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Sikhosana ST, Gumede TP, Malebo NJ, Ogundeji AO, Motloung B. The influence of cellulose content on the morphology, thermal, and mechanical properties of poly(lactic acid)/
Eucomis autumnalis
cellulose biocomposites. POLYM ENG SCI 2023. [DOI: 10.1002/pen.26293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Affiliation(s)
- S. T. Sikhosana
- Department of Life Sciences Central University of Technology Bloemfontein South Africa
| | - T. P. Gumede
- Department of Life Sciences Central University of Technology Bloemfontein South Africa
| | - N. J. Malebo
- Department of Life Sciences Central University of Technology Bloemfontein South Africa
| | - A. O. Ogundeji
- Department of Microbiology and Biochemistry University of Free State Bloemfontein South Africa
| | - B. Motloung
- Department of Life Sciences Central University of Technology Bloemfontein South Africa
- Department of Chemistry and Polymer Science Stellenbosch University Matieland South Africa
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2
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Sharma M, Bhushan S, Sharma D, Kaul S, Dhar MK. A Brief Review of Plant Cell Transfection, Gene Transcript Expression, and Genotypic Integration for Enhancing Compound Production. Methods Mol Biol 2023; 2575:153-179. [PMID: 36301475 DOI: 10.1007/978-1-0716-2716-7_8] [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] [Indexed: 06/16/2023]
Abstract
Plants possess a plethora of important secondary metabolites, which are unique sources of natural pigments, pharmaceutical compounds, food additives, natural pesticides, and other industrial components. The commercial significance of such metabolites/compounds has directed the research toward their production and exploration of methods for enhancement of production. Biotechnological tools are critical in selecting, integrating, multiplying, improving, and analyzing medicinal plants for secondary metabolite production. Out of many techniques that are being explored to enhance secondary metabolite production, "plant cell transfection" is the latest tool to achieve maximum output from the plant source. It is based upon the introduction of foreign DNA into the plant cell relying on physical treatment such as electroporation, cell squeezing, sonoporation, optical transfection nanoparticles, magnetofection, and chemical treatment or biological treatment that depends upon carrier. One of the promising tools that have been exploited is CRISPR-Cas9. Overall, the abovementioned tools focus on the stable transfection of desired gene transcripts. Since the integration and continuous expression of transfected gene of particular trait represents stable transfection of host cell genome, resulting from transfer of required trait to daughter cells ultimately leading to enhanced production of secondary metabolites of interest. This chapter will review a set of biotechnological tools that are candidates for achieving the enhanced bioactive compound production indicated here to be used for drug discovery.
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Affiliation(s)
- Munish Sharma
- Department of Plant Sciences, Central University of Himachal Pradesh, Shahpur, Kangra, Himachal Pradesh, India.
| | - Sakshi Bhushan
- Department of Botany, Central University of Jammu, Jammu, Jammu and Kashmir, India
| | - Deepak Sharma
- Genome Research Laboratory, School of Biotechnology, University of Jammu, Jammu, Jammu and Kashmir, India
| | - Sanjana Kaul
- Genome Research Laboratory, School of Biotechnology, University of Jammu, Jammu, Jammu and Kashmir, India
| | - Manoj K Dhar
- Genome Research Laboratory, School of Biotechnology, University of Jammu, Jammu, Jammu and Kashmir, India
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Nair LG, Agrawal K, Verma P. An insight into the principles of lignocellulosic biomass-based zero-waste biorefineries: a green leap towards imperishable energy-based future. Biotechnol Genet Eng Rev 2022; 38:288-338. [PMID: 35670485 DOI: 10.1080/02648725.2022.2082223] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Lignocellulosic biomass (LCB) is an energy source that has a huge impact in today's world. The depletion of fossil fuels, increased pollution, climatic changes, etc. have led the public and private sectors to move towards sustainability i.e. using LCB for the production of biofuels and value-added compounds. A major bottleneck of the process is the recalcitrant nature of LCB. This can be overcome by using various pretreatment strategies like physical, chemical, biological, physicochemical, etc. Further, the pretreated biomass is made to undergo various steps like hydrolysis, saccharification, etc. for the conversion of value-added products and the remaining waste residues can be further utilized for the synthesis of secondary products thus favouring the zero-waste biorefinery concept. Currently, microorganisms are being explored for their use in biorefinery but the unavailability of commercial strains is a major limitation. Thus, the use of metagenomics can be used to overcome the limitation which is both cost-effective and environmentally friendly. The review deliberates the composition of LCBs, and their recalcitrance nature, followed by the structural changes caused by various pretreatment methods. The further steps in biorefineries, strategies for the development of zero-waste refineries, bottlenecks, and suggestions are also discussed. Special emphasis is given to the use of metagenomics for the discovery of microorganisms efficient for zero-waste biorefineries.
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Affiliation(s)
- Lakshana G Nair
- Bioprocess and Bioenergy Laboratory, Department of Microbiology, Central University of Rajasthan, Kishangarh, Ajmer, India
| | - Komal Agrawal
- Bioprocess and Bioenergy Laboratory, Department of Microbiology, Central University of Rajasthan, Kishangarh, Ajmer, India
| | - Pradeep Verma
- Bioprocess and Bioenergy Laboratory, Department of Microbiology, Central University of Rajasthan, Kishangarh, Ajmer, India
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4
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Genome-wide analysis of the CAD gene family reveals two bona fide CAD genes in oil palm. 3 Biotech 2022; 12:149. [PMID: 35747504 PMCID: PMC9209623 DOI: 10.1007/s13205-022-03208-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 05/21/2022] [Indexed: 11/01/2022] Open
Abstract
Cinnamyl alcohol dehydrogenase (CAD) is the key enzyme for lignin biosynthesis in plants. In this study, genome-wide analysis was performed to identify CAD genes in oil palm (Elaeis guineensis). Phylogenetic analysis was then conducted to select the bona fide EgCADs. The bona fide EgCAD genes and their respective 5' flanking regions were cloned and analysed. Their expression profiles were evaluated in various organs using RT-PCR. Seven EgCAD genes (EgCAD1-7) were identified and divided into four phylogenetic groups. EgCAD1 and EgCAD2 display high sequence similarities with other bona fide CADs and possess all the signature motifs of the bona fide CAD. They also display similar 3D protein structures. Gene expression analysis showed that EgCAD1 was expressed most abundantly in the root tissues, while EgCAD2 was expressed constitutively in all the tissues studied. EgCAD1 possesses only one transcription start site, while EgCAD2 has five. Interestingly, a TC microsatellite was found in the 5' flanking region of EgCAD2. The 5' flanking regions of EgCAD1 and EgCAD2 contain lignin-associated regulatory elements i.e. AC-elements, and other defence-related motifs, including W-box, GT-1 motif and CGTCA-motif. Altogether, these results imply that EgCAD1 and EgCAD2 are bona fide CAD involved in lignin biosynthesis during the normal development of oil palm and in response to stresses. Our findings shed some light on the roles of the bona fide CAD genes in oil palm and pave the way for manipulating lignin content in oil palm through a genetic approach. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03208-0.
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5
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Wang Y, Gui C, Wu J, Gao X, Huang T, Cui F, Liu H, Sethupathy S. Spatio-Temporal Modification of Lignin Biosynthesis in Plants: A Promising Strategy for Lignocellulose Improvement and Lignin Valorization. Front Bioeng Biotechnol 2022; 10:917459. [PMID: 35845403 PMCID: PMC9283729 DOI: 10.3389/fbioe.2022.917459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 06/14/2022] [Indexed: 11/13/2022] Open
Abstract
Lignin is essential for plant growth, structural integrity, biotic/abiotic stress resistance, and water transport. Besides, lignin constitutes 10–30% of lignocellulosic biomass and is difficult to utilize for biofuel production. Over the past few decades, extensive research has uncovered numerous metabolic pathways and genes involved in lignin biosynthesis, several of which have been highlighted as the primary targets for genetic manipulation. However, direct manipulation of lignin biosynthesis is often associated with unexpected abnormalities in plant growth and development for unknown causes, thus limiting the usefulness of genetic engineering for biomass production and utilization. Recent advances in understanding the complex regulatory mechanisms of lignin biosynthesis have revealed new avenues for spatial and temporal modification of lignin in lignocellulosic plants that avoid growth abnormalities. This review explores recent work on utilizing specific transcriptional regulators to modify lignin biosynthesis at both tissue and cellular levels, focusing on using specific promoters paired with functional or regulatory genes to precisely control lignin synthesis and achieve biomass production with desired properties. Further advances in designing more appropriate promoters and other regulators will increase our capacity to modulate lignin content and structure in plants, thus setting the stage for high-value utilization of lignin in the future.
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Affiliation(s)
- Yongli Wang
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
- *Correspondence: Yongli Wang, ; Sivasamy Sethupathy,
| | - Cunjin Gui
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - Jiangyan Wu
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - Xing Gao
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - Ting Huang
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - Fengjie Cui
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Huan Liu
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - Sivasamy Sethupathy
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
- *Correspondence: Yongli Wang, ; Sivasamy Sethupathy,
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6
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Kouhen M, García-Caparrós P, Twyman RM, Abdelly C, Mahmoudi H, Schillberg S, Debez A. Improving environmental stress resilience in crops by genome editing: insights from extremophile plants. Crit Rev Biotechnol 2022; 43:559-574. [PMID: 35606905 DOI: 10.1080/07388551.2022.2042481] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
In basic and applied sciences, genome editing has become an indispensable tool, especially the versatile and adaptable CRISPR/Cas9 system. Using CRISPR/Cas9 in plants has enabled modifications of many valuable traits, including environmental stress tolerance, an essential aspect when it comes to ensuring food security under climate change pressure. The CRISPR toolbox enables faster and more precise plant breeding by facilitating: multiplex gene editing, gene pyramiding, and de novo domestication. In this paper, we discuss the most recent advances in CRISPR/Cas9 and alternative CRISPR-based systems, along with the technical challenges that remain to be overcome. A revision of the latest proof-of-concept and functional characterization studies has indeed provided more insight into the quantitative traits affecting crop yield and stress tolerance. Additionally, we focus on the applications of CRISPR/Cas9 technology in regard to extremophile plants, due to their significance on: industrial, ecological and economic levels. These still unexplored genetic resources could provide the means to harden our crops against the threat of climate change, thus ensuring food security over the next century.
