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Expression of an alkaline feruloyl esterases from thermophilic Chaetomium thermophilum and its boosting effect on delignification of pulp. Enzyme Microb Technol 2021; 150:109859. [PMID: 34489049 DOI: 10.1016/j.enzmictec.2021.109859] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 06/20/2021] [Accepted: 06/23/2021] [Indexed: 11/23/2022]
Abstract
Exploration of feruloyl esterase (FAE) with the resistance to heat and alkali conditions in biobleaching process to improve the separation efficiency of lignocellulose is the key to achieving green papermaking. Herein, we expressed FAEB of C. thermophilum and obtained a thermostable alkaline FAE that can effectively promote the removal of lignin from pulp. The faeB gene was successfully obtained through genomic Blast strategy and high-efficiency expressed under the control of strong alcohol oxidase promoter in Pichia pastoris. The recombinant CtFAEB has an optimal temperature of 65 °C and pH of 7.0. After treated at 65 °C for 1 h, CtFAEB can still retain 63.21 % of its maximum activity, showing a good thermal stability. In addition, the recombinant CtFAEB has broad pH stability and can retain about 56 % of the maximum activity even at pH 11.0. Compared with the effect of mesophilic FAE, pretreatment with thermostable CtFAEB can promote the delignification by laccase and alkaline hydrogen peroxide from the pulp at 70 °C and pH 9.0. Alignment of the protein sequences of CtFAEB and mesophilic FAE suggested that the percentage of amino acids that easily form alpha helix in CtFAEB increases, which enhances its structural rigidity and thereby improves its thermal stability and alkali tolerance. Our study provides an effective method to obtain thermostable and alkaline FAEs, which will promote its application in biobleaching and other biorefining industries.
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Molecular Genetic Characteristics of Different Scenarios of Xylogenesis on the Example of Two Forms of Silver Birch Differing in the Ratio of Structural Elements in the Xylem. PLANTS 2021; 10:plants10081593. [PMID: 34451638 PMCID: PMC8400816 DOI: 10.3390/plants10081593] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/30/2021] [Accepted: 07/30/2021] [Indexed: 11/17/2022]
Abstract
Silver birch (Betula pendula Roth) is an economically important species in Northern Europe. The current research focused on the molecular background of different xylogenesis scenarios in the birch trunks. The study objects were two forms of silver birch, silver birch trees, and Karelian birch trees; the latter form is characterized by the formation of two types of wood, non-figured (straight-grained) and figured, respectively, while it is currently not clear which factors cause this difference. We identified VND/NST/SND genes that regulate secondary cell wall biosynthesis in the birch genome and revealed differences in their expression in association with the formation of xylem with different ratios of structural elements. High expression levels of BpVND7 accompanied differentiation of the type of xylem which is characteristic of the species. At the same time, the appearance of figured wood was accompanied by the low expression levels of the VND genes and increased levels of expression of NST and SND genes. We identified BpARF5 as a crucial regulator of auxin-dependent vascular patterning and its direct target—BpHB8. A decrease in the BpARF5 level expression in differentiating xylem was a specific characteristic of both Karelian birch with figured and non-figured wood. Decreased BpARF5 level expression in non-figured trees accompanied by decreased BpHB8 and VND/NST/SND expression levels compared to figured Karelian birch trees. According to the results obtained, we suggested silver birch forms differing in wood anatomy as valuable objects in studying the regulation of xylogenesis.
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Kasirajan L, Maupin-Furlow JA. Halophilic archaea and their potential to generate renewable fuels and chemicals. Biotechnol Bioeng 2020; 118:1066-1090. [PMID: 33241850 DOI: 10.1002/bit.27639] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 10/27/2020] [Accepted: 11/17/2020] [Indexed: 12/16/2022]
Abstract
Lignocellulosic biofuels and chemicals have great potential to reduce our dependence on fossil fuels and mitigate air pollution by cutting down on greenhouse gas emissions. Chemical, thermal, and enzymatic processes are used to release the sugars from the lignocellulosic biomass for conversion to biofuels. These processes often operate at extreme pH conditions, high salt concentrations, and/or high temperature. These harsh treatments add to the cost of the biofuels, as most known biocatalysts do not operate under these conditions. To increase the economic feasibility of biofuel production, microorganisms that thrive in extreme conditions are considered as ideal resources to generate biofuels and value-added products. Halophilic archaea (haloarchaea) are isolated from hypersaline ecosystems with high salt concentrations approaching saturation (1.5-5 M salt concentration) including environments with extremes in pH and/or temperature. The unique traits of haloarchaea and their enzymes that enable them to sustain catalytic activity in these environments make them attractive resources for use in bioconversion processes that must occur across a wide range of industrial conditions. Biocatalysts (enzymes) derived from haloarchaea occupy a unique niche in organic solvent, salt-based, and detergent industries. This review focuses on the use of haloarchaea and their enzymes to develop and improve biofuel production. The review also highlights how haloarchaea produce value-added products, such as antibiotics, carotenoids, and bioplastic precursors, and can do so using feedstocks considered "too salty" for most microbial processes including wastes from the olive-mill, shell fish, and biodiesel industries.
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Affiliation(s)
- Lakshmi Kasirajan
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA.,Division of Crop Improvement, ICAR Sugarcane Breeding Institute, Coimbatore, India
| | - Julie A Maupin-Furlow
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA.,Genetics Institute, University of Florida, Gainesville, Florida, USA
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The Fungicide Tetramethylthiuram Disulfide Negatively Affects Plant Cell Walls, Infection Thread Walls, and Symbiosomes in Pea ( Pisum sativum L.) Symbiotic Nodules. PLANTS 2020; 9:plants9111488. [PMID: 33158267 PMCID: PMC7694270 DOI: 10.3390/plants9111488] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 10/21/2020] [Accepted: 11/03/2020] [Indexed: 12/26/2022]
Abstract
In Russia, tetramethylthiuram disulfide (TMTD) is a fungicide widely used in the cultivation of legumes, including the pea (Pisum sativum). Application of TMTD can negatively affect nodulation; nevertheless, its effect on the histological and ultrastructural organization of nodules has not previously been investigated. In this study, the effect of TMTD at three concentrations (0.4, 4, and 8 g/kg) on nodule development in three pea genotypes (laboratory lines Sprint-2 and SGE, and cultivar 'Finale') was examined. In SGE, TMTD at 0.4 g/kg reduced the nodule number and shoot and root fresh weights. Treatment with TMTD at 8 g/kg changed the nodule color from pink to green, indicative of nodule senescence. Light and transmission electron microscopy analyses revealed negative effects of TMTD on nodule structure in each genotype. 'Finale' was the most sensitive cultivar to TMTD and Sprint-2 was the most tolerant. The negative effects of TMTD on nodules included the appearance of a senescence zone, starch accumulation, swelling of cell walls accompanied by a loss of electron density, thickening of the infection thread walls, symbiosome fusion, and bacteroid degradation. These results demonstrate how TMTD adversely affects nodules in the pea and will be useful for developing strategies to optimize fungicide use on legume crops.
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Carpita NC, McCann MC. Redesigning plant cell walls for the biomass-based bioeconomy. J Biol Chem 2020; 295:15144-15157. [PMID: 32868456 PMCID: PMC7606688 DOI: 10.1074/jbc.rev120.014561] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 08/30/2020] [Indexed: 01/28/2023] Open
Abstract
Lignocellulosic biomass-the lignin, cellulose, and hemicellulose that comprise major components of the plant cell well-is a sustainable resource that could be utilized in the United States to displace oil consumption from heavy vehicles, planes, and marine-going vessels and commodity chemicals. Biomass-derived sugars can also be supplied for microbial fermentative processing to fuels and chemicals or chemically deoxygenated to hydrocarbons. However, the economic value of biomass might be amplified by diversifying the range of target products that are synthesized in living plants. Genetic engineering of lignocellulosic biomass has previously focused on changing lignin content or composition to overcome recalcitrance, the intrinsic resistance of cell walls to deconstruction. New capabilities to remove lignin catalytically without denaturing the carbohydrate moiety have enabled the concept of the "lignin-first" biorefinery that includes high-value aromatic products. The structural complexity of plant cell-wall components also provides substrates for polymeric and functionalized target products, such as thermosets, thermoplastics, composites, cellulose nanocrystals, and nanofibers. With recent advances in the design of synthetic pathways, lignocellulosic biomass can be regarded as a substrate at various length scales for liquid hydrocarbon fuels, chemicals, and materials. In this review, we describe the architectures of plant cell walls and recent progress in overcoming recalcitrance and illustrate the potential for natural or engineered biomass to be used in the emerging bioeconomy.
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Affiliation(s)
- Nicholas C Carpita
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, USA; Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Maureen C McCann
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA; Center for Plant Biology, Purdue University, West Lafayette, Indiana, USA.
