supply to a rapidly growing global population has highlighted the need to replace petroleum fuels with clean, and sustainable renewable fuels. Biofuels offer a solution to safeguard energy security with reduced ecological footprint and process economics. Over the past years, lignocellulosic biomass has become the most preferred raw material for the production of biofuels, such as fuel, alcohol, biodiesel, and biohydrogen. However, the cost-effective conversion of lignocellulose into biofuels remains an unsolved challenge at the industrial scale. Recently, intensive efforts have been made in lignocellulose feedstock and microbial engineering to address this problem. By improving the biological pathways leading to the polysaccharide, lignin, and lipid biosynthesis, limited success has been achieved, and still needs to improve sustainable biofuel production. Impressive success is being achieved by the retouring metabolic pathways of different microbial hosts. Several robust phenotypes, mostly from bacteria and yeast domains, have been successfully constructed with improved substrate spectrum, product yield and sturdiness against hydrolysate toxins. Cyanobacteria is also being explored for metabolic advancement in recent years, however, it also remained underdeveloped to generate commercialized biofuels. The bacterium Escherichia coli and yeast Saccharomyces cerevisiae strains are also being engineered to have cell surfaces displaying hydrolytic enzymes, which holds much promise for near-term scale-up and biorefinery use. Looking forward, future advances to achieve economically feasible production of lignocellulosic-based biofuels with special focus on designing more efficient metabolic pathways coupled with screening, and engineering of novel enzymes.
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Affiliation(s)
- Abhishek Joshi
- Laboratory of Biomolecular Technology, Department of Botany, Mohanlal Sukhadia University, Udaipur313001, India
| | - Krishan K. Verma
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning - 530007, China
| | - Vishnu D Rajput
- Academy of Biology and Biotechnology, Southern Federal University, 344090, Russia
| | - Tatiana Minkina
- Academy of Biology and Biotechnology, Southern Federal University, 344090, Russia
| | - Jaya Arora
- Laboratory of Biomolecular Technology, Department of Botany, Mohanlal Sukhadia University, Udaipur313001, India,CONTACT Jaya Arora Laboratory of Biomolecular Technology, Department of Botany, Mohanlal Sukhadia University, Udaipur313001, India
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Zhan Y, Cheng J, Liu X, Huang C, Wang J, Han S, Fang G, Meng X, Ragauskas AJ. Assessing the availability of two bamboo species for fermentable sugars by alkaline hydrogen peroxide pretreatment. BIORESOURCE TECHNOLOGY 2022; 349:126854. [PMID: 35176465 DOI: 10.1016/j.biortech.2022.126854] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/09/2022] [Accepted: 02/10/2022] [Indexed: 06/14/2023]
Abstract
This study comprehensively investigated two bamboo species (i.e. Neosinocalamus affinis and Phyllostachys edulis) in terms of their cell wall ultrastructure, chemical compositions, enzymatic saccharification, and lignin structure before and after alkaline hydrogen peroxide pretreatment (AHP). During AHP, Neosinocalamus affinis (NAB) had higher delignification than Phyllostachys edulis (PEB), and thus showed better enzymatic digestibility (93.05% vs 53.57% for glucan). The fundamental chemical behavior of the bamboo lignins was analyzed by fluorescence microscope (FM), confocal Raman microscope (CRM), molecular weight analysis, and 2D HSQC-NMR. Results indicated that the PEB has thicker cell wall and more concentrated lignin in its compound middle lamella and cell corner middle lamella than NAB. Moreover, PEB lignin contains more G units (S/G of 0.95), in evident contrast to that of NAB lignin (S/G of 1.30), which favor the formation of C-C linkages, thus impeding its degradation during the AHP.
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Affiliation(s)
- Yunni Zhan
- Institute of Chemical Industry of Forest Products, Chinese Academy of Forestry, Jiangsu Province Key Laboratory of Biomass Energy and Materials, Nanjing 210042, China
| | - Jinyuan Cheng
- Institute of Chemical Industry of Forest Products, Chinese Academy of Forestry, Jiangsu Province Key Laboratory of Biomass Energy and Materials, Nanjing 210042, China
| | - Xuze Liu
- Institute of Chemical Industry of Forest Products, Chinese Academy of Forestry, Jiangsu Province Key Laboratory of Biomass Energy and Materials, Nanjing 210042, China
| | - Chen Huang
- Institute of Chemical Industry of Forest Products, Chinese Academy of Forestry, Jiangsu Province Key Laboratory of Biomass Energy and Materials, Nanjing 210042, China; Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing 210037, China.