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Affiliation(s)
- Mohamed Kouhen
- Centre of Biotechnology of Borj-Cedria (CBBC), Laboratory of Extremophile Plants (LPE), Hammam-Lif, Tunisia.,Department of Biosciences and Territory, University of Molise, Pesche, Italy
| | - Pedro García-Caparrós
- Agronomy Department of Superior School Engineering, University of Almeria, CIAIMBITAL, Almería, Spain
| | | | - Chedly Abdelly
- Centre of Biotechnology of Borj-Cedria (CBBC), Laboratory of Extremophile Plants (LPE), Hammam-Lif, Tunisia
| | - Henda Mahmoudi
- International Center for Biosaline Agriculture, Academic City, Near Zayed University, Dubai, United Arab Emirates
| | - Stefan Schillberg
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany
| | - Ahmed Debez
- Centre of Biotechnology of Borj-Cedria (CBBC), Laboratory of Extremophile Plants (LPE), Hammam-Lif, Tunisia
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7
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Hlahla JM, Mafa MS, van der Merwe R, Alexander O, Duvenhage MM, Kemp G, Moloi MJ. The Photosynthetic Efficiency and Carbohydrates Responses of Six Edamame ( Glycine max. L. Merrill) Cultivars under Drought Stress. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11030394. [PMID: 35161375 PMCID: PMC8840725 DOI: 10.3390/plants11030394] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/13/2022] [Accepted: 01/14/2022] [Indexed: 05/06/2023]
Abstract
Vegetable-type soybean, also known as edamame, was recently introduced to South Africa. However, there is lack of information on its responses to drought. The aim of this study was to investigate the photosynthetic efficiency and carbohydrates responses of six edamame cultivars under drought stress. Photosynthetic efficiency parameters, including chlorophyll fluorescence and stomatal conductance, were determined using non-invasive methods, while pigments were quantified spectrophotometrically. Non-structural carbohydrates were quantified using Megazyme kits. Structural carbohydrates were determined using Fourier-transform infrared spectroscopy (FTIR) and X-ray diffraction (XRD). Drought stress significantly increased the Fv/Fm and PIabs of AGS429 and UVE17 at pod filling stage. Chlorophyll-a, which was most sensitive to drought, was significantly reduced in AGS429 and UVE17, but chlorophyll-b was relatively stable in all cultivars, except UVE17, which showed a significant decline at flowering stage. AGS354 and AGS429 also showed reduced chlorophyll-b at pod filling. UVE17 showed a significant reduction in carotenoid content and a substantial reduction in stomatal conductance during pod filling. Drought stress during pod filling resulted in a significant increase in the contents of trehalose, sucrose and starch, but glucose was decreased. Chlorophyll-a positively correlated with starch. The FTIR and XRD results suggest that the cell wall of UVE14, followed by UVE8 and AGS429, was the most intact during drought stress. It was concluded that carotenoids, stomatal conductance, starch and hemicellulose could be used as physiological/biochemical indicators of drought tolerance in edamame. This information expands our knowledge of the drought defense responses in edamame, and it is essential for the physiological and biochemical screening of drought tolerance.
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Affiliation(s)
- Jeremiah M. Hlahla
- Department of Plant Sciences-Botany Division, Faculty of Natural and Agricultural Sciences, University of the Free State, 205 Nelson Mandela Drive, Park West, Bloemfontein 9301, South Africa; (J.M.H.); (R.v.d.M.)
| | - Mpho S. Mafa
- Carbohydrates and Enzymology Laboratory (CHEM-LAB), Department of Plant Sciences-Botany Division, University of the Free State, 205 Nelson Mandela Drive, Park West, Bloemfontein 9301, South Africa;
| | - Rouxléne van der Merwe
- Department of Plant Sciences-Botany Division, Faculty of Natural and Agricultural Sciences, University of the Free State, 205 Nelson Mandela Drive, Park West, Bloemfontein 9301, South Africa; (J.M.H.); (R.v.d.M.)
| | - Orbett Alexander
- Department of Chemistry, University of the Free State, 205 Nelson Mandela Drive, Park West, Bloemfontein 9301, South Africa;
| | - Mart-Mari Duvenhage
- Department of Physics, University of the Free State, 205 Nelson Mandela Drive, Park West, Bloemfontein 9301, South Africa;
| | - Gabre Kemp
- Department of Microbiology and Biochemistry, University of the Free State, 205 Nelson Mandela Drive, Park West, Bloemfontein 9301, South Africa;
| | - Makoena J. Moloi
- Department of Plant Sciences-Botany Division, Faculty of Natural and Agricultural Sciences, University of the Free State, 205 Nelson Mandela Drive, Park West, Bloemfontein 9301, South Africa; (J.M.H.); (R.v.d.M.)
- Correspondence: ; Tel.: +27-51-4019483
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8
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Llerena JPP, Figueiredo R, Ferreira SS, Cesarino I, Mazzafera P. Isolation of Promoters and Transcription Factors Involved in the Regulation of Lignin Biosynthesis in Saccharum Species. Methods Mol Biol 2022; 2469:103-118. [PMID: 35508833 DOI: 10.1007/978-1-0716-2185-1_9] [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] [Indexed: 06/14/2023]
Abstract
Sugarcane bagasse has received attention as a raw material for the production of second-generation ethanol (E2G). However, its use is limited because of the cell wall recalcitrance, mostly conferred by lignin. Recently our knowledge of the genes coding for the enzymes of the lignin biosynthesis pathway has increased; however, still little is known about the transcription factors controlling the expression of these genes in sugarcane. Here we describe protocols to optimize the isolation of the promoters of the lignin biosynthetic genes ShCAD8, ShCOMT and ShF5H and the transcription factors (TFs) ShMYB85 and ShMYB58/63 in Saccharum species. To confirm whether these TFs are able to activate the target promoters, a transactivation assay in BY2 protoplasts of Nicotiana tabacum is also detailed.
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Affiliation(s)
| | - Raquel Figueiredo
- Department of Plant Biology, Institute of Biology, State University of Campinas, Campinas, Brazil
- Department of Biology, Faculty of Sciences and LAQV Requimte, Sustainable Chemistry, University of Porto, Porto, Portugal
| | - Sávio Siqueira Ferreira
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX, USA
| | - Igor Cesarino
- Department of Botany, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Paulo Mazzafera
- Department of Plant Biology, Institute of Biology, State University of Campinas, Campinas, Brazil.
- Department of Crop Science, College of Agriculture Luiz de Queiroz, University of São Paulo, Piracicaba, Brazil.
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9
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Biopolymers from Industrial Waste. Biopolymers 2022. [DOI: 10.1007/978-3-030-98392-5_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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10
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Eivazzadeh-Keihan R, Asgharnasl S, Moghim Aliabadi HA, Tahmasebi B, Radinekiyan F, Maleki A, Bahreinizad H, Mahdavi M, Alavijeh MS, Saber R, Lanceros-Méndez S, Shalan AE. Magnetic graphene oxide–lignin nanobiocomposite: a novel, eco-friendly and stable nanostructure suitable for hyperthermia in cancer therapy. RSC Adv 2022; 12:3593-3601. [PMID: 35425373 PMCID: PMC8979318 DOI: 10.1039/d1ra08640e] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 12/27/2021] [Indexed: 01/10/2023] Open
Abstract
A novel nanobiocomposite was designed and synthesized under mild conditions to evaluate its potential in hyperthermia therapy.
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Affiliation(s)
- Reza Eivazzadeh-Keihan
- Catalysts and Organic Synthesis Research Laboratory, Department of Chemistry, Iran University of Science and Technology, Tehran 16846-13114, Iran
| | - Somayeh Asgharnasl
- Catalysts and Organic Synthesis Research Laboratory, Department of Chemistry, Iran University of Science and Technology, Tehran 16846-13114, Iran
| | - Hooman Aghamirza Moghim Aliabadi
- Protein Chemistry Laboratory, Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
- Advanced Chemistry Studies Lab, Department of Chemistry, K. N. Toosi University of Technology, Tehran, Iran
| | - Behnam Tahmasebi
- School of Chemistry, College of Science, University of Tehran, Tehran, Iran
| | - Fateme Radinekiyan
- Catalysts and Organic Synthesis Research Laboratory, Department of Chemistry, Iran University of Science and Technology, Tehran 16846-13114, Iran
| | - Ali Maleki
- Catalysts and Organic Synthesis Research Laboratory, Department of Chemistry, Iran University of Science and Technology, Tehran 16846-13114, Iran
| | - Hossein Bahreinizad
- Mechanical Engineering Department, Sahand University of Technology, Tabriz, Iran
| | - Mohammad Mahdavi
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Reza Saber
- Research Center for Science and Technology in Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Department of Medical Nanotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Senentxu Lanceros-Méndez
- BCMaterials, Basque Center for Materials, Applications and Nanostructures, Martina Casiano, UPV/EHU Science Park, Barrio Sarriena s/n, Leioa 48940, Spain
- IKERBASQUE, Basque Foundation for Science, 48009 Bilbao, Spain
| | - Ahmed Esmail Shalan
- BCMaterials, Basque Center for Materials, Applications and Nanostructures, Martina Casiano, UPV/EHU Science Park, Barrio Sarriena s/n, Leioa 48940, Spain
- Central Metallurgical Research and Development Institute (CMRDI), P. O. Box 87, Helwan, Cairo 11421, Egypt
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Mohan C, Easterling M, Yau YY. Gene Editing Technologies for Sugarcane Improvement: Opportunities and Limitations. SUGAR TECH : AN INTERNATIONAL JOURNAL OF SUGAR CROPS & RELATED INDUSTRIES 2022; 24:369-385. [PMID: 34667393 PMCID: PMC8517945 DOI: 10.1007/s12355-021-01045-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Accepted: 08/07/2021] [Indexed: 05/05/2023]
Abstract
Plant-based biofuels present a promising alternative to depleting non-renewable fuel resources. One of the benefits of biofuel is reduced environmental impact, including reduction in greenhouse gas emission which causes climate change. Sugarcane is one of the most important bioenergy crops. Sugarcane juice is used to produce table sugar and first-generation biofuel (e.g., bioethanol). Sugarcane bagasse is also a potential material for second-generation cellulosic biofuel production. Researchers worldwide are striving to improve sugarcane biomass yield and quality by a variety of means including biotechnological tools. This paper reviews the use of sugarcane as a feedstock for biofuel production, and gene manipulation tools and approaches, including RNAi and genome-editing tools, such as TALENs and CRISPR-Cas9, for improving its quality. The specific focus here is on CRISPR system because it is low cost, simple in design and versatile compared to other genome-editing tools. The advance of CRISPR-Cas9 technology has transformed plant research with its ability to precisely delete, insert or replace genes in recent years. Lignin is the primary material responsible for biomass recalcitrance in biofuel production. The use of genome editing technology to modify lignin composition and distribution in sugarcane cell wall has been realized. The current and potential applications of genome editing technology for sugarcane improvement are discussed. The advantages and limitations of utilizing RNAi and TALEN techniques in sugarcane improvement are discussed as well.
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Affiliation(s)
- Chakravarthi Mohan
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil
| | - Mona Easterling
- Department of Natural Sciences, Northeastern State University, Broken Arrow, OK 74014 USA
- Northeast Campus, Tulsa Community College, 3727 East Apache St, Tulsa, OK 74115 USA
| | - Yuan-Yeu Yau
- Department of Natural Sciences, Northeastern State University, Broken Arrow, OK 74014 USA
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12
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Wang X, Chao N, Zhang A, Kang J, Jiang X, Gai Y. Systematic Analysis and Biochemical Characterization of the Caffeoyl Shikimate Esterase Gene Family in Poplar. Int J Mol Sci 2021; 22:ijms222413366. [PMID: 34948162 PMCID: PMC8704367 DOI: 10.3390/ijms222413366] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/09/2021] [Accepted: 12/10/2021] [Indexed: 02/07/2023] Open
Abstract
Caffeoyl shikimate esterase (CSE) hydrolyzes caffeoyl shikimate into caffeate and shikimate in the phenylpropanoid pathway. In this study, we performed a systematic analysis of the CSE gene family and investigated the possible roles of CSE and CSE-like genes in Populus. We conducted a genome-wide analysis of the CSE gene family, including functional and phylogenetic analyses of CSE and CSE-like genes, using the poplar (Populus trichocarpa) genome. Eighteen CSE and CSE-like genes were identified in the Populus genome, and five phylogenetic groups were identified from phylogenetic analysis. CSEs in Group Ia, which were proposed as bona fide CSEs, have probably been lost in most monocots except Oryza sativa. Primary functional classification showed that PoptrCSE1 and PoptrCSE2 had putative function in lignin biosynthesis. In addition, PoptrCSE2, along with PoptrCSE12, might also respond to stress with a function in cell wall biosynthesis. Enzymatic assay of PoptoCSE1 (Populus tomentosa), -2 and -12 showed that PoptoCSE1 and -2 maintained CSE activity. PoptoCSE1 and 2 had similar biochemical properties, tissue expression patterns and subcellular localization. Most of the PoptrCSE-like genes are homologs of AtMAGL (monoacylglycerol lipase) genes in Arabidopsis and may function as MAG lipase in poplar. Our study provides a systematic understanding of this novel gene family and suggests the function of CSE in monolignol biosynthesis in Populus.