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Yang Y, Kang L, Wu R, Chen Y, Lu C. Genome-wide identification and characterization of UDP-glucose dehydrogenase family genes in moso bamboo and functional analysis of PeUGDH4 in hemicellulose synthesis. Sci Rep 2020; 10:10124. [PMID: 32576917 PMCID: PMC7311537 DOI: 10.1038/s41598-020-67227-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 06/04/2020] [Indexed: 01/24/2023] Open
Abstract
Uridine diphosphate glucose dehydrogenases (UGDHs) are critical for synthesizing many nucleotide sugars and help promote the carbohydrate metabolism related to cell wall synthesis. In plants, UGDHs are encoded by a small gene family. Genome-wide analyses of these genes have been conducted in Glycine max and Arabidopsis thaliana, however, the UGDH gene family has not been comprehensively and systematically investigated in moso bamboo (Phyllostachys edulis), which is a special woody grass monocotyledonous species. In this study, we identified nine putative PeUGDH genes. Furthermore, analysis of gene duplication events and divergences revealed that the expansion of the PeUGDH family was mainly due to segmental and tandem duplications approximately 4.76–83.16 million years ago. An examination of tissue-specific PeUGDH expression indicated that more than 77% of the genes were predominantly expressed in the stem. Based on relative expression levels among PeUGDH members in different tissues in moso bamboo, PeUGDH4 was selected for detailed analysis. The results of subcellular localization indicated that PeUGDH4-GFP fusion proteins was observed to be localized in the cytoplasm. The ectopic overexpression of PeUGDH4 in Arabidopsis significantly increased the contents of hemicellulose and soluble sugar, suggesting that PeUGDH4 acts as a key enzyme involved in bamboo cell wall synthesis.
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Affiliation(s)
- Ying Yang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China.,College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Lan Kang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China.,College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Ruihua Wu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China.,College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Yuzhen Chen
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China.,College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Cunfu Lu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China. .,College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.
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Knoblauch J, Knoblauch M, Vasina VV, Peters WS. Sieve elements rapidly develop 'nacreous walls' following injury - a common wounding response? THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 102:797-808. [PMID: 31883138 DOI: 10.1111/tpj.14665] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 11/19/2019] [Accepted: 12/09/2019] [Indexed: 06/10/2023]
Abstract
Thick glistening cell walls occur in sieve tubes of all major land plant taxa. Historically, these 'nacreous walls' have been considered a diagnostic feature of sieve elements; they represent a conundrum, though, in the context of the widely accepted pressure-flow theory as they severely constrict sieve tubes. We employed the cucurbit Gerrardanthus macrorhizus as a model to study nacreous walls in sieve elements by standard and in situ confocal microscopy and electron microscopy, focusing on changes in functional sieve tubes that occur when prepared for microscopic observation. Over 90% of sieve elements in tissue sections processed for microscopy by standard methods exhibit nacreous walls. Sieve elements in whole, live plants that were actively transporting as shown by phloem-mobile tracers, lacked nacreous walls and exhibited open lumina of circular cross-sections instead, an appropriate structure for Münch-type mass flow of the cell contents. Puncturing of transporting sieve elements with micropipettes triggered the rapid (<1 min) development of nacreous walls that occluded the cell lumen almost completely. We conclude that nacreous walls are preparation artefacts rather than structural features of transporting sieve elements. Nacreous walls in land plants resemble the reversibly swellable walls found in various algae, suggesting that they may function in turgor buffering, the amelioration of osmotic stress, wounding-induced sieve tube occlusion, and possibly local defence responses of the phloem.
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Affiliation(s)
- Jan Knoblauch
- School of Biological Sciences, Washington State University, PO Box 644236, Pullman, WA, 99164, USA
| | - Michael Knoblauch
- School of Biological Sciences, Washington State University, PO Box 644236, Pullman, WA, 99164, USA
| | - Viktoriya V Vasina
- School of Biological Sciences, Washington State University, PO Box 644236, Pullman, WA, 99164, USA
| | - Winfried S Peters
- School of Biological Sciences, Washington State University, PO Box 644236, Pullman, WA, 99164, USA
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Yang JH, Lee KH, Du Q, Yang S, Yuan B, Qi L, Wang H. A membrane-associated NAC domain transcription factor XVP interacts with TDIF co-receptor and regulates vascular meristem activity. THE NEW PHYTOLOGIST 2020; 226:59-74. [PMID: 31660587 DOI: 10.1111/nph.16289] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 10/24/2019] [Indexed: 05/22/2023]
Abstract
Vascular stem cell maintenance is regulated by a peptide signaling involving Tracheary Element Differentiation Inhibitory Factor (TDIF) and Receptor TDR/PXY (Phloem intercalated with Xylem) and co-receptor BAK1 (BRI1-associated receptor kinase1). The regulatory mechanism of this signaling pathway is largely unknown despite its importance in stem cell maintenance in the vascular meristem. We report that activation of a NAC domain transcription factor XVP leads to precocious Xylem differentiation, disruption of Vascular Patterning, and reduced cell numbers in vascular bundles. We combined molecular and genetic studies to elucidate the biological functions of XVP. XVP is expressed in the cambium, localized on the plasma membrane and forms a complex with TDIF co-receptors PXY-BAK1. Simultaneous mutation of XVP and its close homologous NAC048 enhances TDIF signaling. In addition, genetics analysis indicated that XVP promotes xylem differentiation through a known master regulator VASCULAR-RELATED NAC-DOMAIN6 (VND6). Expression analyses indicate that XVP activates CLAVATA3/ESR (CLE)-related protein 44 (CLE44), the coding gene of TDIF, whereas TDIF represses XVP expression, suggesting a feedback mechanism. Therefore, XVP functions as a negative regulator of the TDIF-PXY module and fine-tunes TDIF signaling in vascular development. These results shed new light on the mechanism of vascular stem cell maintenance.
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Affiliation(s)
- Jung Hyun Yang
- Department of Plant Science and Landscape Architecture, University of Connecticut, 1376 Storrs Rd, Storrs, CT, 06269, USA
| | - Kwang-Hee Lee
- Department of Plant Science and Landscape Architecture, University of Connecticut, 1376 Storrs Rd, Storrs, CT, 06269, USA
| | - Qian Du
- Department of Plant Science and Landscape Architecture, University of Connecticut, 1376 Storrs Rd, Storrs, CT, 06269, USA
| | - Shuo Yang
- Department of Plant Science and Landscape Architecture, University of Connecticut, 1376 Storrs Rd, Storrs, CT, 06269, USA
| | - Bingjian Yuan
- Department of Plant Science and Landscape Architecture, University of Connecticut, 1376 Storrs Rd, Storrs, CT, 06269, USA
| | - Liying Qi
- Department of Plant Science and Landscape Architecture, University of Connecticut, 1376 Storrs Rd, Storrs, CT, 06269, USA
| | - Huanzhong Wang
- Department of Plant Science and Landscape Architecture, University of Connecticut, 1376 Storrs Rd, Storrs, CT, 06269, USA
- Institute for System Genomics, University of Connecticut, Storrs, CT, 06269, USA
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Mohapatra S, Mishra SS, Bhalla P, Thatoi H. Engineering grass biomass for sustainable and enhanced bioethanol production. PLANTA 2019; 250:395-412. [PMID: 31236698 DOI: 10.1007/s00425-019-03218-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Accepted: 06/18/2019] [Indexed: 06/09/2023]
Abstract
Bioethanol from lignocellulosic biomass is a promising step for the future energy requirements. Grass is a potential lignocellulosic biomass which can be utilised for biorefinery-based bioethanol production. Grass biomass is a suitable feedstock for bioethanol production due to its all the year around production, requirement of less fertile land and noninterference with food system. However, the processes involved, i.e. pretreatment, enzymatic hydrolysis and fermentation for bioethanol production from grass biomass, are both time consuming and costly. Developing the grass biomass in planta for enhanced bioethanol production is a promising step for maximum utilisation of this valuable feedstock and, thus, is the focus of the present review. Modern breeding techniques and transgenic processes are attractive methods which can be utilised for development of the feedstock. However, the outcomes are not always predictable and the time period required for obtaining a robust variety is generation dependent. Sophisticated genome editing technologies such as synthetic genetic circuits (SGC) or clustered regularly interspaced short palindromic repeats (CRISPR) systems are advantageous for induction of desired traits/heritable mutations in a foreseeable genome location in the 1st mutant generation. Although, its application in grass biomass for bioethanol is limited, these sophisticated techniques are anticipated to exhibit more flexibility in engineering the expression pattern for qualitative and qualitative traits. Nevertheless, the fundamentals rendered by the genetics of the transgenic crops will remain the basis of such developments for obtaining biorefinery-based bioethanol concepts from grass biomass. Grasses which are abundant and widespread in nature epitomise attractive lignocellulosic feedstocks for bioethanol production. The complexity offered by the grass cell wall in terms of lignin recalcitrance and its binding to polysaccharides forms a barricade for its commercialization as a biofuel feedstock. Inspired by the possibilities for rewiring the genetic makeup of grass biomass for reduced lignin and lignin-polysaccharide linkages along with increase in carbohydrates, innovative approaches for in planta modifications are forging ahead. In this review, we highlight the progress made in the field of transgenic grasses for bioethanol production and focus our understanding on improvements of simple breeding techniques and post-harvest techniques for development in shortening of lignin-carbohydrate and carbohydrate-carbohydrate linkages. Further, we discuss about the designer lignins which are aimed for qualitable lignins and also emphasise on remodelling of polysaccharides and mixed-linkage glucans for enhancing carbohydrate content and in planta saccharification efficiency. As a final point, we discuss the role of synthetic genetic circuits and CRISPR systems in targeted improvement of cell wall components without compromising the plant growth and health. It is anticipated that this review can provide a rational approach towards a better understanding of application of in planta genetic engineering aspects for designing synthetic genetic circuits which can promote grass feedstocks for biorefinery-based bioethanol concepts.