| | - Jia Wang
- Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing 210037, China
| | - Shanming Han
- Institute of Chemical Industry of Forest Products, Chinese Academy of Forestry, Jiangsu Province Key Laboratory of Biomass Energy and Materials, Nanjing 210042, China
| | - Guigan Fang
- Institute of Chemical Industry of Forest Products, Chinese Academy of Forestry, Jiangsu Province Key Laboratory of Biomass Energy and Materials, Nanjing 210042, China; Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing 210037, China
| | - Xianzhi Meng
- Department of Chemical and Biomolecular Engineering, University of Tennessee Knoxville, Knoxville, TN 37996, USA
| | - Arthur J Ragauskas
- Department of Chemical and Biomolecular Engineering, University of Tennessee Knoxville, Knoxville, TN 37996, USA; Department of Forestry, Wildlife, and Fisheries, Center for Renewable Carbon, The University of Tennessee Institute of Agriculture, Knoxville, TN 37996, USA; Joint Institute for Biological Science, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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Yao T, Feng K, Xie M, Barros J, Tschaplinski TJ, Tuskan GA, Muchero W, Chen JG. Phylogenetic Occurrence of the Phenylpropanoid Pathway and Lignin Biosynthesis in Plants. FRONTIERS IN PLANT SCIENCE 2021; 12:704697. [PMID: 34484267 PMCID: PMC8416159 DOI: 10.3389/fpls.2021.704697] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 07/19/2021] [Indexed: 05/19/2023]
Abstract
The phenylpropanoid pathway serves as a rich source of metabolites in plants and provides precursors for lignin biosynthesis. Lignin first appeared in tracheophytes and has been hypothesized to have played pivotal roles in land plant colonization. In this review, we summarize recent progress in defining the lignin biosynthetic pathway in lycophytes, monilophytes, gymnosperms, and angiosperms. In particular, we review the key structural genes involved in p-hydroxyphenyl-, guaiacyl-, and syringyl-lignin biosynthesis across plant taxa and consider and integrate new insights on major transcription factors, such as NACs and MYBs. We also review insight regarding a new transcriptional regulator, 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase, canonically identified as a key enzyme in the shikimate pathway. We use several case studies, including EPSP synthase, to illustrate the evolution processes of gene duplication and neo-functionalization in lignin biosynthesis. This review provides new insights into the genetic engineering of the lignin biosynthetic pathway to overcome biomass recalcitrance in bioenergy crops.
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Affiliation(s)
- Tao Yao
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Kai Feng
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Meng Xie
- Biology Department, Brookhaven National Laboratory, Upton, NY, United States
| | - Jaime Barros
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX, United States
| | - Timothy J. Tschaplinski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Gerald A. Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Wellington Muchero
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
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Sattar MN, Iqbal Z, Al-Khayri JM, Jain SM. Induced Genetic Variations in Fruit Trees Using New Breeding Tools: Food Security and Climate Resilience. PLANTS (BASEL, SWITZERLAND) 2021; 10:1347. [PMID: 34371550 PMCID: PMC8309169 DOI: 10.3390/plants10071347] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 06/23/2021] [Accepted: 06/28/2021] [Indexed: 12/22/2022]
Abstract
Fruit trees provide essential nutrients to humans by contributing to major agricultural outputs and economic growth globally. However, major constraints to sustainable agricultural productivity are the uncontrolled proliferation of the population, and biotic and abiotic stresses. Tree mutation breeding has been substantially improved using different physical and chemical mutagens. Nonetheless, tree plant breeding has certain crucial bottlenecks including a long life cycle, ploidy level, occurrence of sequence polymorphisms, nature of parthenocarpic fruit development and linkage. Genetic engineering of trees has focused on boosting quality traits such as productivity, wood quality, and resistance to biotic and abiotic stresses. Recent technological advances in genome editing provide a unique opportunity for the genetic improvement of woody plants. This review examines application of the CRISPR-Cas system to reduce disease susceptibility, alter plant architecture, enhance fruit quality, and improve yields. Examples are discussed of the contemporary CRISPR-Cas system to engineer easily scorable PDS genes, modify lignin, and to alter the flowering onset, fertility, tree architecture and certain biotic stresses.