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Affiliation(s)
- Xuechun Wang
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; (X.W.); (N.C.); (A.Z.); (J.K.); (X.J.)
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory, National Forestry and Grassland Administration, Beijing 100083, China
- National Engineering Laboratory for Tree Breeding, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing 100083, China
| | - Nan Chao
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; (X.W.); (N.C.); (A.Z.); (J.K.); (X.J.)
- Jiangsu Key Laboratory of Sericutural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212018, China
| | - Aijing Zhang
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; (X.W.); (N.C.); (A.Z.); (J.K.); (X.J.)
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory, National Forestry and Grassland Administration, Beijing 100083, China
- National Engineering Laboratory for Tree Breeding, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing 100083, China
| | - Jiaqi Kang
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; (X.W.); (N.C.); (A.Z.); (J.K.); (X.J.)
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory, National Forestry and Grassland Administration, Beijing 100083, China
- National Engineering Laboratory for Tree Breeding, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing 100083, China
| | - Xiangning Jiang
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; (X.W.); (N.C.); (A.Z.); (J.K.); (X.J.)
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory, National Forestry and Grassland Administration, Beijing 100083, China
- National Engineering Laboratory for Tree Breeding, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing 100083, China
| | - Ying Gai
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; (X.W.); (N.C.); (A.Z.); (J.K.); (X.J.)
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory, National Forestry and Grassland Administration, Beijing 100083, China
- National Engineering Laboratory for Tree Breeding, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing 100083, China
- Correspondence: ; Tel.: +86-10-6233-8063
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Xin A, Herburger K. Precursor biosynthesis regulation of lignin, suberin and cutin. PROTOPLASMA 2021; 258:1171-1178. [PMID: 34120228 DOI: 10.1007/s00709-021-01676-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 06/01/2021] [Indexed: 06/12/2023]
Abstract
The extracellular matrix of plants can contain the hydrophobic biopolymers lignin, suberin and/or cutin, which provide mechanical strength and limit water loss and pathogen invasion. Due to their remarkable chemical resistance, these polymers have a high potential in various biotechnological applications and can replace petrol-based resources, for example, in the packing industry. However, despite the importance of these polymers, the regulation of their precursor biosynthesis is far from being fully understood. This is particularly true for suberin and cutin, which hinders efforts to engineer their formation in plants and produce customised biopolymers. This review brings attention to knowledge gaps in the current research and highlights some of the most recent findings on transcription factors that regulate lignin, suberin and cutin precursor biosynthesis. Finally, we also briefly discuss how some of the remaining knowledge gaps can be closed.
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Affiliation(s)
- Anzhou Xin
- Section for Plant Glycobiology, Department of Plant and Environmental Sciences, University of Copenhagen, 1871, Frederiksberg, Denmark
| | - Klaus Herburger
- Section for Plant Glycobiology, Department of Plant and Environmental Sciences, University of Copenhagen, 1871, Frederiksberg, Denmark.
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14
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Lin CY, Sun Y, Song J, Chen HC, Shi R, Yang C, Liu J, Tunlaya-Anukit S, Liu B, Loziuk PL, Williams CM, Muddiman DC, Lin YCJ, Sederoff RR, Wang JP, Chiang VL. Enzyme Complexes of Ptr4CL and PtrHCT Modulate Co-enzyme A Ligation of Hydroxycinnamic Acids for Monolignol Biosynthesis in Populus trichocarpa. FRONTIERS IN PLANT SCIENCE 2021; 12:727932. [PMID: 34691108 PMCID: PMC8527181 DOI: 10.3389/fpls.2021.727932] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 09/13/2021] [Indexed: 06/13/2023]
Abstract
Co-enzyme A (CoA) ligation of hydroxycinnamic acids by 4-coumaric acid:CoA ligase (4CL) is a critical step in the biosynthesis of monolignols. Perturbation of 4CL activity significantly impacts the lignin content of diverse plant species. In Populus trichocarpa, two well-studied xylem-specific Ptr4CLs (Ptr4CL3 and Ptr4CL5) catalyze the CoA ligation of 4-coumaric acid to 4-coumaroyl-CoA and caffeic acid to caffeoyl-CoA. Subsequently, two 4-hydroxycinnamoyl-CoA:shikimic acid hydroxycinnamoyl transferases (PtrHCT1 and PtrHCT6) mediate the conversion of 4-coumaroyl-CoA to caffeoyl-CoA. Here, we show that the CoA ligation of 4-coumaric and caffeic acids is modulated by Ptr4CL/PtrHCT protein complexes. Downregulation of PtrHCTs reduced Ptr4CL activities in the stem-differentiating xylem (SDX) of transgenic P. trichocarpa. The Ptr4CL/PtrHCT interactions were then validated in vivo using biomolecular fluorescence complementation (BiFC) and protein pull-down assays in P. trichocarpa SDX extracts. Enzyme activity assays using recombinant proteins of Ptr4CL and PtrHCT showed elevated CoA ligation activity for Ptr4CL when supplemented with PtrHCT. Numerical analyses based on an evolutionary computation of the CoA ligation activity estimated the stoichiometry of the protein complex to consist of one Ptr4CL and two PtrHCTs, which was experimentally confirmed by chemical cross-linking using SDX plant protein extracts and recombinant proteins. Based on these results, we propose that Ptr4CL/PtrHCT complexes modulate the metabolic flux of CoA ligation for monolignol biosynthesis during wood formation in P. trichocarpa.
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Affiliation(s)
- Chien-Yuan Lin
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Yi Sun
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Jina Song
- Department of Electrical and Computer Engineering, North Carolina State University, Raleigh, NC, United States
| | - Hsi-Chuan Chen
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
| | - Rui Shi
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
| | - Chenmin Yang
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
| | - Jie Liu
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
| | - Sermsawat Tunlaya-Anukit
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
| | - Baoguang Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- Department of Forestry, Beihua University, Jilin, China
| | - Philip L. Loziuk
- W.M. Keck FTMS Laboratory, Department of Chemistry, North Carolina State University, Raleigh, NC, United States
| | - Cranos M. Williams
- Department of Electrical and Computer Engineering, North Carolina State University, Raleigh, NC, United States
| | - David C. Muddiman
- W.M. Keck FTMS Laboratory, Department of Chemistry, North Carolina State University, Raleigh, NC, United States
| | - Ying-Chung Jimmy Lin
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Ronald R. Sederoff
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
| | - Jack P. Wang
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Vincent L. Chiang
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
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15
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Optimization of hydrolases production from cassava peels by Trametes polyzona BKW001. SCIENTIFIC AFRICAN 2021. [DOI: 10.1016/j.sciaf.2021.e00835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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16
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Reijngoud J, Arentshorst M, Ruijmbeek C, Reid I, Alazi ED, Punt PJ, Tsang A, Ram AFJ. Loss of function of the carbon catabolite repressor CreA leads to low but inducer-independent expression from the feruloyl esterase B promoter in Aspergillus niger. Biotechnol Lett 2021; 43:1323-1336. [PMID: 33738610 PMCID: PMC8197723 DOI: 10.1007/s10529-021-03104-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 02/08/2021] [Indexed: 11/26/2022]
Abstract
Objective
With the aim to decipher the mechanisms involved in the transcriptional regulation of feruloyl esterase encoded by faeB, a genetic screen was performed to isolate A. niger mutants displaying inducer-independent expression from the faeB promoter.
Result PfaeB-amdS and PfaeB-lux dual reporter strains were constructed and used to isolate trans-acting mutants in which the expression of both reporters was increased, based on the ability to grow on acetamide plates and higher luciferase activity, respectively. The genetic screen on the non-inducing carbon source D-fructose yielded in total 111 trans-acting mutants. The genome of one of the mutants was sequenced and revealed several SNPs, including a point mutation in the creA gene encoding a transcription factor known to be involved in carbon catabolite repression. Subsequently, all mutants were analyzed for defects in carbon catabolite repression by determining sensitivity towards allyl alcohol. All except four of the 111 mutants were sensitive to allyl alcohol, indicating that the vast majority of the mutants are defective in carbon catabolite repression. The creA gene of 32 allyl alcohol sensitive mutants was sequenced and 27 of them indeed contained a mutation in the creA gene. Targeted deletion of creA in the reporter strain confirmed that the loss of CreA results in constitutive expression from the faeB promoter. Conclusion
Loss of function of CreA leads to low but inducer-independent expression from the faeB promoter in A. niger. Supplementary Information The online version contains supplementary material available at 10.1007/s10529-021-03104-2.
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Affiliation(s)
- Jos Reijngoud
- Molecular Microbiology and Biotechnology, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
- Bioscienz, Goeseelsstraat 10, 4817 MV, Breda, The Netherlands
| | - Mark Arentshorst
- Molecular Microbiology and Biotechnology, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Claudine Ruijmbeek
- Molecular Microbiology and Biotechnology, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Ian Reid
- Centre for Structural and Functional Genomics, Concordia University, Montreal, Canada
| | - Ebru Demirci Alazi
- Molecular Microbiology and Biotechnology, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Peter J Punt
- Molecular Microbiology and Biotechnology, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
- Dutch DNA Biotech, Hugo R Kruytgebouw 4-Noord, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Adrian Tsang
- Centre for Structural and Functional Genomics, Concordia University, Montreal, Canada
| | - Arthur F J Ram
- Molecular Microbiology and Biotechnology, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands.
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17
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Chao N, Qi Q, Li S, Ruan B, Jiang X, Gai Y. Characterization and functional analysis of the Hydroxycinnamoyl-CoA: shikimate hydroxycinnamoyl transferase (HCT) gene family in poplar. PeerJ 2021; 9:e10741. [PMID: 33665007 PMCID: PMC7916539 DOI: 10.7717/peerj.10741] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 12/18/2020] [Indexed: 12/24/2022] Open
Abstract
Hydroxycinnamoyl-CoA: shikimate hydroxycinnamoyl transferase (HCT) divides the mass flux to H, G and S units in monolignol biosynthesis and affects lignin content. Ten HCT homologs were identified in the Populus trichocarpa (Torr. & Gray) genome. Both genome duplication and tandem duplication resulted in the expansion of HCT orthologs in Populus. Comprehensive analysis including motif analysis, phylogenetic analysis, expression profiles and co-expression analysis revealed the divergence and putative function of these candidate PoptrHCTs. PoptrHCT1 and 2 were identified as likely involved in lignin biosynthesis. PoptrHCT9 and 10- are likely to be involved in plant development and the response to cold stress. Similar functional divergence was also identified in Populus tomentosa Carr. Enzymatic assay of PtoHCT1 showed that PtoHCT1 was able to synthesize caffeoyl shikimate using caffeoyl-CoA and shikimic acid as substrates.