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Affiliation(s)
- Sonali Mohapatra
- Department of Biotechnology, College of Engineering and Technology, Biju Patnaik University of Technology, Bhubaneswar, 751003, India.
| | - Suruchee Samparana Mishra
- Department of Biotechnology, College of Engineering and Technology, Biju Patnaik University of Technology, Bhubaneswar, 751003, India
| | - Prerna Bhalla
- Bhupat and Jyoti Mehta School of Biosciences Building, Indian Institute of Technology Madras, Chennai, India
| | - Hrudayanath Thatoi
- Department of Biotechnology, North Orissa University, Sriram Chandra Vihar, Takatpur, Baripada, 757003, Odisha, India
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Javaid R, Sabir A, Sheikh N, Ferhan M. Recent Advances in Applications of Acidophilic Fungi to Produce Chemicals. Molecules 2019; 24:E786. [PMID: 30813221 PMCID: PMC6412211 DOI: 10.3390/molecules24040786] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 07/28/2018] [Accepted: 08/08/2018] [Indexed: 12/16/2022] Open
Abstract
Processing of fossil fuels is the major environmental issue today. Biomass utilization for the production of chemicals presents an alternative to simple energy generation by burning. Lignocellulosic biomass (cellulose, hemicellulose and lignin) is abundant and has been used for variety of purposes. Among them, lignin polymer having phenyl-propanoid subunits linked together either through C-C bonds or ether linkages can produce chemicals. It can be depolymerized by fungi using their enzyme machinery (laccases and peroxidases). Both acetic acid and formic acid production by certain fungi contribute significantly to lignin depolymerization. Fungal natural organic acids production is thought to have many key roles in nature depending upon the type of fungi producing them. Biological conversion of lignocellulosic biomass is beneficial over physiochemical processes. Laccases, copper containing proteins oxidize a broad spectrum of inorganic as well as organic compounds but most specifically phenolic compounds by radical catalyzed mechanism. Similarly, lignin peroxidases (LiP), heme containing proteins perform a vital part in oxidizing a wide variety of aromatic compounds with H₂O₂. Lignin depolymerization yields value-added compounds, the important ones are aromatics and phenols as well as certain polymers like polyurethane and carbon fibers. Thus, this review will provide a concept that biological modifications of lignin using acidophilic fungi can generate certain value added and environmentally friendly chemicals.
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Affiliation(s)
- Rehman Javaid
- Lignin Valorization & Nanomaterials Lab, Centre for Applied Molecular Biology (CAMB), University of the Punjab, 87-West Canal Bank Road, Thokar Niaz Baig, 53700 Lahore, Pakistan.
- Cell and Molecular Biology Lab, Department of Zoology, University of the Punjab Quaid-e Azam Campus, 54590 Lahore, Pakistan.
| | - Aqsa Sabir
- Lignin Valorization & Nanomaterials Lab, Centre for Applied Molecular Biology (CAMB), University of the Punjab, 87-West Canal Bank Road, Thokar Niaz Baig, 53700 Lahore, Pakistan.
| | - Nadeem Sheikh
- Lignin Valorization & Nanomaterials Lab, Centre for Applied Molecular Biology (CAMB), University of the Punjab, 87-West Canal Bank Road, Thokar Niaz Baig, 53700 Lahore, Pakistan.
- Cell and Molecular Biology Lab, Department of Zoology, University of the Punjab Quaid-e Azam Campus, 54590 Lahore, Pakistan.
| | - Muhammad Ferhan
- Lignin Valorization & Nanomaterials Lab, Centre for Applied Molecular Biology (CAMB), University of the Punjab, 87-West Canal Bank Road, Thokar Niaz Baig, 53700 Lahore, Pakistan.
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Zhao K, Lin F, Romero-Gamboa SP, Saha P, Goh HJ, An G, Jung KH, Hazen SP, Bartley LE. Rice Genome-Scale Network Integration Reveals Transcriptional Regulators of Grass Cell Wall Synthesis. FRONTIERS IN PLANT SCIENCE 2019; 10:1275. [PMID: 31681374 PMCID: PMC6813959 DOI: 10.3389/fpls.2019.01275] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 09/12/2019] [Indexed: 05/07/2023]
Abstract
Grasses have evolved distinct cell wall composition and patterning relative to dicotyledonous plants. However, despite the importance of this plant family, transcriptional regulation of its cell wall biosynthesis is poorly understood. To identify grass cell wall-associated transcription factors, we constructed the Rice Combined mutual Ranked Network (RCRN). The RCRN covers >90% of annotated rice (Oryza sativa) genes, is high quality, and includes most grass-specific cell wall genes, such as mixed-linkage glucan synthases and hydroxycinnamoyl acyltransferases. Comparing the RCRN and an equivalent Arabidopsis network suggests that grass orthologs of most genetically verified eudicot cell wall regulators also control this process in grasses, but some transcription factors vary significantly in network connectivity between these divergent species. Reverse genetics, yeast-one-hybrid, and protoplast-based assays reveal that OsMYB61a activates a grass-specific acyltransferase promoter, which confirms network predictions and supports grass-specific cell wall synthesis genes being incorporated into conserved regulatory circuits. In addition, 10 of 15 tested transcription factors, including six novel Wall-Associated regulators (WAP1, WACH1, WAHL1, WADH1, OsMYB13a, and OsMYB13b), alter abundance of cell wall-related transcripts when transiently expressed. The results highlight the quality of the RCRN for examining rice biology, provide insight into the evolution of cell wall regulation, and identify network nodes and edges that are possible leads for improving cell wall composition.
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Affiliation(s)
- Kangmei Zhao
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
| | - Fan Lin
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
| | | | - Prasenjit Saha
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
| | - Hyung-Jung Goh
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, South Korea
| | - Gynheung An
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, South Korea
| | - Ki-Hong Jung
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, South Korea
| | - Samuel P. Hazen
- Department of Biology, University of Massachusetts, Amherst, MA, United States
| | - Laura E. Bartley
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
- *Correspondence: Laura E. Bartley,
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Otulak-Kozieł K, Kozieł E, Lockhart BEL. Plant Cell Wall Dynamics in Compatible and Incompatible Potato Response to Infection Caused by Potato Virus Y (PVY NTN). Int J Mol Sci 2018; 19:ijms19030862. [PMID: 29543714 PMCID: PMC5877723 DOI: 10.3390/ijms19030862] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 03/12/2018] [Accepted: 03/13/2018] [Indexed: 02/04/2023] Open
Abstract
The cell wall provides the structure of the plant, and also acts as a barier against biotic stress. The vein necrosis strain of Potato virus Y (PVYNTN) induces necrotic disease symptoms that affect both plant growth and yield. Virus infection triggers a number of inducible basal defense responses, including defense proteins, especially those involved in cell wall metabolism. This study investigates the comparison of cell wall host dynamics induced in a compatible (potato cv. Irys) and incompatible (potato cv. Sárpo Mira with hypersensitive reaction gene Ny-Smira) PVYNTN–host–plant interaction. Ultrastructural analyses revealed numerous cell wall changes induced by virus infection. Furthermore, the localization of essential defensive wall-associated proteins in susceptible and resistant potato host to PVYNTN infection were investigated. The data revealed a higher level of detection of pathogenesis-related protein 2 (PR-2) in a compatible compared to an incompatible (HR) interaction. Immunofluorescence analyses indicated that hydroxyproline-rich glycoproteins (HRGP) (extensin) synthesis was induced, whereas that of cellulose synthase catalytic subunits (CesA4) decreased as a result of PVYNTN infection. The highest level of extensin localization was found in HR potato plants. Proteins involved in cell wall metabolism play a crucial role in the interaction because they affect the spread of the virus. Analysis of CesA4, PR-2 and HRGP deposition within the apoplast and symplast confirmed the active trafficking of these proteins as a step-in potato cell wall remodeling in response to PVYNTN infection. Therefore, cell wall reorganization may be regarded as an element of “signWALLing”—involving apoplast and symplast activation as a specific response to viruses.
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Affiliation(s)
- Katarzyna Otulak-Kozieł
- Department of Botany, Faculty of Agriculture and Biology, Warsaw University of Life Sciences-SGGW, 159 Nowoursynowska St., 02-776 Warsaw, Poland.
| | - Edmund Kozieł
- Department of Botany, Faculty of Agriculture and Biology, Warsaw University of Life Sciences-SGGW, 159 Nowoursynowska St., 02-776 Warsaw, Poland.
| | - Benham E L Lockhart
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, USA.