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Affiliation(s)
- Muhammad Naeem Sattar
- Central Laboratories, King Faisal University, Al-Ahsa 31982, Saudi Arabia; (M.N.S.); (Z.I.)
| | - Zafar Iqbal
- Central Laboratories, King Faisal University, Al-Ahsa 31982, Saudi Arabia; (M.N.S.); (Z.I.)
| | - Jameel M. Al-Khayri
- Department of Agricultural Biotechnology, College of Agriculture and Food Sciences, King Faisal University, Al-Ahsa 31982, Saudi Arabia
| | - S. Mohan Jain
- Department of Agricultural Sciences, PL-27, University of Helsinki, 00014 Helsinki, Finland;
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22
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Coleman HD, Brunner AM, Tsai CJ. Synergies and Entanglement in Secondary Cell Wall Development and Abiotic Stress Response in Trees. FRONTIERS IN PLANT SCIENCE 2021; 12:639769. [PMID: 33815447 PMCID: PMC8018706 DOI: 10.3389/fpls.2021.639769] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 03/01/2021] [Indexed: 06/12/2023]
Abstract
A major challenge for sustainable food, fuel, and fiber production is simultaneous genetic improvement of yield, biomass quality, and resilience to episodic environmental stress and climate change. For Populus and other forest trees, quality traits involve alterations in the secondary cell wall (SCW) of wood for traditional uses, as well as for a growing diversity of biofuels and bioproducts. Alterations in wood properties that are desirable for specific end uses can have negative effects on growth and stress tolerance. Understanding of the diverse roles of SCW genes is necessary for the genetic improvement of fast-growing, short-rotation trees that face perennial challenges in their growth and development. Here, we review recent progress into the synergies and antagonisms of SCW development and abiotic stress responses, particularly, the roles of transcription factors, SCW biogenesis genes, and paralog evolution.
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Affiliation(s)
| | - Amy M. Brunner
- Department of Forest Resources and Environmental Conservation, Virginia Tech, Blacksburg, VA, United States
| | - Chung-Jui Tsai
- Department of Plant Biology, University of Georgia, Athens, GA, United States
- Department of Genetics, University of Georgia, Athens, GA, United States
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA, United States
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Zhang Y, Showalter AM. CRISPR/Cas9 Genome Editing Technology: A Valuable Tool for Understanding Plant Cell Wall Biosynthesis and Function. FRONTIERS IN PLANT SCIENCE 2020; 11:589517. [PMID: 33329650 PMCID: PMC7714752 DOI: 10.3389/fpls.2020.589517] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 10/23/2020] [Indexed: 05/05/2023]
Abstract
For the past 5 years, clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) technology has appeared in the molecular biology research spotlight. As a game-changing player in genome editing, CRISPR/Cas9 technology has revolutionized animal research, including medical research and human gene therapy as well as plant science research, particularly for crop improvement. One of the most common applications of CRISPR/Cas9 is to generate genetic knock-out mutants. Recently, several multiplex genome editing approaches utilizing CRISPR/Cas9 were developed and applied in various aspects of plant research. Here we summarize these approaches as they relate to plants, particularly with respect to understanding the biosynthesis and function of the plant cell wall. The plant cell wall is a polysaccharide-rich cell structure that is vital to plant cell formation, growth, and development. Humans are heavily dependent on the byproducts of the plant cell wall such as shelter, food, clothes, and fuel. Genes involved in the assembly of the plant cell wall are often highly redundant. To identify these redundant genes, higher-order knock-out mutants need to be generated, which is conventionally done by genetic crossing. Compared with genetic crossing, CRISPR/Cas9 multi-gene targeting can greatly shorten the process of higher-order mutant generation and screening, which is especially useful to characterize cell wall related genes in plant species that require longer growth time. Moreover, CRISPR/Cas9 makes it possible to knock out genes when null T-DNA mutants are not available or are genetically linked. Because of these advantages, CRISPR/Cas9 is becoming an ideal and indispensable tool to perform functional studies in plant cell wall research. In this review, we provide perspectives on how to design CRISPR/Cas9 to achieve efficient gene editing and multi-gene targeting in plants. We also discuss the recent development of the virus-based CRISPR/Cas9 system and the application of CRISPR/Cas9 to knock in genes. Lastly, we summarized current progress on using CRISPR/Cas9 for the characterization of plant cell wall-related genes.
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Affiliation(s)
- Yuan Zhang
- Molecular and Cellular Biology Program, Ohio University, Athens, OH, United States
- Department of Environmental & Plant Biology, Ohio University, Athens, OH, United States
| | - Allan M. Showalter
- Molecular and Cellular Biology Program, Ohio University, Athens, OH, United States
- Department of Environmental & Plant Biology, Ohio University, Athens, OH, United States
- *Correspondence: Allan M. Showalter,
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