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Affiliation(s)
- Nan Chao
- School of Life Science, Tsinghua University, Beijing, China.,College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China.,School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Qi Qi
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China.,College of Horticulture, China Agricultural University, Beijing, China
| | - Shuang Li
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Brent Ruan
- Department of Agricultural and Biological Engineering, University of Illinois at Urbana Champaign, Urbana Champaign, IL, USA
| | - Xiangning Jiang
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China.,National Engineering Laboratory for Tree Breeding, the Tree and Ornamental Plant Breeding and Biotechnology Laboratory of Chinese Forestry Administration, Beijing, China
| | - Ying Gai
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China.,National Engineering Laboratory for Tree Breeding, the Tree and Ornamental Plant Breeding and Biotechnology Laboratory of Chinese Forestry Administration, Beijing, China
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18
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Genome-wide analysis of general phenylpropanoid and monolignol-specific metabolism genes in sugarcane. Funct Integr Genomics 2021; 21:73-99. [PMID: 33404914 DOI: 10.1007/s10142-020-00762-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 11/23/2020] [Accepted: 11/27/2020] [Indexed: 10/22/2022]
Abstract
Lignin is the main component of secondary cell walls and is essential for plant development and defense. However, lignin is recognized as a major recalcitrant factor for efficiency of industrial biomass processing. Genes involved in general phenylpropanoid and monolignol-specific metabolism in sugarcane have been previously analyzed at the transcriptomic level. Nevertheless, the number of genes identified in this species is still very low. The recently released sugarcane genome sequence has allowed the genome-wide characterization of the 11 gene families involved in the monolignol biosynthesis branch of the phenylpropanoid pathway. After an exhaustive analysis of sugarcane genomes, 438 haplotypes derived from 175 candidate genes from Saccharum spontaneum and 144 from Saccharum hybrid R570 were identified as associated with this biosynthetic route. The phylogenetic analyses, combined with the search for protein conserved residues involved in the catalytic activity of the encoded enzymes, were employed to identify the family members potentially involved in developmental lignification. Accordingly, 15 candidates were identified as bona fide lignin biosynthesis genes: PTAL1, PAL2, C4H4, 4CL1, HCT1, HCT2, C3'H1, C3'H2, CCoAOMT1, COMT1, F5H1, CCR1, CCR2, CAD2, and CAD7. For this core set of lignin biosynthetic genes, we searched for the chromosomal location, the gene expression pattern, the promoter cis-acting elements, and microRNA targets. Altogether, our results present a comprehensive characterization of sugarcane general phenylpropanoid and monolignol-specific genes, providing the basis for further functional studies focusing on lignin biosynthesis manipulation and biotechnological strategies to improve sugarcane biomass utilization.
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19
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Weiss R, Guebitz GM, Pellis A, Nyanhongo GS. Harnessing the Power of Enzymes for Tailoring and Valorizing Lignin. Trends Biotechnol 2020; 38:1215-1231. [PMID: 32423726 DOI: 10.1016/j.tibtech.2020.03.010] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 03/17/2020] [Accepted: 03/19/2020] [Indexed: 02/07/2023]
Abstract
Lignin, a structural component of lignocellulosic plants, is an alternative raw material with enormous potential to replace diminishing fossil-based resources for the sustainable production of many chemicals and materials. Unfortunately, lignin's heterogeneity, low reactivity, and strong intra- and intermolecular hydrogen interactions and modifications introduced during the pulping process present significant technical challenges. However, the increasing ability to tailor lignin biosynthesis pathways by targeting enzymes and the continued discovery of more robust biocatalysts are enabling the synthesis of novel valuable products. This review summarizes how enzymes involved in lignin biosynthesis pathways and microbial enzymes are being harnessed to produce chemicals and materials and to upgrade lignin properties for the synthesis of a variety of value-added lignin industrial products.
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Affiliation(s)
- Renate Weiss
- University of Natural Resources and Life Sciences, Vienna, Institute of Environmental Biotechnology, Konrad Lorenz Straße 20, 3430, Tulln an der Donau, Austria
| | - Georg M Guebitz
- University of Natural Resources and Life Sciences, Vienna, Institute of Environmental Biotechnology, Konrad Lorenz Straße 20, 3430, Tulln an der Donau, Austria; Austrian Centre for Industrial Biotechnology (ACIB), Konrad Lorenz Strasse 20, 3430, Tulln an der Donau, Austria
| | - Alessandro Pellis
- University of Natural Resources and Life Sciences, Vienna, Institute of Environmental Biotechnology, Konrad Lorenz Straße 20, 3430, Tulln an der Donau, Austria
| | - Gibson S Nyanhongo
- University of Natural Resources and Life Sciences, Vienna, Institute of Environmental Biotechnology, Konrad Lorenz Straße 20, 3430, Tulln an der Donau, Austria; Austrian Centre for Industrial Biotechnology (ACIB), Konrad Lorenz Strasse 20, 3430, Tulln an der Donau, Austria.
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20
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Straub CT, Bing RG, Wang JP, Chiang VL, Adams MWW, Kelly RM. Use of the lignocellulose-degrading bacterium Caldicellulosiruptor bescii to assess recalcitrance and conversion of wild-type and transgenic poplar. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:43. [PMID: 32180826 PMCID: PMC7065347 DOI: 10.1186/s13068-020-01675-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 02/04/2020] [Indexed: 06/10/2023]
Abstract
BACKGROUND Biological conversion of lignocellulosic biomass is significantly hindered by feedstock recalcitrance, which is typically assessed through an enzymatic digestion assay, often preceded by a thermal and/or chemical pretreatment. Here, we assay 17 lines of unpretreated transgenic black cottonwood (Populus trichocarpa) utilizing a lignocellulose-degrading, metabolically engineered bacterium, Caldicellulosiruptor bescii. The poplar lines were assessed by incubation with an engineered C. bescii strain that solubilized and converted the hexose and pentose carbohydrates to ethanol and acetate. The resulting fermentation titer and biomass solubilization were then utilized as a measure of biomass recalcitrance and compared to data previously reported on the transgenic poplar samples. RESULTS Of the 17 transgenic poplar lines examined with C. bescii, a wide variation in solubilization and fermentation titer was observed. While the wild type poplar control demonstrated relatively high recalcitrance with a total solubilization of only 20% and a fermentation titer of 7.3 mM, the transgenic lines resulted in solubilization ranging from 15 to 79% and fermentation titers from 6.8 to 29.6 mM. Additionally, a strong inverse correlation (R 2 = 0.8) between conversion efficiency and lignin content was observed with lower lignin samples more easily converted and solubilized by C. bescii. CONCLUSIONS Feedstock recalcitrance can be significantly reduced with transgenic plants, but finding the correct modification may require a large sample set to identify the most advantageous genetic modifications for the feedstock. Utilizing C. bescii as a screening assay for recalcitrance, poplar lines with down-regulation of coumarate 3-hydroxylase 3 (C3H3) resulted in the highest degrees of solubilization and conversion by C. bescii. One such line, with a growth phenotype similar to the wild-type, generated more than three times the fermentation products of the wild-type poplar control, suggesting that excellent digestibility can be achieved without compromising fitness of the tree.
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Affiliation(s)
- Christopher T. Straub
- Department of Chemical and Biomolecular Engineering, North Carolina State University, EB-1, 911 Partners Way, Raleigh, NC 27695-7905 USA
| | - Ryan G. Bing
- Department of Chemical and Biomolecular Engineering, North Carolina State University, EB-1, 911 Partners Way, Raleigh, NC 27695-7905 USA
| | - Jack P. Wang
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695 USA
| | - Vincent L. Chiang
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695 USA
| | - Michael W. W. Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602 USA
| | - Robert M. Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University, EB-1, 911 Partners Way, Raleigh, NC 27695-7905 USA
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21
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Functional Characteristics of Caffeoyl Shikimate Esterase in Larix Kaempferi and Monolignol Biosynthesis in Gymnosperms. Int J Mol Sci 2019; 20:ijms20236071. [PMID: 31810184 PMCID: PMC6929169 DOI: 10.3390/ijms20236071] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 11/19/2019] [Accepted: 11/26/2019] [Indexed: 02/06/2023] Open
Abstract
Caffeoyl shikimate esterase (CSE) has been reported to be involved in lignin biosynthesis; however, studies of CSE in gymnosperms are lacking. In this study, CSE was successfully cloned from Larix kaempferi (LkCSE) based on Larix laricina transcriptome screening. LkCSE was likely to have catalytic activity based on homologous sequence alignment and phylogenetic analyses of CSEs from different species. In vitro assays with the recombinant enzyme validated the catalytic activity of LkCSE, indicating its function in converting caffeoyl shikimate into caffeate and shikimate. Additionally, the optimum reaction pH and temperature of LkCSE were determined to be 6.0 and 30 °C, respectively. The values of Km and Vmax of CSE for caffeoyl shikimate were 98.11 μM and 14.44 nM min-1, respectively. Moreover, LkCSE was observed to have tissue expression specificity and was abundantly expressed in stems and leaves, especially stems, which was 50 times higher than the expression levels of roots. Lastly, translational fusion assays using LkCSE fused with green fluorescent proteins (GFP) in tobacco leaves indicated that LkCSE was localized in the plasma membrane and endoplasmic reticulum (ER). These results revealed that CSE clearly functions in gymnosperms and it is possible for LkCSE to interact with other ER-resident proteins and regulate mass flux in the monolignol biosynthesis pathway.
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22
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Yang Y, Yoo CG, Rottmann W, Winkeler KA, Collins CM, Gunter LE, Jawdy SS, Yang X, Pu Y, Ragauskas AJ, Tuskan GA, Chen JG. PdWND3A, a wood-associated NAC domain-containing protein, affects lignin biosynthesis and composition in Populus. BMC PLANT BIOLOGY 2019; 19:486. [PMID: 31711424 PMCID: PMC6849256 DOI: 10.1186/s12870-019-2111-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 10/31/2019] [Indexed: 05/21/2023]
Abstract
BACKGROUND Plant secondary cell wall is a renewable feedstock for biofuels and biomaterials production. Arabidopsis VASCULAR-RELATED NAC DOMAIN (VND) has been demonstrated to be a key transcription factor regulating secondary cell wall biosynthesis. However, less is known about its role in the woody species. RESULTS Here we report the functional characterization of Populus deltoides WOOD-ASSOCIATED NAC DOMAIN protein 3 (PdWND3A), a sequence homolog of Arabidopsis VND4 and VND5 that are members of transcription factor networks regulating secondary cell wall biosynthesis. PdWND3A was expressed at higher level in the xylem than in other tissues. The stem tissues of transgenic P. deltoides overexpressing PdWND3A (OXPdWND3A) contained more vessel cells than that of wild-type plants. Furthermore, lignin content and lignin monomer syringyl and guaiacyl (S/G) ratio were higher in OXPdWND3A transgenic plants than in wild-type plants. Consistent with these observations, the expression of FERULATE 5-HYDROXYLASE1 (F5H1), encoding an enzyme involved in the biosynthesis of sinapyl alcohol (S unit monolignol), was elevated in OXPdWND3A transgenic plants. Saccharification analysis indicated that the rate of sugar release was reduced in the transgenic plants. In addition, OXPdWND3A transgenic plants produced lower amounts of biomass than wild-type plants. CONCLUSIONS PdWND3A affects lignin biosynthesis and composition and negatively impacts sugar release and biomass production.
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Affiliation(s)
- Yongil Yang
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Chang Geun Yoo
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- UT-ORNL Joint Institute for Biological Science, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | | | | | | | - Lee E. Gunter
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Sara S. Jawdy
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Xiaohan Yang
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Yunqiao Pu
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- UT-ORNL Joint Institute for Biological Science, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Arthur J. Ragauskas
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- UT-ORNL Joint Institute for Biological Science, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Department of Chemical and Biomolecular Engineering & Department of Forestry, Wildlife, and Fisheries, University of Tennessee, Knoxville, TN 37996 USA
| | - Gerald A. Tuskan
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Jin-Gui Chen
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
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23
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Bhatia R, Dalton S, Roberts LA, Moron-Garcia OM, Iacono R, Kosik O, Gallagher JA, Bosch M. Modified expression of ZmMYB167 in Brachypodium distachyon and Zea mays leads to increased cell wall lignin and phenolic content. Sci Rep 2019; 9:8800. [PMID: 31217516 PMCID: PMC6584667 DOI: 10.1038/s41598-019-45225-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 05/31/2019] [Indexed: 01/01/2023] Open
Abstract
One of the challenges to enable targeted modification of lignocellulosic biomass from grasses for improved biofuel and biochemical production lies within our limited understanding of the transcriptional control of secondary cell wall biosynthesis. Here, we investigated the role of the maize MYB transcription factor ZmMYB167 in secondary cell wall biosynthesis and how modified ZmMYB167 expression in two distinct grass model species affects plant biomass and growth phenotypes. Heterologous expression of ZmMYB167 in the C3 model system Brachypodium led to mild dwarf phenotypes, increased lignin (~7% to 13%) and S-lignin monomer (~11% to 16%) content, elevated concentrations of cell wall-bound p-coumaric acid (~15% to 24%) and reduced biomass sugar release (~20%) compared to controls. Overexpression of ZmMYB167 in the C4 model system Zea mays increased lignin (~4% to 13%), p-coumaric acid (~8% to 52%) and ferulic acid (~13% to 38%) content but did not affect plant growth and development nor biomass recalcitrance. Taken together, modifying ZmMYB167 expression represents a target to alter lignin and phenolic content in grasses. The ZmMYB167 expression-induced discrepancies in plant phenotypic and biomass properties between the two grass model systems highlight the challenges and opportunities for MYB transcription factor-based genetic engineering approaches of grass biomass.