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Sun H, Zhao W, Mao X, Li Y, Wu T, Chen F. High-value biomass from microalgae production platforms: strategies and progress based on carbon metabolism and energy conversion. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:227. [PMID: 30151055 PMCID: PMC6100726 DOI: 10.1186/s13068-018-1225-6] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 08/09/2018] [Indexed: 05/13/2023]
Abstract
Microalgae are capable of producing sustainable bioproducts and biofuels by using carbon dioxide or other carbon substances in various cultivation modes. It is of great significance to exploit microalgae for the economical viability of biofuels and the revenues from high-value bioproducts. However, the industrial performance of microalgae is still challenged with potential conflict between cost of microalgae cultivation and revenues from them, which is mainly ascribed to the lack of comprehensive understanding of carbon metabolism and energy conversion. In this review, we provide an overview of the recent advances in carbon and energy fluxes of light-dependent reaction, Calvin-Benson-Bassham cycle, tricarboxylic acid cycle, glycolysis pathway and processes of product biosynthesis in microalgae, with focus on the increased photosynthetic and carbon efficiencies. Recent strategies for the enhanced production of bioproducts and biofuels from microalgae are discussed in detail. Approaches to alter microbial physiology by controlling light, nutrient and other environmental conditions have the advantages of increasing biomass concentration and product yield through the efficient carbon conversion. Engineering strategies by regulating carbon partitioning and energy route are capable of improving the efficiencies of photosynthesis and carbon conversion, which consequently realize high-value biomass. The coordination of carbon and energy fluxes is emerging as the potential strategy to increase efficiency of carbon fixation and product biosynthesis. To achieve more desirable high-value products, coordination of multi-stage cultivation with engineering and stress-based strategies occupies significant positions in a long term.
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Affiliation(s)
- Han Sun
- Institute for Food & Bioresource Engineering, College of Engineering, Peking University, Beijing, 100871 China
- BIC-ESAT, College of Engineering, Peking University, Beijing, 100871 China
| | - Weiyang Zhao
- Institute for Food & Bioresource Engineering, College of Engineering, Peking University, Beijing, 100871 China
- BIC-ESAT, College of Engineering, Peking University, Beijing, 100871 China
| | - Xuemei Mao
- Institute for Food & Bioresource Engineering, College of Engineering, Peking University, Beijing, 100871 China
- BIC-ESAT, College of Engineering, Peking University, Beijing, 100871 China
| | - Yuelian Li
- Institute for Food & Bioresource Engineering, College of Engineering, Peking University, Beijing, 100871 China
- BIC-ESAT, College of Engineering, Peking University, Beijing, 100871 China
| | - Tao Wu
- Institute for Food & Bioresource Engineering, College of Engineering, Peking University, Beijing, 100871 China
- BIC-ESAT, College of Engineering, Peking University, Beijing, 100871 China
| | - Feng Chen
- Institute for Food & Bioresource Engineering, College of Engineering, Peking University, Beijing, 100871 China
- BIC-ESAT, College of Engineering, Peking University, Beijing, 100871 China
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14
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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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15
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Bryan AC, Jawdy S, Gunter L, Gjersing E, Sykes R, Hinchee MAW, Winkeler KA, Collins CM, Engle N, Tschaplinski TJ, Yang X, Tuskan GA, Muchero W, Chen JG. Knockdown of a laccase in Populus deltoides confers altered cell wall chemistry and increased sugar release. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:2010-20. [PMID: 26997157 PMCID: PMC5043505 DOI: 10.1111/pbi.12560] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 03/01/2016] [Accepted: 03/12/2016] [Indexed: 05/07/2023]
Abstract
Plant laccases are thought to function in the oxidation of monolignols which leads to higher order lignin formation. Only a hand-full of laccases in plants have been functionally evaluated, and as such little is known about the breadth of their impact on cell wall chemistry or structure. Here, we describe a previously uncharacterized laccase from Populus, encoded by locus Potri.008G064000, whose reduced expression resulted in transgenic Populus trees with changes in syringyl/guaiacyl ratios as well as altered sugar release phenotypes. These phenotypes are consistent with plant biomass exhibiting reduced recalcitrance. Interestingly, the transgene effect on recalcitrance is dependent on a mild pretreatment prior to chemical extraction of sugars. Metabolite profiling suggests the transgene modulates phenolics that are associated with the cell wall structure. We propose that this particular laccase has a range of functions related to oxidation of phenolics and conjugation of flavonoids that interact with lignin in the cell wall.
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Affiliation(s)
- Anthony C Bryan
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Sara Jawdy
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Lee Gunter
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Erica Gjersing
- The Biosciences Center, National Renewable Energy Laboratory, Golden, CO, USA
| | - Robert Sykes
- The Biosciences Center, National Renewable Energy Laboratory, Golden, CO, USA
| | | | | | | | - Nancy Engle
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Timothy J Tschaplinski
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Xiaohan Yang
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Gerald A Tuskan
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Wellington Muchero
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
| | - Jin-Gui Chen
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
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Expression, purification and biochemical characterization of AtFUT1, a xyloglucan-specific fucosyltransferase from Arabidopsis thaliana. Biochimie 2016; 128-129:183-92. [PMID: 27580247 DOI: 10.1016/j.biochi.2016.08.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 08/25/2016] [Indexed: 12/29/2022]
Abstract
Efforts to identify genes and characterize enzymes involved in the biosynthesis of plant cell wall polysaccharides have yet to produce and purify to homogeneity an active plant cell wall synthesizing enzyme suitable for structural studies. In Arabidopsis, the last step of xyloglucan (XG) biosynthesis is catalyzed by fucosyltransferase 1 (AtFUT1), which transfers l-fucose from GDP-β-l-fucose to a specific galactose on the XG core. Here, we describe the production of a soluble form of AtFUT1 (HisΔ68-AtFUT1) and its purification to milligram quantities. An active form of AtFUT1 was produced in an insect cell culture medium, using a large-scale expression system, and purified in a two-step protocol. Characterization of purified HisΔ68-AtFUT1 revealed that the enzyme behaves as a non-covalent homodimer in solution. A bioluminescent transferase assay confirmed HisΔ68-AtFUT1 activity on its substrates, namely GDP-fucose and tamarind XG, with calculated Km values of 42 μM and 0.31 μM, respectively. Moreover, the length of the XG-derived acceptor quantitatively affected fucosyltransferase activity in a size-dependent manner. The affinity of HisΔ68-AtFUT1 for tamarind XG and GDP was determined using isothermal titration calorimetry (ITC). Interestingly, ITC data suggest that HisΔ68-AtFUT1 undergoes conformational changes in the presence of its first co-substrate (XG or GDP), which then confers greater affinity for the second co-substrate. The procedure described in this study can potentially be transferred to other enzymes involved in plant cell wall synthesis.
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17
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CAZyChip: dynamic assessment of exploration of glycoside hydrolases in microbial ecosystems. BMC Genomics 2016; 17:671. [PMID: 27552843 PMCID: PMC4994258 DOI: 10.1186/s12864-016-2988-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 08/02/2016] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Microorganisms constitute a reservoir of enzymes involved in environmental carbon cycling and degradation of plant polysaccharides through their production of a vast variety of Glycoside Hydrolases (GH). The CAZyChip was developed to allow a rapid characterization at transcriptomic level of these GHs and to identify enzymes acting on hydrolysis of polysaccharides or glycans. RESULTS This DNA biochip contains the signature of 55,220 bacterial GHs available in the CAZy database. Probes were designed using two softwares, and microarrays were directly synthesized using the in situ ink-jet technology. CAZyChip specificity and reproducibility was validated by hybridization of known GHs RNA extracted from recombinant E. coli strains, which were previously identified by a functional metagenomic approach. The GHs arsenal was also studied in bioprocess conditions using rumen derived microbiota. CONCLUSIONS The CAZyChip appears to be a user friendly tool for profiling the expression of a large variety of GHs. It can be used to study temporal variations of functional diversity, thereby facilitating the identification of new efficient candidates for enzymatic conversions from various ecosystems.
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Culbertson AT, Smith AL, Cook MD, Zabotina OA. Truncations of xyloglucan xylosyltransferase 2 provide insights into the roles of the N- and C-terminus. PHYTOCHEMISTRY 2016; 128:12-19. [PMID: 27193738 DOI: 10.1016/j.phytochem.2016.03.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 03/04/2016] [Accepted: 03/30/2016] [Indexed: 06/05/2023]
Abstract
Xyloglucan is the most abundant hemicellulose in the primary cell wall of dicotyledonous plants. In Arabidopsis, three xyloglucan xylosyltransferases, XXT1, XXT2, and XXT5, participate in xylosylation of the xyloglucan backbone. Despite the importance of these enzymes, there is a lack of information on their structure and the critical residues required for substrate binding and transferase activity. In this study, the roles of different domains of XX2 in protein expression and catalytic activity were investigated by constructing a series of N- and C-terminal truncations. XXT2 with an N-terminal truncation of 31 amino acids after the predicted transmembrane domain showed the highest protein expression, but truncations of more than 31 residues decreased protein expression and catalytic activity. XXT2 constructs with C-terminal truncations showed increased protein expression but decreased activity, particularly for truncations of 44 or more amino acids. Site-directed mutagenesis was also used to investigate six positively charged residues near the C-terminus and found that four of the mutants showed decreased enzymatic activity. We conclude that the N- and C-termini of XXT2 have important roles in protein folding and enzymatic activity: the stem region (particularly the N-terminus of the catalytic domain) is critical for protein folding and the C-terminus is essential for enzymatic activity but not for protein folding.