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Affiliation(s)
- Rakesh Bhatia
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Plas Gogerddan, Aberystwyth, SY23 3EE, UK.
| | - Sue Dalton
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Plas Gogerddan, Aberystwyth, SY23 3EE, UK
| | - Luned A Roberts
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Plas Gogerddan, Aberystwyth, SY23 3EE, UK
| | - Odin M Moron-Garcia
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Plas Gogerddan, Aberystwyth, SY23 3EE, UK
| | - Rosario Iacono
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Plas Gogerddan, Aberystwyth, SY23 3EE, UK
| | - Ondrej Kosik
- Rothamsted Research, West Common, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - Joe A Gallagher
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Plas Gogerddan, Aberystwyth, SY23 3EE, UK
| | - Maurice Bosch
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Plas Gogerddan, Aberystwyth, SY23 3EE, UK.
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24
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Pazhany AS, Henry RJ. Genetic Modification of Biomass to Alter Lignin Content and Structure. Ind Eng Chem Res 2019. [DOI: 10.1021/acs.iecr.9b01163] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Adhini S. Pazhany
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, 4072 Queensland, Australia
- ICAR - Sugarcane Breeding Institute, Coimbatore, 641 007 Tamil Nadu, India
| | - Robert J. Henry
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, 4072 Queensland, Australia
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25
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Abstract
We used primers designed on conserved gene regions of several species to isolate the most expressed genes of the lignin pathway in four Saccharum species. S. officinarum and S. barberi have more sucrose in the culms than S. spontaneum and S. robustum, but less polysaccharides and lignin in the cell wall. S. spontaneum, and S. robustum had the lowest S/G ratio and a lower rate of saccharification in mature internodes. Surprisingly, except for CAD, 4CL, and CCoAOMT for which we found three, two, and two genes, respectively, only one gene was found for the other enzymes and their sequences were highly similar among the species. S. spontaneum had the highest expression for most genes. CCR and CCoAOMT B presented the highest expression; 4CL and F5H showed increased expression in mature tissues; C3H and CCR had higher expression in S. spontaneum, and one of the CADs isolated (CAD B) had higher expression in S. officinarum. The similarity among the most expressed genes isolated from these species was unexpected and indicated that lignin biosynthesis is conserved in Saccharum including commercial varieties Thus the lignin biosynthesis control in sugarcane may be only fully understood with the knowledge of the promotor region of each gene.
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Mohapatra S, Mishra C, Merritt BB, Pattathil S, Thatoi H. Evaluating the Role of Ultrasonication-Assisted Alkali Pretreatment and Enzymatic Hydrolysis on Cellwall Polysaccharides of Pennisetum
Grass Varieties as Potential Biofuel Feedstock. ChemistrySelect 2019. [DOI: 10.1002/slct.201802187] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Sonali Mohapatra
- Department of Biotechnology; College of Engineering and Technology; Biju Pattnaik University of Technology; Bhubaneswar- 751003 India
| | - Chinmaya Mishra
- Department of Biotechnology; College of Engineering and Technology; Biju Pattnaik University of Technology; Bhubaneswar- 751003 India
| | - Brian B Merritt
- Complex Carbohydrate Research Center; University of Georgia, GA 30602 USA and BioEnergy Science Center (BESC); Oak Ridge National Laboratory; Oak Ridge, TN 37831 USA
| | - Sivakumar Pattathil
- Complex Carbohydrate Research Center; University of Georgia, GA 30602 USA and BioEnergy Science Center (BESC); Oak Ridge National Laboratory; Oak Ridge, TN 37831 USA
| | - Hrudayanath Thatoi
- Department of Biotechnology; North Orissa University; Sriram Chandra vihar, Takatpur Baripada- 757003, Odisha India
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27
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Kang X, Kirui A, Dickwella Widanage MC, Mentink-Vigier F, Cosgrove DJ, Wang T. Lignin-polysaccharide interactions in plant secondary cell walls revealed by solid-state NMR. Nat Commun 2019; 10:347. [PMID: 30664653 PMCID: PMC6341099 DOI: 10.1038/s41467-018-08252-0] [Citation(s) in RCA: 205] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 12/19/2018] [Indexed: 01/16/2023] Open
Abstract
Lignin is a complex aromatic biopolymer that strengthens and waterproofs plant secondary cell walls, enabling mechanical stability in trees and long-distance water transport in xylem. Lignin removal is a key step in paper production and biomass conversion to biofuels, motivating efforts to re-engineer lignin biosynthesis. However, the physical nature of lignin's interactions with wall polysaccharides is not well understood. Here we show that lignin self-aggregates to form highly hydrophobic and dynamically unique nanodomains, with extensive surface contacts to xylan. Solid-state NMR spectroscopy of intact maize stems, supported by dynamic nuclear polarization, reveals that lignin has abundant electrostatic interactions with the polar motifs of xylan. Lignin preferentially binds xylans with 3-fold or distorted 2-fold helical screw conformations, indicative of xylans not closely associated with cellulose. These findings advance our knowledge of the molecular-level organization of lignocellulosic biomass, providing the structural foundation for optimization of post-harvest processing for biofuels and biomaterials.
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Affiliation(s)
- Xue Kang
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Alex Kirui
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, USA
| | | | | | - Daniel J Cosgrove
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Tuo Wang
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, USA.
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28
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Huang J, Xia T, Li G, Li X, Li Y, Wang Y, Wang Y, Chen Y, Xie G, Bai FW, Peng L, Wang L. Overproduction of native endo-β-1,4-glucanases leads to largely enhanced biomass saccharification and bioethanol production by specific modification of cellulose features in transgenic rice. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:11. [PMID: 30636971 PMCID: PMC6325865 DOI: 10.1186/s13068-018-1351-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 12/29/2018] [Indexed: 05/03/2023]
Abstract
BACKGROUND Genetic modification of plant cell walls has been implemented to reduce lignocellulosic recalcitrance for biofuel production. Plant glycoside hydrolase family 9 (GH9) comprises endo-β-1,4-glucanase in plants. Few studies have examined the roles of GH9 in cell wall modification. In this study, we independently overexpressed two genes from GH9B subclasses (OsGH9B1 and OsGH9B3) and examined cell wall features and biomass saccharification in transgenic rice plants. RESULTS Compared with the wild type (WT, Nipponbare), the OsGH9B1 and OsGH9B3 transgenic rice plants, respectively, contained much higher OsGH9B1 and OsGH9B3 protein levels and both proteins were observed in situ with nonspecific distribution in the plant cells. The transgenic lines exhibited significantly increased cellulase activity in vitro than the WT. The OsGH9B1 and OsGH9B3 transgenic plants showed a slight alteration in three wall polymer compositions (cellulose, hemicelluloses, and lignin), in their stem mechanical strength and biomass yield, but were significantly decreased in the cellulose degree of polymerization (DP) and lignocellulose crystalline index (CrI) by 21-22%. Notably, the crude cellulose substrates of the transgenic lines were more efficiently digested by cellobiohydrolase (CBHI) than those of the WT, indicating the significantly increased amounts of reducing ends of β-1,4-glucans in cellulose microfibrils. Finally, the engineered lines generated high sugar yields after mild alkali pretreatments and subsequent enzymatic hydrolysis, resulting in the high bioethanol yields obtained at 22.5% of dry matter. CONCLUSIONS Overproduction of OsGH9B1/B3 enzymes should have specific activity in the postmodification of cellulose microfibrils. The increased reducing ends of β-1,4-glucan chains for reduced cellulose DP and CrI positively affected biomass enzymatic saccharification. Our results demonstrate a potential strategy for genetic modification of cellulose microfibrils in bioenergy crops.
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Affiliation(s)
- Jiangfeng Huang
- Biomass and Bioenergy Research Centre, College of Plant Science and Technology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010070 China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Agriculture, Guangxi University, Nanning, 530004 China
| | - Tao Xia
- Biomass and Bioenergy Research Centre, College of Plant Science and Technology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Guanhua Li
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010070 China
| | - Xianliang Li
- College of Bioengineering, Jingchu University of Technology, Jingmen, 448000 China
| | - Ying Li
- Biomass and Bioenergy Research Centre, College of Plant Science and Technology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Yanting Wang
- Biomass and Bioenergy Research Centre, College of Plant Science and Technology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Youmei Wang
- Biomass and Bioenergy Research Centre, College of Plant Science and Technology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Yuanyuan Chen
- Biomass and Bioenergy Research Centre, College of Plant Science and Technology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Guosheng Xie
- Biomass and Bioenergy Research Centre, College of Plant Science and Technology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Feng-Wu Bai
- State Key Laboratory of Microbial Metabolism, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Liangcai Peng
- Biomass and Bioenergy Research Centre, College of Plant Science and Technology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
- State Key Laboratory of Microbial Metabolism, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Lingqiang Wang
- Biomass and Bioenergy Research Centre, College of Plant Science and Technology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
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29
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Barros J, Temple S, Dixon RA. Development and commercialization of reduced lignin alfalfa. Curr Opin Biotechnol 2018; 56:48-54. [PMID: 30268938 DOI: 10.1016/j.copbio.2018.09.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 09/07/2018] [Accepted: 09/11/2018] [Indexed: 10/28/2022]
Abstract
Reducing lignin content in forage legumes can improve digestibility and, correspondingly, animal performance, and alfalfa (Medicago sativa) is the first genetically engineered crop commercialized for improved forage digestibility. Lignin reduction was achieved by downregulating the gene encoding caffeoyl-CoA 3-O-methyltransferase (CCoAOMT), and development of the commercial product, branded as HarvXtra, required the coordination of two research institutions and two companies, and more than 15 years of research and field trials. Lignin modification has positive impacts on forage management. Future developments will likely stack lignin modification with additional forage quality traits.
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Affiliation(s)
- Jaime Barros
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX 76203, United States; Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States
| | - Stephen Temple
- Forage Genetics International, West Salem, WI 54669, United States
| | - Richard A Dixon
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX 76203, United States; Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States.
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30
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Kasirajan L, Hoang NV, Furtado A, Botha FC, Henry RJ. Transcriptome analysis highlights key differentially expressed genes involved in cellulose and lignin biosynthesis of sugarcane genotypes varying in fiber content. Sci Rep 2018; 8:11612. [PMID: 30072760 PMCID: PMC6072797 DOI: 10.1038/s41598-018-30033-4] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 07/20/2018] [Indexed: 12/20/2022] Open
Abstract
Sugarcane (Saccharum spp. hybrids) is a potential lignocellulosic feedstock for biofuel production due to its exceptional biomass accumulation ability, high convertible carbohydrate content and a favorable energy input/output ratio. Genetic modification of biofuel traits to improve biomass conversion requires an understanding of the regulation of carbohydrate and lignin biosynthesis. RNA-Seq was used to investigate the transcripts differentially expressed between the immature and mature tissues of the sugarcane genotypes varying in fiber content. Most of the differentially expressed transcripts were found to be down-regulated during stem maturation, highlighting their roles in active secondary cell-wall development in the younger tissues of both high and low fiber genotypes. Several cellulose synthase genes (including CesA2, CesA4, CesA7 and COBRA-like protein), lignin biosynthesis-related genes (ρ-coumarate 3-hydroxylase, ferulate 5-hydroxylase, cinnamyl alcohol dehydrogenase and gentiobiase) and transcription regulators for the secondary cell-wall synthesis (including LIM, MYB, PLATZ, IAA24, C2H2 and C2C2 DOF zinc finger gene families) were exclusively differentially expressed between immature and mature tissues of high fiber genotypes. These findings reveal target genes for subsequent research on the regulation of cellulose and lignin metabolism.