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Affiliation(s)
- Alan T Culbertson
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - Adrienne L Smith
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - Matthew D Cook
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - Olga A Zabotina
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011, USA.
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19
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Culbertson AT, Tietze AA, Tietze D, Chou YH, Smith AL, Young ZT, Zabotina OA. A homology model of Xyloglucan Xylosyltransferase 2 reveals critical amino acids involved in substrate binding. Glycobiology 2016; 26:961-972. [DOI: 10.1093/glycob/cww050] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 04/14/2016] [Indexed: 11/14/2022] Open
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20
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Repeated cultivation: non-cell disruption extraction of astaxanthin for Haematococcus pluvialis. Sci Rep 2016; 6:20578. [PMID: 26838183 PMCID: PMC4738327 DOI: 10.1038/srep20578] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 01/06/2016] [Indexed: 11/19/2022] Open
Abstract
The operation of cell disruption is indispensable but cost much in microalgae industry. To be simplified, two different reaction mechanisms await in the cell to respond to moderated or stressed environment. The physical and chemical changes of enzyme and turgor pressure of cell in this conversion play an important role in the enhancement of biomass and metabolites. Repeated turgor pressure (based on the structure and mechanics of cell wall) and converted enzyme system (based on photosynthesis) were used to loosen cell wall and then repeated cultivation of Haematococcus pluvialis for astaxanthin extraction was proposed. There was no significant difference of extraction yield between the broken cell (94.75 ± 3.13%) and non-broken cell (92.32 ± 3.24%) treated by the repeated cultivation. Meanwhile, fed-batch culture according to the relationship among pH and nutrient concentration was used to enhance the biomass of Haematococcus pluvialis with the dry cell weight of 1.63 ± 0.07 g/L.
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Transcriptome analysis of secondary cell wall development in Medicago truncatula. BMC Genomics 2016; 17:23. [PMID: 26728635 PMCID: PMC4700669 DOI: 10.1186/s12864-015-2330-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 12/17/2015] [Indexed: 11/18/2022] Open
Abstract
Background Legumes are important to humans by providing food, feed and raw materials for industrial utilizations. Some legumes, such as alfalfa, are potential bioenergy crops due to their high biomass productivity. Global transcriptional profiling has been successfully used to identify genes and regulatory pathways in secondary cell wall thickening in Arabidopsis, but such transcriptome data is lacking in legumes. Results A systematic microarray assay and high through-put real time PCR analysis of secondary cell wall development were performed along stem maturation in Medicago truncatula. More than 11,000 genes were differentially expressed during stem maturation, and were categorized into 10 expression clusters. Among these, 279 transcription factor genes were correlated with lignin/cellulose biosynthesis, therefore representing putative regulators of secondary wall development. The b-ZIP, NAC, WRKY, C2H2 zinc finger (ZF), homeobox, and HSF gene families were over-represented. Gene co-expression network analysis was employed to identify transcription factors that may regulate the biosynthesis of lignin, cellulose and hemicellulose. As a complementary approach to microarray, real-time PCR analysis was used to characterize the expression of 1,045 transcription factors in the stem samples, and 64 of these were upregulated more than 5-fold during stem maturation. Reverse genetics characterization of a cellulose synthase gene in cluster 10 confirmed its function in xylem development. Conclusions This study provides a useful transcriptome and expression resource for understanding cell wall development, which is pivotal to enhance biomass production in legumes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2330-6) contains supplementary material, which is available to authorized users.
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Yang JH, Wang H. Molecular Mechanisms for Vascular Development and Secondary Cell Wall Formation. FRONTIERS IN PLANT SCIENCE 2016; 7:356. [PMID: 27047525 PMCID: PMC4801872 DOI: 10.3389/fpls.2016.00356] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 03/07/2016] [Indexed: 05/18/2023]
Abstract
Vascular tissues are important for transporting water and nutrients throughout the plant and as physical support of upright growth. The primary constituents of vascular tissues, xylem, and phloem, are derived from the meristematic vascular procambium and cambium. Xylem cells develop secondary cell walls (SCWs) that form the largest part of plant lignocellulosic biomass that serve as a renewable feedstock for biofuel production. For the last decade, research on vascular development and SCW biosynthesis has seen rapid progress due to the importance of these processes to plant biology and to the biofuel industry. Plant hormones, transcriptional regulators and peptide signaling regulate procambium/cambium proliferation, vascular patterning, and xylem differentiation. Transcriptional regulatory pathways play a pivot role in SCW biosynthesis. Although most of these discoveries are derived from research in Arabidopsis, many genes have shown conserved functions in biofuel feedstock species. Here, we review the recent advances in our understanding of vascular development and SCW formation and discuss potential biotechnological uses.
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Affiliation(s)
- Jung Hyun Yang
- Department of Plant Science and Landscape Architecture, University of ConnecticutStorrs, CT, USA
| | - Huanzhong Wang
- Department of Plant Science and Landscape Architecture, University of ConnecticutStorrs, CT, USA
- Institute for Systems Genomics, University of ConnecticutStorrs, CT, USA
- *Correspondence: Huanzhong Wang,
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23
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Zhang HM, Talbot MJ, McCurdy DW, Patrick JW, Offler CE. Calcium-dependent depletion zones in the cortical microtubule array coincide with sites of, but do not regulate, wall ingrowth papillae deposition in epidermal transfer cells. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:6021-33. [PMID: 26136268 PMCID: PMC4566988 DOI: 10.1093/jxb/erv317] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Trans-differentiation to a transfer-cell morphology is characterized by the localized deposition of wall ingrowth papillae that protrude into the cytosol. Whether the cortical microtubule array directs wall ingrowth papillae formation was investigated using a Vicia faba cotyledon culture system in which their adaxial epidermal cells were spontaneously induced to trans-differentiate to transfer cells. During deposition of wall ingrowth papillae, the aligned cortical microtubule arrays in precursor epidermal cells were reorganized into a randomized array characterized by circular depletion zones. Concurrence of the temporal appearance, spatial pattern, and size of depletion zones and wall ingrowth papillae was consistent with each papilla occupying a depletion zone. Surprisingly, microtubules appeared not to regulate construction of wall ingrowth papillae, as neither depolymerization nor stabilization of cortical microtubules changed their deposition pattern or morphology. Moreover, the size and spatial pattern of depletion zones was unaltered when the formation of wall ingrowth papillae was blocked by inhibiting cellulose biosynthesis. In contrast, the depletion zones were absent when the cytosolic calcium plumes, responsible for directing wall ingrowth papillae formation, were blocked or dissipated. Thus, we conclude that the depletion zones within the cortical microtubule array result from localized depolymerization of microtubules initiated by elevated cytosolic Ca(2+) levels at loci where wall ingrowth papillae are deposited. The physiological significance of the depletion zones as a mechanism to accommodate the construction of wall ingrowth papillae without compromising maintenance of the plasma membrane-microtubule inter-relationship is discussed.
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Affiliation(s)
- Hui-ming Zhang
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Mark J Talbot
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia CSIRO Agriculture, Canberra, ACT 2601, Australia
| | - David W McCurdy
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia
| | - John W Patrick
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Christina E Offler
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia
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Nakano Y, Yamaguchi M, Endo H, Rejab NA, Ohtani M. NAC-MYB-based transcriptional regulation of secondary cell wall biosynthesis in land plants. FRONTIERS IN PLANT SCIENCE 2015; 6:288. [PMID: 25999964 PMCID: PMC4419676 DOI: 10.3389/fpls.2015.00288] [Citation(s) in RCA: 274] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2015] [Accepted: 04/09/2015] [Indexed: 05/08/2023]
Abstract
Plant cells biosynthesize primary cell walls (PCW) in all cells and produce secondary cell walls (SCWs) in specific cell types that conduct water and/or provide mechanical support, such as xylem vessels and fibers. The characteristic mechanical stiffness, chemical recalcitrance, and hydrophobic nature of SCWs result from the organization of SCW-specific biopolymers, i.e., highly ordered cellulose, hemicellulose, and lignin. Synthesis of these SCW-specific biopolymers requires SCW-specific enzymes that are regulated by SCW-specific transcription factors. In this review, we summarize our current knowledge of the transcriptional regulation of SCW formation in plant cells. Advances in research on SCW biosynthesis during the past decade have expanded our understanding of the transcriptional regulation of SCW formation, particularly the functions of the NAC and MYB transcription factors. Focusing on the NAC-MYB-based transcriptional network, we discuss the regulatory systems that evolved in land plants to modify the cell wall to serve as a key component of structures that conduct water and provide mechanical support.