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Affiliation(s)
- Lakshmi Kasirajan
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Queensland, 4072, Australia
- ICAR-Sugarcane Breeding Institute, Coimbatore, 641007, Tamil Nadu, India
| | - Nam V Hoang
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Queensland, 4072, Australia
- College of Agriculture and Forestry, Hue University, Hue, Vietnam
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Queensland, 4072, Australia
| | - Frederik C Botha
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Queensland, 4072, Australia
- Sugar Research Australia, Indooroopilly, Queensland, 4068, Australia
| | - Robert J Henry
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Queensland, 4072, Australia.
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31
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Gunasekara C, Zhang K, Deng W, Brown L, Wei H. TGMI: an efficient algorithm for identifying pathway regulators through evaluation of triple-gene mutual interaction. Nucleic Acids Res 2018; 46:e67. [PMID: 29579312 PMCID: PMC6009660 DOI: 10.1093/nar/gky210] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 03/07/2018] [Accepted: 03/12/2018] [Indexed: 12/20/2022] Open
Abstract
Despite their important roles, the regulators for most metabolic pathways and biological processes remain elusive. Presently, the methods for identifying metabolic pathway and biological process regulators are intensively sought after. We developed a novel algorithm called triple-gene mutual interaction (TGMI) for identifying these regulators using high-throughput gene expression data. It first calculated the regulatory interactions among triple gene blocks (two pathway genes and one transcription factor (TF)), using conditional mutual information, and then identifies significantly interacted triple genes using a newly identified novel mutual interaction measure (MIM), which was substantiated to reflect strengths of regulatory interactions within each triple gene block. The TGMI calculated the MIM for each triple gene block and then examined its statistical significance using bootstrap. Finally, the frequencies of all TFs present in all significantly interacted triple gene blocks were calculated and ranked. We showed that the TFs with higher frequencies were usually genuine pathway regulators upon evaluating multiple pathways in plants, animals and yeast. Comparison of TGMI with several other algorithms demonstrated its higher accuracy. Therefore, TGMI will be a valuable tool that can help biologists to identify regulators of metabolic pathways and biological processes from the exploded high-throughput gene expression data in public repositories.
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Affiliation(s)
- Chathura Gunasekara
- School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA
- Program of Computational Science and Engineering, Michigan Technological University, MI 49931, USA
| | - Kui Zhang
- Department of Mathematical Sciences Michigan Technological University, Houghton, MI 49931, USA
| | - Wenping Deng
- School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA
| | - Laura Brown
- Department of Computer Science, Michigan Technological University, MI 49931, USA
| | - Hairong Wei
- School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA
- Program of Computational Science and Engineering, Michigan Technological University, MI 49931, USA
- Department of Computer Science, Michigan Technological University, MI 49931, USA
- Life Science and Technology Institute, Michigan Technological University, Houghton, MI 49931, USA
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
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32
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Cauley AN, Wilson JN. Functionalized lignin biomaterials for enhancing optical properties and cellular interactions of dyes. Biomater Sci 2018; 5:2114-2121. [PMID: 28831468 DOI: 10.1039/c7bm00518k] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We report a library of functionalized lignins and demonstrate their utility as nanocontainers for organic dyes in biologically relevant applications. Kraft lignin was modified via SN2 reaction at the phenolic -OH group utilizing a mild base, potassium carbonate, and various alkyl halides, several bearing additional functionalities, with dimethylsulfoxide as solvent. The resulting phenoxy ethers were characterized by 1H-NMR and IR spectroscopy, as well as DLS and SEM to evaluate their morphology and supramolecular organization. Lignin modified with long-chain hydrocarbon tails was found to effectively encapsulate DiD, a cyanine dye, decrease aggregation, enhance optical transitions and exert a photoprotective effect. The dye-lignin assemblies were also examined as imaging agents, via confocal microscopy, and found to accumulate intracellularly with no leaching of the dye to hydrophobic subcellular components observed. Lignin functionalized with short chain carboxylic acids interacts with ligands directed at the norepinephrine transporter (NET), suggesting applications in sequestration of neuroactive compounds.
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Affiliation(s)
- Anthony N Cauley
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, FL 33124, USA.
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33
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Llerena JPP, Araújo P, Mazzafera P. Optimization of RT-PCR reactions in studies with genes of lignin biosynthetic route in Saccharum spontaneum. AN ACAD BRAS CIENC 2018; 90:509-519. [PMID: 29641770 DOI: 10.1590/0001-3765201820170250] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 05/19/2017] [Indexed: 11/22/2022] Open
Abstract
Saccharum spontaneum has been used for the development of energy cane a crop aimed to be used for the production of second-generation ethanol, or lignocellulosic ethanol. Lignin is a main challenge in the conversion of cell wall sugars into ethanol. In our studies to isolate the genes the lignin biosynthesis in S. spontaneum we have had great difficulty in RT-PCR reactions. Thus, we evaluated the effectiveness of different additives in the amplification of these genes. While COMT and CCoAOMT genes did not need any additives for other genes there was no amplification (HCT, F5H, 4CL and CCR) or the yield was very low (CAD and C4H). The application of supplementary cDNA was enough to overcome the non-specificity and low yield for C4H and C3H, while the addition of 0.04% BSA + 2% formamide was effective to amplify 4CL, CCR, F5H and CCR. HCT was amplified only by addition of 0.04% BSA + 2% formamide + 0.1 M trehalose and amplification of PAL was possible with addition of 2% of DMSO. Besides optimization of expression assays, the results show that additives can act independently or synergistically.
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Affiliation(s)
- Juan P P Llerena
- Universidade Estadual de Campinas, Laboratório de Fisiologia Molecular das Plantas, Departamento de Biologia Vegetal, Instituto de Biologia, Rua Monteiro Lobato, 255, Caixa Postal 6109, 13083-862 Campinas, SP, Brazil
| | - Pedro Araújo
- Universidade Estadual de Campinas, Laboratório de Genoma Funcional, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Rua Monteiro Lobato, 255, 13083-862 Campinas, SP, Brazil
| | - Paulo Mazzafera
- Universidade Estadual de Campinas, Laboratório de Fisiologia Molecular das Plantas, Departamento de Biologia Vegetal, Instituto de Biologia, Rua Monteiro Lobato, 255, Caixa Postal 6109, 13083-862 Campinas, SP, Brazil.,Universidade de São Paulo, Escola Superior de Agricultura Luiz de Queiroz, Departamento de Produção Vegetal, Av. Pádua Dias, 11, Caixa Postal 9, 34294-100 Piracicaba, SP, Brazil
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34
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Controllable modification of polymer membranes by LDDLT plasma flow: Grafting acidic ILs into PPF membrane for catalytic performance. J Memb Sci 2018. [DOI: 10.1016/j.memsci.2018.02.044] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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35
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Rodrigues Mota T, Matias de Oliveira D, Marchiosi R, Ferrarese-Filho O, Dantas dos Santos W. Plant cell wall composition and enzymatic deconstruction. AIMS BIOENGINEERING 2018. [DOI: 10.3934/bioeng.2018.1.63] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
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36
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Li J, Tang W, Zhang YW, Chen KN, Wang C, Liu Y, Zhan Q, Wang C, Wang SB, Xie SQ, Wang L. Genome-Wide Association Studies for Five Forage Quality-Related Traits in Sorghum ( Sorghum bicolor L.). FRONTIERS IN PLANT SCIENCE 2018; 9:1146. [PMID: 30186292 PMCID: PMC6111974 DOI: 10.3389/fpls.2018.01146] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 07/18/2018] [Indexed: 05/20/2023]
Abstract
Understanding the genetic function of the forage quality-related traits, including crude protein (CP), neutral detergent fiber (NDF), acid detergent fiber (ADF), hemicellulose (HC), and cellulose (CL) contents, is essential for the identification of forage quality genes and selection of effective molecular markers in sorghum. In this study, we genotyped 245 sorghum accessions by 85,585 single-nucleotide polymorphisms (SNPs) and obtained the phenotypic data from four environments. The SNPs and phenotypic data were applied to multi-locus genome-wide association studies (GWAS) with the mrMLM software. A total of 42 SNPs were identified to be associated with the five forage quality-related traits. Moreover, three and two quantitative trait nucleotides (QTNs) were simultaneously detected among them by three and two multi-locus methods, respectively. One QTN on chromosome 5 was found to be associated simultaneously with CP, NDF, and ADF. Furthermore, 3, 2, 2, 5, and 2 candidate genes were identified to be responsible for CP, NDF, ADF, HC, and CL contents, respectively. These results provided insightful information of the forage quality-related traits and would facilitate the genetic improvement of sorghum forage quality in the future.
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Affiliation(s)
- Jieqin Li
- College of Agriculture, Anhui Science and Technology University, Fengyang, China
| | - Weijie Tang
- College of Horticulture, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, China
| | - Ya-Wen Zhang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Kai-Ning Chen
- College of Horticulture, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Chenchen Wang
- College of Agriculture, Anhui Science and Technology University, Fengyang, China
| | - Yanlong Liu
- College of Agriculture, Anhui Science and Technology University, Fengyang, China
| | - Qiuwen Zhan
- College of Agriculture, Anhui Science and Technology University, Fengyang, China
| | - Chunming Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, China
| | - Shi-Bo Wang
- College of Horticulture, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Shang-Qian Xie
- College of Horticulture, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China
- *Correspondence: Shang-Qian Xie
| | - Lihua Wang
- College of Agriculture, Anhui Science and Technology University, Fengyang, China
- Lihua Wang
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37
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Bhatia R, Gallagher JA, Gomez LD, Bosch M. Genetic engineering of grass cell wall polysaccharides for biorefining. PLANT BIOTECHNOLOGY JOURNAL 2017; 15:1071-1092. [PMID: 28557198 PMCID: PMC5552484 DOI: 10.1111/pbi.12764] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 05/17/2017] [Accepted: 05/24/2017] [Indexed: 05/10/2023]
Abstract
Grasses represent an abundant and widespread source of lignocellulosic biomass, which has yet to fulfil its potential as a feedstock for biorefining into renewable and sustainable biofuels and commodity chemicals. The inherent recalcitrance of lignocellulosic materials to deconstruction is the most crucial limitation for the commercial viability and economic feasibility of biomass biorefining. Over the last decade, the targeted genetic engineering of grasses has become more proficient, enabling rational approaches to modify lignocellulose with the aim of making it more amenable to bioconversion. In this review, we provide an overview of transgenic strategies and targets to tailor grass cell wall polysaccharides for biorefining applications. The bioengineering efforts and opportunities summarized here rely primarily on (A) reprogramming gene regulatory networks responsible for the biosynthesis of lignocellulose, (B) remodelling the chemical structure and substitution patterns of cell wall polysaccharides and (C) expressing lignocellulose degrading and/or modifying enzymes in planta. It is anticipated that outputs from the rational engineering of grass cell wall polysaccharides by such strategies could help in realizing an economically sustainable, grass-derived lignocellulose processing industry.
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Affiliation(s)
- Rakesh Bhatia
- Institute of Biological, Environmental and Rural Sciences (IBERS)Aberystwyth UniversityAberystwythUK
| | - Joe A. Gallagher
- Institute of Biological, Environmental and Rural Sciences (IBERS)Aberystwyth UniversityAberystwythUK
| | | | - Maurice Bosch
- Institute of Biological, Environmental and Rural Sciences (IBERS)Aberystwyth UniversityAberystwythUK
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38
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Millwood R, Nageswara-Rao M, Ye R, Terry-Emert E, Johnson CR, Hanson M, Burris JN, Kwit C, Stewart CN. Pollen-mediated gene flow from transgenic to non-transgenic switchgrass (Panicum virgatum L.) in the field. BMC Biotechnol 2017; 17:40. [PMID: 28464851 PMCID: PMC5414321 DOI: 10.1186/s12896-017-0363-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 04/25/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Switchgrass is C4 perennial grass species that is being developed as a cellulosic bioenergy feedstock. It is wind-pollinated and considered to be an obligate outcrosser. Genetic engineering has been used to alter cell walls for more facile bioprocessing and biofuel yield. Gene flow from transgenic cultivars would likely be of regulatory concern. In this study we investigated pollen-mediated gene flow from transgenic to nontransgenic switchgrass in a 3-year field experiment performed in Oliver Springs, Tennessee, U.S.A. using a modified Nelder wheel design. The planted area (0.6 ha) contained sexually compatible pollen source and pollen receptor switchgrass plants. One hundred clonal switchgrass 'Alamo' plants transgenic for an orange-fluorescent protein (OFP) and hygromycin resistance were used as the pollen source; whole plants, including pollen, were orange-fluorescent. To assess pollen movement, pollen traps were placed at 10 m intervals from the pollen-source plot in the four cardinal directions extending to 20 m, 30 m, 30 m, and 100 m to the north, south, west, and east, respectively. To assess pollination rates, nontransgenic 'Alamo 2' switchgrass clones were planted in pairs adjacent to pollen traps. RESULTS In the eastward direction there was a 98% decrease in OFP pollen grains from 10 to 100 m from the pollen-source plot (Poisson regression, F1,8 = 288.38, P < 0.0001). At the end of the second and third year, 1,820 F1 seeds were collected from pollen recipient-plots of which 962 (52.9%) germinated and analyzed for their transgenic status. Transgenic progeny production detected in each pollen-recipient plot decreased with increased distance from the edge of the transgenic plot (Poisson regression, F1,15 = 12.98, P < 0.003). The frequency of transgenic progeny detected in the eastward plots (the direction of the prevailing wind) ranged from 79.2% at 10 m to 9.3% at 100 m. CONCLUSIONS In these experiments we found transgenic pollen movement and hybridization rates to be inversely associated with distance. However, these data suggest pollen-mediated gene flow is likely to occur up to, at least, 100 m. This study gives baseline data useful to determine isolation distances and other management practices should transgenic switchgrass be grown commercially in relevant environments.
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Affiliation(s)
- Reginald Millwood
- Department of Plant Sciences, University of Tennessee, 252 Ellington Plant Sciences, 2431 Joe Johnson Dr., Knoxville, TN, 37996, USA
| | - Madhugiri Nageswara-Rao
- Department of Plant Sciences, University of Tennessee, 252 Ellington Plant Sciences, 2431 Joe Johnson Dr., Knoxville, TN, 37996, USA.,Department of Biology, New Mexico State University, PO Box 30001, MSC 3AF, Las Cruces, NM, USA
| | - Rongjian Ye
- Department of Plant Sciences, University of Tennessee, 252 Ellington Plant Sciences, 2431 Joe Johnson Dr., Knoxville, TN, 37996, USA
| | - Ellie Terry-Emert
- Department of Plant Sciences, University of Tennessee, 252 Ellington Plant Sciences, 2431 Joe Johnson Dr., Knoxville, TN, 37996, USA
| | - Chelsea R Johnson
- Department of Plant Sciences, University of Tennessee, 252 Ellington Plant Sciences, 2431 Joe Johnson Dr., Knoxville, TN, 37996, USA
| | - Micaha Hanson
- Department of Plant Sciences, University of Tennessee, 252 Ellington Plant Sciences, 2431 Joe Johnson Dr., Knoxville, TN, 37996, USA
| | - Jason N Burris
- Department of Plant Sciences, University of Tennessee, 252 Ellington Plant Sciences, 2431 Joe Johnson Dr., Knoxville, TN, 37996, USA
| | - Charles Kwit
- Department of Forestry, Wildlife and Fisheries, University of Tennessee, 274 Ellington Plant Sciences, 2431 Joe Johnson Dr., Knoxville, TN, 37996, USA
| | - C Neal Stewart
- Department of Plant Sciences, University of Tennessee, 252 Ellington Plant Sciences, 2431 Joe Johnson Dr., Knoxville, TN, 37996, USA.
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Biotechnology for bioenergy dedicated trees: meeting future energy demands. ACTA ACUST UNITED AC 2017; 73:15-32. [DOI: 10.1515/znc-2016-0185] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 03/26/2017] [Indexed: 11/15/2022]
Abstract
Abstract
With the increase in human demands for energy, purpose-grown woody crops could be part of the global renewable energy solution, especially in geographical regions where plantation forestry is feasible and economically important. In addition, efficient utilization of woody feedstocks would engage in mitigating greenhouse gas emissions, decreasing the challenge of food and energy security, and resolving the conflict between land use for food or biofuel production. This review compiles existing knowledge on biotechnological and genomics-aided improvements of biomass performance of purpose-grown poplar, willow, eucalyptus and pine species, and their relative hybrids, for efficient and sustainable bioenergy applications. This includes advancements in tree in vitro regeneration, and stable expression or modification of selected genes encoding desirable traits, which enhanced growth and yield, wood properties, site adaptability, and biotic and abiotic stress tolerance. Genetic modifications used to alter lignin/cellulose/hemicelluloses ratio and lignin composition, towards effective lignocellulosic feedstock conversion into cellulosic ethanol, are also examined. Biotech-trees still need to pass challengeable regulatory authorities’ processes, including biosafety and risk assessment analyses prior to their commercialization release. Hence, strategies developed to contain transgenes, or to mitigate potential transgene flow risks, are discussed.
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40
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Nanda S, Mohanty JN, Mishra R, Joshi RK. Metabolic Engineering of Phenylpropanoids in Plants. REFERENCE SERIES IN PHYTOCHEMISTRY 2017. [DOI: 10.1007/978-3-319-28669-3_30] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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41
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Zheng Y, Shi J, Tu M, Cheng YS. Principles and Development of Lignocellulosic Biomass Pretreatment for Biofuels. ADVANCES IN BIOENERGY 2017. [DOI: 10.1016/bs.aibe.2017.03.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Jung JH, Kannan B, Dermawan H, Moxley GW, Altpeter F. Precision breeding for RNAi suppression of a major 4-coumarate:coenzyme A ligase gene improves cell wall saccharification from field grown sugarcane. PLANT MOLECULAR BIOLOGY 2016; 92:505-517. [PMID: 27549390 DOI: 10.1007/s11103-016-0527-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 08/08/2016] [Indexed: 05/02/2023]
Abstract
Sugarcane (Saccharum spp. hybrids) is a major feedstock for commercial bioethanol production. The recent integration of conversion technologies that utilize lignocellulosic sugarcane residues as well as sucrose from stem internodes has elevated bioethanol yields. RNAi suppression of lignin biosynthetic enzymes is a successful strategy to improve the saccharification of lignocellulosic biomass. 4-coumarate:coenzyme A ligase (4CL) is a key enzyme in the biosynthesis of phenylpropanoid metabolites, such as lignin and flavonoids. Identifying a major 4CL involved in lignin biosynthesis among multiple isoforms with functional divergence is key to manipulate lignin biosynthesis. In this study, two full length 4CL genes (Sh4CL1 and Sh4CL2) were isolated and characterized in sugarcane. Phylogenetic, expression and RNA interference (RNAi) analysis confirmed that Sh4CL1 is a major lignin biosynthetic gene. An intragenic precision breeding strategy may facilitate the regulatory approval of the genetically improved events and was used for RNAi suppression of Sh4CL1. Both, the RNAi inducing cassette and the expression cassette for the mutated ALS selection marker consisted entirely of DNA sequences from sugarcane or the sexually compatible species Sorghum bicolor. Field grown sugarcane with intragenic RNAi suppression of Sh4CL1 resulted in reduction of the total lignin content by up to 16.5 % along with altered monolignol ratios without reduction in biomass yield. Mature, field grown, intragenic sugarcane events displayed 52-76 % improved saccharification efficiency of lignocellulosic biomass compared to wild type (WT) controls. This demonstrates for the first time that an intragenic approach can add significant value to lignocellulosic feedstocks for biofuel and biochemical production.
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Affiliation(s)
- Je Hyeong Jung
- Agronomy Department, IFAS, University of Florida, PO Box 110500, Gainesville, FL, 32611, USA
- Institute of Life Science and Natural Resources, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul, 02841, South Korea
| | - Baskaran Kannan
- Agronomy Department, IFAS, University of Florida, PO Box 110500, Gainesville, FL, 32611, USA
| | - Hugo Dermawan
- Agronomy Department, IFAS, University of Florida, PO Box 110500, Gainesville, FL, 32611, USA
| | | | - Fredy Altpeter
- Agronomy Department, IFAS, University of Florida, PO Box 110500, Gainesville, FL, 32611, USA.
- Plant Molecular and Cellular Biology Program, IFAS, University of Florida, PO Box 110300, Gainesville, FL, 32611, USA.
- University of Florida Genetics Institute, PO Box 103610, Gainesville, FL, 32610, USA.
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Sangha AK, Petridis L, Cheng X, Smith JC. Relative Binding Affinities of Monolignols to Horseradish Peroxidase. J Phys Chem B 2016; 120:7635-40. [DOI: 10.1021/acs.jpcb.6b00789] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Amandeep K. Sangha
- UT/ORNL
Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Department of Biochemistry and Cellular
and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Loukas Petridis
- UT/ORNL
Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Xiaolin Cheng
- UT/ORNL
Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Department of Biochemistry and Cellular
and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Jeremy C. Smith
- UT/ORNL
Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Department of Biochemistry and Cellular
and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
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Li J, Fan F, Wang L, Zhan Q, Wu P, Du J, Yang X, Liu Y. Cloning and expression analysis of cinnamoyl-CoA reductase (CCR) genes in sorghum. PeerJ 2016; 4:e2005. [PMID: 27231650 PMCID: PMC4878380 DOI: 10.7717/peerj.2005] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2016] [Accepted: 04/13/2016] [Indexed: 11/20/2022] Open
Abstract
Cinnamoyl-CoA reductase (CCR) is the first enzyme in the monolignol-specific branch of the lignin biosynthetic pathway. In this research, three sorghum CCR genes including SbCCR1, SbCCR2-1 and SbCCR2-2 were cloned and characterized. Analyses of the structure and phylogeny of the three CCR genes showed evolutionary conservation of the functional domains and divergence of function. Transient expression assays in Nicotiana benthamiana leaves demonstrated that the three CCR proteins were localized in the cytoplasm. The expression analysis showed that the three CCR genes were induced by drought. But in 48 h, the expression levels of SbCCR1 and SbCCR2-2 did not differ between CK and the drought treatment; while the expression level of SbCCR2-1 in the drought treatment was higher than in CK. The expression of the SbCCR1 and SbCCR2-1 genes was not induced by sorghum aphid [Melanaphis sacchari (Zehntner)] attack, but SbCCR2-2 was significantly induced by sorghum aphid attack. It is suggested that SbCCR2-2 is involved in the process of pest defense. Absolute quantitative real-time PCR revealed that the three CCR genes were mainly expressed in lignin deposition organs. The gene copy number of SbCCR1 was significantly higher than those of SbCCR2-1 and SbCCR2-2 in the tested tissues, especially in stem. The results provide new insight into the functions of the three CCR genes in sorghum.