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Affiliation(s)
- Yoshimi Nakano
- Graduate School of Biological Sciences, Nara Institute of Science and TechnologyIkoma, Japan
| | - Masatoshi Yamaguchi
- Division of Strategic Research and Development, Graduate School of Science and Engineering, Saitama UniversitySaitama, Japan
- PRESTO (Precursory Research for Embryonic Science and Technology), Japan Science and Technology AgencyKawaguchi, Japan
| | - Hitoshi Endo
- Graduate School of Biological Sciences, Nara Institute of Science and TechnologyIkoma, Japan
| | - Nur Ardiyana Rejab
- Graduate School of Biological Sciences, Nara Institute of Science and TechnologyIkoma, Japan
- Faculty of Science, Institute of Biological Sciences, University of MalayaKuala Lumpur, Malaysia
| | - Misato Ohtani
- Graduate School of Biological Sciences, Nara Institute of Science and TechnologyIkoma, Japan
- Biomass Engineering Program Cooperation Division, RIKEN Center for Sustainable Resource ScienceYokohama, Japan
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25
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San Clemente H, Jamet E. WallProtDB, a database resource for plant cell wall proteomics. PLANT METHODS 2015; 11:2. [PMID: 25614757 PMCID: PMC4302427 DOI: 10.1186/s13007-015-0045-y] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 01/06/2015] [Indexed: 05/18/2023]
Abstract
BACKGROUND During the last fifteen years, cell wall proteomics has become a major research field with the publication of more than 50 articles describing plant cell wall proteomes. The WallProtDB database has been designed as a tool to facilitate the inventory, the interpretation of cell wall proteomics data and the comparisons between cell wall proteomes. RESULTS WallProtDB (http://www.polebio.lrsv.ups-tlse.fr/WallProtDB/) presently contains 2170 proteins and ESTs identified experimentally in 36 cell wall proteomics studies performed on 11 different plant species. Two criteria have to be met for entering WallProtDB. First one is related to the identification of proteins. Only proteins identified in plant with available genomic or ESTs data are considered to ensure unambiguous identification. Second criterion is related to the difficulty to obtain clean cell wall fractions. Indeed, since cell walls constitute an open compartment difficult to isolate, numerous proteins predicted to be intracellular and/or having functions inside the cell have been identified in cell wall extracts. Then, except proteins predicted to be plasma membrane proteins, only proteins having a predicted signal peptide and no known intracellular retention signal are included in the database. In addition, WallProtDB contains information about the strategies used to obtain cell wall protein extracts and to identify proteins by mass spectrometry and bioinformatics. Mass spectrometry data are included when available. All the proteins of WallProtDB are linked to ProtAnnDB, another database, which contains structural and functional bioinformatics annotations of proteins as well as links to other databases (Aramemnon, CAZy, Planet, Phytozome). A list of references in the cell wall proteomics field is also provided. CONCLUSIONS WallProtDB aims at becoming a cell wall proteome reference database. It can be updated at any time on request and provide a support for sharing cell wall proteomics data and literature references with researchers interested in plant cell wall biology.
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Affiliation(s)
- Hélène San Clemente
- />Université de Toulouse; UPS; UMR 5546, Laboratoire de Recherche en Sciences Végétales, BP 42617, F-31326 Castanet-Tolosan, France
- />CNRS; UMR 5546, BP 42617, F-31326 Castanet-Tolosan, France
| | - Elisabeth Jamet
- />Université de Toulouse; UPS; UMR 5546, Laboratoire de Recherche en Sciences Végétales, BP 42617, F-31326 Castanet-Tolosan, France
- />CNRS; UMR 5546, BP 42617, F-31326 Castanet-Tolosan, France
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Lund CH, Bromley JR, Stenbæk A, Rasmussen RE, Scheller HV, Sakuragi Y. A reversible Renilla luciferase protein complementation assay for rapid identification of protein-protein interactions reveals the existence of an interaction network involved in xyloglucan biosynthesis in the plant Golgi apparatus. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:85-97. [PMID: 25326916 PMCID: PMC4265154 DOI: 10.1093/jxb/eru401] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
A growing body of evidence suggests that protein-protein interactions (PPIs) occur amongst glycosyltransferases (GTs) required for plant glycan biosynthesis (e.g. cell wall polysaccharides and N-glycans) in the Golgi apparatus, and may control the functions of these enzymes. However, identification of PPIs in the endomembrane system in a relatively fast and simple fashion is technically challenging, hampering the progress in understanding the functional coordination of the enzymes in Golgi glycan biosynthesis. To solve the challenges, we adapted and streamlined a reversible Renilla luciferase protein complementation assay (Rluc-PCA), originally reported for use in human cells, for transient expression in Nicotiana benthamiana. We tested Rluc-PCA and successfully identified luminescence complementation amongst Golgi-localizing GTs known to form a heterodimer (GAUT1 and GAUT7) and those which homooligomerize (ARAD1). In contrast, no interaction was shown between negative controls (e.g. GAUT7, ARAD1, IRX9). Rluc-PCA was used to investigate PPIs amongst Golgi-localizing GTs involved in biosynthesis of hemicelluloses. Although no PPI was identified among six GTs involved in xylan biosynthesis, Rluc-PCA confirmed three previously proposed interactions and identified seven novel PPIs amongst GTs involved in xyloglucan biosynthesis. Notably, three of the novel PPIs were confirmed by a yeast-based split-ubiquitin assay. Finally, Gateway-enabled expression vectors were generated, allowing rapid construction of fusion proteins to the Rluc reporters and epitope tags. Our results show that Rluc-PCA coupled with transient expression in N. benthamiana is a fast and versatile method suitable for analysis of PPIs between Golgi resident proteins in an easy and mid-throughput fashion in planta.
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Affiliation(s)
- Christian H Lund
- University of Copenhagen, Department of Plant Biology and Biotechnology, Frederiksberg, DK-1871, Denmark
| | - Jennifer R Bromley
- University of Copenhagen, Department of Plant Biology and Biotechnology, Frederiksberg, DK-1871, Denmark Joint BioEnergy Institute, Feedstocks Division, Emeryville, CA 94608, USA Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Anne Stenbæk
- University of Copenhagen, Department of Plant Biology and Biotechnology, Frederiksberg, DK-1871, Denmark
| | - Randi E Rasmussen
- University of Copenhagen, Department of Plant Biology and Biotechnology, Frederiksberg, DK-1871, Denmark
| | - Henrik V Scheller
- Joint BioEnergy Institute, Feedstocks Division, Emeryville, CA 94608, USA Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Yumiko Sakuragi
- University of Copenhagen, Department of Plant Biology and Biotechnology, Frederiksberg, DK-1871, Denmark
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Kalluri UC, Yin H, Yang X, Davison BH. Systems and synthetic biology approaches to alter plant cell walls and reduce biomass recalcitrance. PLANT BIOTECHNOLOGY JOURNAL 2014; 12:1207-16. [PMID: 25363806 PMCID: PMC4265275 DOI: 10.1111/pbi.12283] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Revised: 09/11/2014] [Accepted: 09/12/2014] [Indexed: 05/19/2023]
Abstract
Fine-tuning plant cell wall properties to render plant biomass more amenable to biofuel conversion is a colossal challenge. A deep knowledge of the biosynthesis and regulation of plant cell wall and a high-precision genome engineering toolset are the two essential pillars of efforts to alter plant cell walls and reduce biomass recalcitrance. The past decade has seen a meteoric rise in use of transcriptomics and high-resolution imaging methods resulting in fresh insights into composition, structure, formation and deconstruction of plant cell walls. Subsequent gene manipulation approaches, however, commonly include ubiquitous mis-expression of a single candidate gene in a host that carries an intact copy of the native gene. The challenges posed by pleiotropic and unintended changes resulting from such an approach are moving the field towards synthetic biology approaches. Synthetic biology builds on a systems biology knowledge base and leverages high-precision tools for high-throughput assembly of multigene constructs and pathways, precision genome editing and site-specific gene stacking, silencing and/or removal. Here, we summarize the recent breakthroughs in biosynthesis and remodelling of major secondary cell wall components, assess the impediments in obtaining a systems-level understanding and explore the potential opportunities in leveraging synthetic biology approaches to reduce biomass recalcitrance.
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Affiliation(s)
- Udaya C Kalluri
- BioEnergy Science Center and Biosciences Division, Oak Ridge National LaboratoryOak Ridge, TN, USA
- * Correspondence (Tel 1 865 576 9495, fax 1 865 576 9939; email )
| | - Hengfu Yin
- Biosciences Division, Oak Ridge National LaboratoryOak Ridge, TN, USA
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National LaboratoryOak Ridge, TN, USA
| | - Brian H Davison
- BioEnergy Science Center and Biosciences Division, Oak Ridge National LaboratoryOak Ridge, TN, USA
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Sablok G, Fu Y, Bobbio V, Laura M, Rotino GL, Bagnaresi P, Allavena A, Velikova V, Viola R, Loreto F, Li M, Varotto C. Fuelling genetic and metabolic exploration of C 3 bioenergy crops through the first reference transcriptome of Arundo donax L. PLANT BIOTECHNOLOGY JOURNAL 2014; 12. [PMCID: PMC4285118 DOI: 10.1111/pbi.12159] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The development of inexpensive and highly productive biomass sources of biofuel is a priority in global climate change biology. Arundo donax, also known as the giant reed, is recognized as one of the most promising nonfood bioenergy crops in Europe. Despite its relevance, to date no genomic resources are available to support the characterization of the developmental, adaptive and metabolic traits underlying the high productivity of this nonmodel species. We hereby present the first report on the de novo assembly of bud, culm, leaf and root transcriptomes of A. donax, which can be accessed through a customized BLAST server (http://ecogenomics.fmach.it/arundo/) for mining and exploring the genetic potential of this species. Based on functional annotation and homology comparison to 19 prospective biofuel Poaceae species, we provide the first genomic view of this so far unexplored crop and indicate the model species with highest potential for comparative genomics approaches. The analysis of the transcriptome reveals strong differences in the enrichment of the Gene Ontology categories and the relative expression among different organs, which can guide future efforts for functional genomics or genetic improvement of A. donax. A set of homologs to key genes involved in lignin, cellulose, starch, lipid metabolism and in the domestication of other crops is discussed to provide a platform for possible enhancement of productivity and saccharification efficiency in A. donax.
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Affiliation(s)
- Gaurav Sablok
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund MachS. Michele all'Adige, TN, Italy
| | - Yuan Fu
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund MachS. Michele all'Adige, TN, Italy
- Dipartimento di Biotecnologie, Università degli Studi di VeronaVerona, Italy
| | - Valentina Bobbio
- Dipartimento di Scienze della Terra, dell'Ambiente e della Vita, Università degli Studi di GenovaGenova, Italy
- Unità di Ricerca per la Floricoltura e le Specie Ornamentali, Consiglio per la Ricerca e la Sperimentazione in AgricolturaSanremo, IM, Italy
| | - Marina Laura
- Unità di Ricerca per la Floricoltura e le Specie Ornamentali, Consiglio per la Ricerca e la Sperimentazione in AgricolturaSanremo, IM, Italy
| | - Giuseppe L Rotino
- Unità di Ricerca per l'Orticoltura, Consiglio per la Ricerca e la Sperimentazione in AgricolturaMontanaso Lombardo, LO, Italy
| | - Paolo Bagnaresi
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Genomics Research CentreFiorenzuola D'Arda, PC, Italy
| | - Andrea Allavena
- Unità di Ricerca per la Floricoltura e le Specie Ornamentali, Consiglio per la Ricerca e la Sperimentazione in AgricolturaSanremo, IM, Italy
| | - Violeta Velikova
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund MachS. Michele all'Adige, TN, Italy
- Bulgarian Academy of Sciences, Institute of Plant Physiology and GeneticsSofia, Bulgaria
| | - Roberto Viola
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund MachS. Michele all'Adige, TN, Italy
| | - Francesco Loreto
- Dipartimento di Scienze Bio-Agroalimentari (DISBA), Consiglio Nazionale delle Ricerche (CNR)Roma, Italy
| | - Mingai Li
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund MachS. Michele all'Adige, TN, Italy
| | - Claudio Varotto
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund MachS. Michele all'Adige, TN, Italy
- * Correspondence (fax +39 0461 650 956; email )
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Yin Y, Johns MA, Cao H, Rupani M. A survey of plant and algal genomes and transcriptomes reveals new insights into the evolution and function of the cellulose synthase superfamily. BMC Genomics 2014; 15:260. [PMID: 24708035 PMCID: PMC4023592 DOI: 10.1186/1471-2164-15-260] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Accepted: 03/31/2014] [Indexed: 11/30/2022] Open
Abstract
Background Enzymes of the cellulose synthase (CesA) family and CesA-like (Csl) families are responsible for the synthesis of celluloses and hemicelluloses, and thus are of great interest to bioenergy research. We studied the occurrences and phylogenies of CesA/Csl families in diverse plants and algae by comprehensive data mining of 82 genomes and transcriptomes. Results We found that 1) charophytic green algae (CGA) have orthologous genes in CesA, CslC and CslD families; 2) liverwort genes are found in the CesA, CslA, CslC and CslD families; 3) The fern Pteridium aquilinum not only has orthologs in these conserved families but also in the CslB, CslH and CslE families; 4) basal angiosperms, e.g. Aristolochia fimbriata, have orthologs in these families too; 5) gymnosperms have genes forming clusters ancestral to CslB/H and to CslE/J/G respectively; 6) CslG is found in switchgrass and basal angiosperms; 7) CslJ is widely present in dicots and monocots; 8) CesA subfamilies have already diversified in ferns. Conclusions We speculate that: (i) ferns and horsetails might both have CslH enzymes, responsible for the synthesis of mixed-linkage glucans and (ii) CslD and similar genes might be responsible for the synthesis of mannans in CGA. Our findings led to a more detailed model of cell wall evolution and suggested that gene loss played an important role in the evolution of Csl families. We also demonstrated the usefulness of transcriptome data in the study of plant cell wall evolution and diversity.
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Affiliation(s)
- Yanbin Yin
- Department of Biological Sciences, Northern Illinois University, Montgomery Hall 325A, DeKalb, IL 60115-2857, USA.
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Zhang Q, Cheetamun R, Dhugga KS, Rafalski JA, Tingey SV, Shirley NJ, Taylor J, Hayes K, Beatty M, Bacic A, Burton RA, Fincher GB. Spatial gradients in cell wall composition and transcriptional profiles along elongating maize internodes. BMC PLANT BIOLOGY 2014; 14:27. [PMID: 24423166 PMCID: PMC3927872 DOI: 10.1186/1471-2229-14-27] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Accepted: 12/27/2013] [Indexed: 05/11/2023]
Abstract
BACKGROUND The elongating maize internode represents a useful system for following development of cell walls in vegetative cells in the Poaceae family. Elongating internodes can be divided into four developmental zones, namely the basal intercalary meristem, above which are found the elongation, transition and maturation zones. Cells in the basal meristem and elongation zones contain mainly primary walls, while secondary cell wall deposition accelerates in the transition zone and predominates in the maturation zone. RESULTS The major wall components cellulose, lignin and glucuronoarabinoxylan (GAX) increased without any abrupt changes across the elongation, transition and maturation zones, although GAX appeared to increase more between the elongation and transition zones. Microarray analyses show that transcript abundance of key glycosyl transferase genes known to be involved in wall synthesis or re-modelling did not match the increases in cellulose, GAX and lignin. Rather, transcript levels of many of these genes were low in the meristematic and elongation zones, quickly increased to maximal levels in the transition zone and lower sections of the maturation zone, and generally decreased in the upper maturation zone sections. Genes with transcript profiles showing this pattern included secondary cell wall CesA genes, GT43 genes, some β-expansins, UDP-Xylose synthase and UDP-Glucose pyrophosphorylase, some xyloglucan endotransglycosylases/hydrolases, genes involved in monolignol biosynthesis, and NAM and MYB transcription factor genes. CONCLUSIONS The data indicated that the enzymic products of genes involved in cell wall synthesis and modification remain active right along the maturation zone of elongating maize internodes, despite the fact that corresponding transcript levels peak earlier, near or in the transition zone.
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Affiliation(s)
- Qisen Zhang
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, 5064 Adelaide, South Australia, Australia
| | - Roshan Cheetamun
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of Botany, University of Melbourne, 3010 Parkville, Victoria, Australia
| | - Kanwarpal S Dhugga
- Genetic Discovery Group, Crop Genetics Research and Development, Pioneer Hi-Bred International Inc. 7300 NW 62nd Avenue, 50131-1004 Johnston, IA, USA
| | - J Antoni Rafalski
- Genetic Discovery Group, DuPont Crop Genetics Research, DuPont Experimental Station, Building E353, 198803 Wilmington, DE, USA
| | - Scott V Tingey
- Genetic Discovery Group, DuPont Crop Genetics Research, DuPont Experimental Station, Building E353, 198803 Wilmington, DE, USA
| | - Neil J Shirley
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, 5064 Adelaide, South Australia, Australia
| | - Jillian Taylor
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, 5064 Adelaide, South Australia, Australia
| | - Kevin Hayes
- Genetic Discovery Group, Crop Genetics Research and Development, Pioneer Hi-Bred International Inc. 7300 NW 62nd Avenue, 50131-1004 Johnston, IA, USA
| | - Mary Beatty
- Genetic Discovery Group, Crop Genetics Research and Development, Pioneer Hi-Bred International Inc. 7300 NW 62nd Avenue, 50131-1004 Johnston, IA, USA
| | - Antony Bacic
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of Botany, University of Melbourne, 3010 Parkville, Victoria, Australia
| | - Rachel A Burton
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, 5064 Adelaide, South Australia, Australia
| | - Geoffrey B Fincher
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, 5064 Adelaide, South Australia, Australia
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Frei M. Lignin: characterization of a multifaceted crop component. ScientificWorldJournal 2013; 2013:436517. [PMID: 24348159 PMCID: PMC3848262 DOI: 10.1155/2013/436517] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Accepted: 09/24/2013] [Indexed: 11/17/2022] Open
Abstract
Lignin is a plant component with important implications for various agricultural disciplines. It confers rigidity to cell walls, and is therefore associated with tolerance to abiotic and biotic stresses and the mechanical stability of plants. In animal nutrition, lignin is considered an antinutritive component of forages as it cannot be readily fermented by rumen microbes. In terms of energy yield from biomass, the role of lignin depends on the conversion process. It contains more gross energy than other cell wall components and therefore confers enhanced heat value in thermochemical processes such as direct combustion. Conversely, it negatively affects biological energy conversion processes such as bioethanol or biogas production, as it inhibits microbial fermentation of the cell wall. Lignin from crop residues plays an important role in the soil organic carbon cycling, as it constitutes a recalcitrant carbon pool affecting nutrient mineralization and carbon sequestration. Due to the significance of lignin in several agricultural disciplines, the modification of lignin content and composition by breeding is becoming increasingly important. Both mapping of quantitative trait loci and transgenic approaches have been adopted to modify lignin in crops. However, breeding goals must be defined considering the conflicting role of lignin in different agricultural disciplines.