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Affiliation(s)
- Jieqin Li
- College of Agriculture, Anhui Science and Technology University , Fengyang , China
| | - Feifei Fan
- College of Agriculture, Anhui Science and Technology University , Fengyang , China
| | - Lihua Wang
- College of Agriculture, Anhui Science and Technology University , Fengyang , China
| | - Qiuwen Zhan
- College of Agriculture, Anhui Science and Technology University , Fengyang , China
| | - Peijin Wu
- College of Agriculture, Anhui Science and Technology University , Fengyang , China
| | - Junli Du
- College of Agriculture, Anhui Science and Technology University , Fengyang , China
| | - Xiaocui Yang
- College of Agriculture, Anhui Science and Technology University , Fengyang , China
| | - Yanlong Liu
- College of Agriculture, Anhui Science and Technology University , Fengyang , China
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Liu Y, He C. Regulation of plant reactive oxygen species (ROS) in stress responses: learning from AtRBOHD. PLANT CELL REPORTS 2016; 35:995-1007. [PMID: 26883222 DOI: 10.1007/s00299-016-1950-x] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 02/02/2016] [Indexed: 05/18/2023]
Abstract
Reactive oxygen species (ROS) are constantly produced in plants, as the metabolic by-products or as the signaling components in stress responses. High levels of ROS are harmful to plants. In contrast, ROS play important roles in plant physiology, including abiotic and biotic tolerance, development, and cellular signaling. Therefore, ROS production needs to be tightly regulated to balance their function. Respiratory burst oxidase homologue (RBOH) proteins, also known as plant nicotinamide adenine dinucleotide phosphate oxidases, are well studied enzymatic ROS-generating systems in plants. The regulatory mechanisms of RBOH-dependent ROS production in stress responses have been intensively studied. This has greatly advanced our knowledge of the mechanisms that regulate plant ROS production. This review attempts to integrate the regulatory mechanisms of RBOHD-dependent ROS production by discussing the recent advance. AtRBOHD-dependent ROS production could provide a valuable reference for studying ROS production in plant stress responses.
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Affiliation(s)
- Yukun Liu
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, College of Forestry, Southwest Forestry University, 300 Bailong Si, Kunming, 650224, Yunnan, People's Republic of China.
- Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, College of Forestry, Southwest Forestry University, 300 Bailong Si, Kunming, 650224, Yunnan, People's Republic of China.
| | - Chengzhong He
- Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, College of Forestry, Southwest Forestry University, 300 Bailong Si, Kunming, 650224, Yunnan, People's Republic of China
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Wang W, Li R, Zhu Q, Tang X, Zhao Q. Transcriptomic and physiological analysis of common duckweed Lemna minor responses to NH4(+) toxicity. BMC PLANT BIOLOGY 2016; 16:92. [PMID: 27091123 PMCID: PMC4835947 DOI: 10.1186/s12870-016-0774-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 04/11/2016] [Indexed: 05/29/2023]
Abstract
BACKGROUND Plants can suffer ammonium (NH4 (+)) toxicity, particularly when NH4 (+) is supplied as the sole nitrogen source. However, our knowledge about the underlying mechanisms of NH4 (+) toxicity is still largely unknown. Lemna minor, a model duckweed species, can grow well in high NH4 (+) environment but to some extent can also suffer toxic effects. The transcriptomic and physiological analysis of L. minor responding to high NH4 (+) may provide us some interesting and useful information not only in toxic processes, but also in tolerance mechanisms. RESULTS The L. minor cultured in the Hoagland solution were used as the control (NC), and in two NH4 (+) concentrations (NH4 (+) was the sole nitrogen source), 84 mg/L (A84) and 840 mg/L (A840) were used as stress treatments. The NH4 (+) toxicity could inhibit the growth of L. minor. Reactive oxygen species (ROS) and cell death were studied using stained fronds under toxic levels of NH4 (+). The malondialdehyde content and the activities of superoxide dismutase and peroxidase increased from NC to A840, rather than catalase and ascorbate peroxidase. A total of 6.62G nucleotides were generated from the three distinct libraries. A total of 14,207 differentially expressed genes (DEGs) among 70,728 unigenes were obtained. All the DEGs could be clustered into 7 profiles. Most DEGs were down-regulated under NH4 (+) toxicity. The genes required for lignin biosynthesis in phenylpropanoid biosynthesis pathway were up-regulated. ROS oxidative-related genes and programmed cell death (PCD)-related genes were also analyzed and indicated oxidative damage and PCD occurring under NH4 (+) toxicity. CONCLUSIONS The first large transcriptome study in L. minor responses to NH4 (+) toxicity was reported in this work. NH4 (+) toxicity could induce ROS accumulation that causes oxidative damage and thus induce cell death in L. minor. The antioxidant enzyme system was activated under NH4 (+) toxicity for ROS scavenging. The phenylpropanoid pathway was stimulated under NH4 (+) toxicity. The increased lignin biosynthesis might play an important role in NH4 (+) toxicity resistance.
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Affiliation(s)
- Wenguo Wang
- />Biogas Institute of Ministry of Agriculture, Section 4-13, Renmin Road South, Chengdu, 610041 Sichuan PR China
- />Key Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agriculture, Section 4-13, Renmin Road South, Chengdu, 610041 Sichuan PR China
| | - Rui Li
- />Faculty of Biotechnology Industry, Chengdu University, 1 Shiling Street, Chengluo Road, 610106 Chengdu, Sichuan PR China
| | - Qili Zhu
- />Biogas Institute of Ministry of Agriculture, Section 4-13, Renmin Road South, Chengdu, 610041 Sichuan PR China
- />Key Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agriculture, Section 4-13, Renmin Road South, Chengdu, 610041 Sichuan PR China
| | - Xiaoyu Tang
- />Biogas Institute of Ministry of Agriculture, Section 4-13, Renmin Road South, Chengdu, 610041 Sichuan PR China
- />Key Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agriculture, Section 4-13, Renmin Road South, Chengdu, 610041 Sichuan PR China
| | - Qi Zhao
- />Faculty of Biotechnology Industry, Chengdu University, 1 Shiling Street, Chengluo Road, 610106 Chengdu, Sichuan PR China
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Scully ED, Gries T, Funnell-Harris DL, Xin Z, Kovacs FA, Vermerris W, Sattler SE. Characterization of novel Brown midrib 6 mutations affecting lignin biosynthesis in sorghum. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2016; 58:136-49. [PMID: 26172142 DOI: 10.1111/jipb.12375] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 07/07/2015] [Indexed: 05/23/2023]
Abstract
The presence of lignin reduces the quality of lignocellulosic biomass for forage materials and feedstock for biofuels. In C4 grasses, the brown midrib phenotype has been linked to mutations to genes in the monolignol biosynthesis pathway. For example, the Bmr6 gene in sorghum (Sorghum bicolor) has been previously shown to encode cinnamyl alcohol dehydrogenase (CAD), which catalyzes the final step of the monolignol biosynthesis pathway. Mutations in this gene have been shown to reduce the abundance of lignin, enhance digestibility, and improve saccharification efficiencies and ethanol yields. Nine sorghum lines harboring five different bmr6 alleles were identified in an EMS-mutagenized TILLING population. DNA sequencing of Bmr6 revealed that the majority of the mutations impacted evolutionarily conserved amino acids while three-dimensional structural modeling predicted that all of these alleles interfered with the enzyme's ability to bind with its NADPH cofactor. All of the new alleles reduced in vitro CAD activity levels and enhanced glucose yields following saccharification. Further, many of these lines were associated with higher reductions in acid detergent lignin compared to lines harboring the previously characterized bmr6-ref allele. These bmr6 lines represent new breeding tools for manipulating biomass composition to enhance forage and feedstock quality.
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Affiliation(s)
- Erin D Scully
- Grain, Forage, and Bioenergy Research Unit, USDA-ARS, Lincoln, NE, 68583, USA
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
| | - Tammy Gries
- Grain, Forage, and Bioenergy Research Unit, USDA-ARS, Lincoln, NE, 68583, USA
| | - Deanna L Funnell-Harris
- Grain, Forage, and Bioenergy Research Unit, USDA-ARS, Lincoln, NE, 68583, USA
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
| | - Zhanguo Xin
- Plant Stress and Germplasm Development Unit, USDA-ARS, Lubbock, TX, 79414, USA
| | - Frank A Kovacs
- Department of Chemistry, University of Nebraska-Kearney, Kearney, NE, 68849, USA
| | - Wilfred Vermerris
- Department of Microbiology & Cell Science and UF Genetics Institute, University of Florida, Gainesville, FL, 32610, USA
| | - Scott E Sattler
- Grain, Forage, and Bioenergy Research Unit, USDA-ARS, Lincoln, NE, 68583, USA
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
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48
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Amore A, Ciesielski PN, Lin CY, Salvachúa D, Sànchez i Nogué V. Development of Lignocellulosic Biorefinery Technologies: Recent Advances and Current Challenges. Aust J Chem 2016. [DOI: 10.1071/ch16022] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Recent developments of the biorefinery concept are described within this review, which focuses on the efforts required to make the lignocellulosic biorefinery a sustainable and economically viable reality. Despite the major research and development endeavours directed towards this goal over the past several decades, the integrated production of biofuel and other bio-based products still needs to be optimized from both technical and economical perspectives. This review will highlight recent progress towards the optimization of the major biorefinery processes, including biomass pretreatment and fractionation, saccharification of sugars, and conversion of sugars and lignin into fuels and chemical precursors. In addition, advances in genetic modification of biomass structure and composition for the purpose of enhancing the efficacy of conversion processes, which is emerging as a powerful tool for tailoring biomass fated for the biorefinery, will be overviewed. The continual improvement of these processes and their integration in the format of a modern biorefinery is paving the way for a sustainable bio-economy which will displace large portions of petroleum-derived fuels and chemicals with renewable substitutes.
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Tong Z, Li H, Zhang R, Ma L, Dong J, Wang T. Co-downregulation of the hydroxycinnamoyl-CoA:shikimate hydroxycinnamoyl transferase and coumarate 3-hydroxylase significantly increases cellulose content in transgenic alfalfa (Medicago sativa L.). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 239:230-7. [PMID: 26398807 DOI: 10.1016/j.plantsci.2015.08.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 08/06/2015] [Accepted: 08/06/2015] [Indexed: 05/04/2023]
Abstract
Lignin is a component of the cell wall that is essential for growth, development, structure and pathogen resistance in plants, but high lignin is an obstacle to the conversion of cellulose to ethanol for biofuel. Genetically modifying lignin and cellulose contents can be a good approach to overcoming that obstacle. Alfalfa (Medicago sativa L.) is rich in lignocellulose biomass and used as a model plant for the genetic modification of lignin in this study. Two key enzymes in the lignin biosynthesis pathway-hydroxycinnamoyl -CoA:shikimate hydroxycinnamoyl transferase (HCT) and coumarate 3-hydroxylase (C3H)-were co-downregulated. Compared to wild-type plants, the lignin content in the modified strain was reduced by 38%, cellulose was increased by 86.1%, enzyme saccharification efficiency was increased by 10.9%, and cell wall digestibility was increased by 13.0%. The modified alfalfa exhibited a dwarf phenotype, but normal above ground biomass. This approach provides a new strategy for reducing lignin and increasing cellulose contents and creates a new genetically modified crop with enhanced value for biofuel.
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Affiliation(s)
- Zongyong Tong
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China; Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Heng Li
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
| | - Rongxue Zhang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
| | - Lei Ma
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
| | - Jiangli Dong
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
| | - Tao Wang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China; National Energy R&D Center for Non-food Biomass, China Agricultural University, Beijing 100193, China.
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50
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Engineering Plant Biomass Lignin Content and Composition for Biofuels and Bioproducts. ENERGIES 2015. [DOI: 10.3390/en8087654] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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