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Affiliation(s)
- Michael Frei
- Division of Abiotic Stress Tolerance in Crops, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Karlrobert-Kreiten Straße 13, 53115 Bonn, Germany
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32
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Dynamic metabolic flux analysis of plant cell wall synthesis. Metab Eng 2013; 18:78-85. [DOI: 10.1016/j.ymben.2013.04.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Revised: 03/14/2013] [Accepted: 04/16/2013] [Indexed: 11/21/2022]
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Vanholme B, Desmet T, Ronsse F, Rabaey K, Breusegem FV, Mey MD, Soetaert W, Boerjan W. Towards a carbon-negative sustainable bio-based economy. FRONTIERS IN PLANT SCIENCE 2013; 4:174. [PMID: 23761802 PMCID: PMC3669761 DOI: 10.3389/fpls.2013.00174] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2013] [Accepted: 05/16/2013] [Indexed: 05/17/2023]
Abstract
The bio-based economy relies on sustainable, plant-derived resources for fuels, chemicals, materials, food and feed rather than on the evanescent usage of fossil resources. The cornerstone of this economy is the biorefinery, in which renewable resources are intelligently converted to a plethora of products, maximizing the valorization of the feedstocks. Innovation is a prerequisite to move a fossil-based economy toward sustainable alternatives, and the viability of the bio-based economy depends on the integration between plant (green) and industrial (white) biotechnology. Green biotechnology deals with primary production through the improvement of biomass crops, while white biotechnology deals with the conversion of biomass into products and energy. Waste streams are minimized during these processes or partly converted to biogas, which can be used to power the processing pipeline. The sustainability of this economy is guaranteed by a third technology pillar that uses thermochemical conversion to valorize waste streams and fix residual carbon as biochar in the soil, hence creating a carbon-negative cycle. These three different multidisciplinary pillars interact through the value chain of the bio-based economy.
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Affiliation(s)
- Bartel Vanholme
- Department of Plant Systems Biology, Flanders Institute for BiotechnologyGent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent UniversityGent, Belgium
| | - Tom Desmet
- Department of Biochemical and Microbial Technology, Centre of Expertise – Industrial Biotechnology and Biocatalysis, Ghent UniversityGent, Belgium
| | - Frederik Ronsse
- Department of Biosystems Engineering, Ghent UniversityGent, Belgium
| | - Korneel Rabaey
- Laboratory of Microbial Ecology and Technology, Ghent UniversityGent, Belgium
- Centre for Microbial Electrosynthesis, The University of QueenslandBrisbane, Australia
- Advanced Water Management Centre, The University of QueenslandBrisbane, Australia
| | - Frank Van Breusegem
- Department of Plant Systems Biology, Flanders Institute for BiotechnologyGent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent UniversityGent, Belgium
| | - Marjan De Mey
- Department of Biochemical and Microbial Technology, Centre of Expertise – Industrial Biotechnology and Biocatalysis, Ghent UniversityGent, Belgium
| | - Wim Soetaert
- Department of Biochemical and Microbial Technology, Centre of Expertise – Industrial Biotechnology and Biocatalysis, Ghent UniversityGent, Belgium
| | - Wout Boerjan
- Department of Plant Systems Biology, Flanders Institute for BiotechnologyGent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent UniversityGent, Belgium
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Wells T, Ragauskas AJ. Biotechnological opportunities with the β-ketoadipate pathway. Trends Biotechnol 2012; 30:627-37. [DOI: 10.1016/j.tibtech.2012.09.008] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Revised: 09/24/2012] [Accepted: 09/26/2012] [Indexed: 01/18/2023]
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Grene R, Klumas C, Suren H, Yang K, Collakova E, Myers E, Heath LS, Holliday JA. Mining and visualization of microarray and metabolomic data reveal extensive cell wall remodeling during winter hardening in Sitka spruce (Picea sitchensis). FRONTIERS IN PLANT SCIENCE 2012; 3:241. [PMID: 23112803 PMCID: PMC3482696 DOI: 10.3389/fpls.2012.00241] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 10/10/2012] [Indexed: 05/18/2023]
Abstract
Microarray gene expression profiling is a powerful technique to understand complex developmental processes, but making biologically meaningful inferences from such studies has always been challenging. We previously reported a microarray study of the freezing acclimation period in Sitka spruce (Picea sitchensis) in which a large number of candidate genes for climatic adaptation were identified. In the current paper, we apply additional systems biology tools to these data to further probe changes in the levels of genes and metabolites and activities of associated pathways that regulate this complex developmental transition. One aspect of this adaptive process that is not well understood is the role of the cell wall. Our data suggest coordinated metabolic and signaling responses leading to cell wall remodeling. Co-expression of genes encoding proteins associated with biosynthesis of structural and non-structural cell wall carbohydrates was observed, which may be regulated by ethylene signaling components. At the same time, numerous genes, whose products are putatively localized to the endomembrane system and involved in both the synthesis and trafficking of cell wall carbohydrates, were up-regulated. Taken together, these results suggest a link between ethylene signaling and biosynthesis, and targeting of cell wall related gene products during the period of winter hardening. Automated Layout Pipeline for Inferred NEtworks (ALPINE), an in-house plugin for the Cytoscape visualization environment that utilizes the existing GeneMANIA and Mosaic plugins, together with the use of visualization tools, provided images of proposed signaling processes that became active over the time course of winter hardening, particularly at later time points in the process. The resulting visualizations have the potential to reveal novel, hypothesis-generating, gene association patterns in the context of targeted subcellular location.
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Affiliation(s)
- Ruth Grene
- Department of Plant Pathology, Physiology, and Weed Science, Virginia TechBlacksburg, VA, USA
- *Correspondence: Ruth Grene, Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA 24061, USA. e-mail:
| | - Curtis Klumas
- Department of Plant Pathology, Physiology, and Weed Science, Virginia TechBlacksburg, VA, USA
- Genetics, Bioinformatics and Computational Biology Program, Virginia TechBlacksburg, VA, USA
| | - Haktan Suren
- Genetics, Bioinformatics and Computational Biology Program, Virginia TechBlacksburg, VA, USA
- Department of Forest Resources and Environmental Conservation, Virginia TechBlacksburg, VA, USA
| | - Kuan Yang
- Department of Plant Pathology, Physiology, and Weed Science, Virginia TechBlacksburg, VA, USA
- Genetics, Bioinformatics and Computational Biology Program, Virginia TechBlacksburg, VA, USA
| | - Eva Collakova
- Department of Plant Pathology, Physiology, and Weed Science, Virginia TechBlacksburg, VA, USA
| | - Elijah Myers
- Genetics, Bioinformatics and Computational Biology Program, Virginia TechBlacksburg, VA, USA
- Department of Computer Science, Virginia TechBlacksburg, VA, USA
| | - Lenwood S. Heath
- Department of Computer Science, Virginia TechBlacksburg, VA, USA
| | - Jason A. Holliday
- Department of Forest Resources and Environmental Conservation, Virginia TechBlacksburg, VA, USA
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Liepman AH, Cavalier DM. The CELLULOSE SYNTHASE-LIKE A and CELLULOSE SYNTHASE-LIKE C families: recent advances and future perspectives. FRONTIERS IN PLANT SCIENCE 2012; 3:109. [PMID: 22654891 PMCID: PMC3359485 DOI: 10.3389/fpls.2012.00109] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2012] [Accepted: 05/07/2012] [Indexed: 05/08/2023]
Abstract
The CELLULOSE SYNTHASE (CESA) superfamily of proteins contains several sub-families of closely related CELLULOSE SYNTHASE-LIKE (CSL) sequences. Among these, the CSLA and CSLC families are closely related to each other and are the most evolutionarily divergent from the CESA family. Significant progress has been made with the functional characterization of CSLA and CSLC genes, which have been shown to encode enzymes with 1,4-β-glycan synthase activities involved in the biosynthesis of mannan and possibly xyloglucan backbones, respectively. This review examines recent work on the CSLA and CSLC families from evolutionary, molecular, and biochemical perspectives. We pose a series of questions, whose answers likely will provide further insight about the specific functions of members of the CSLA and CSLC families and about plant polysaccharide biosynthesis is general.
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Affiliation(s)
- Aaron H. Liepman
- Biology Department, Eastern Michigan University, Ypsilanti, MI, USA
| | - David M. Cavalier
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, USA
- *Correspondence: David M. Cavalier, Great Lakes Bioenergy Research Center, Michigan State University, 612 Wilson Road, Room 110 Plant Biology Laboratories, East Lansing, MI 48826, USA. e-mail:
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