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Luo C, Akhtar M, Min W, Bai X, Ma T, Liu C. Domain of unknown function (DUF) proteins in plants: function and perspective. PROTOPLASMA 2024; 261:397-410. [PMID: 38158398 DOI: 10.1007/s00709-023-01917-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 12/08/2023] [Indexed: 01/03/2024]
Abstract
Domains of unknown function (DUFs), which are deposited in the protein family database (Pfam), are protein domains with conserved amino acid sequences and uncharacterized functions. Proteins with the same DUF were classified as DUF families. Although DUF families are generally not essential for the survival of plants, they play roles in plant development and adaptation. Characterizing the functions of DUFs is important for deciphering biological puzzles. DUFs were generally studied through forward and reverse genetics. Some novelty approaches, especially the determination of crystal structures and interaction partners of the DUFs, should attract more attention. This review described the identification of DUF genes by genome-wide and transcriptome-wide analyses, summarized the function of DUF-containing proteins, and addressed the prospects for future studies in DUFs in plants.
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Affiliation(s)
- Chengke Luo
- School of Agriculture, Ningxia University, Yinchuan, 750021, China
| | - Maryam Akhtar
- College of Life Sciences, Northwest Normal University, Lanzhou, 730070, China
| | - Weifang Min
- School of Agriculture, Ningxia University, Yinchuan, 750021, China
| | - Xiaorong Bai
- School of Agriculture, Ningxia University, Yinchuan, 750021, China
| | - Tianli Ma
- School of Agriculture, Ningxia University, Yinchuan, 750021, China
| | - Caixia Liu
- School of Agriculture, Ningxia University, Yinchuan, 750021, China.
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Dang Z, Wang Y, Wang M, Cao L, Ruan N, Huang Y, Li F, Xu Q, Chen W. The Fragile culm19 (FC19) mutation largely improves plant lodging resistance, biomass saccharification, and cadmium resistance by remodeling cell walls in rice. JOURNAL OF HAZARDOUS MATERIALS 2023; 458:132020. [PMID: 37429191 DOI: 10.1016/j.jhazmat.2023.132020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 06/17/2023] [Accepted: 07/06/2023] [Indexed: 07/12/2023]
Abstract
Cell wall is essential for plant upright growth, biomass saccharification, and stress resistance. Although cell wall modification is suggested as an effective means to increase biomass saccharification, it is a challenge to maintain normal plant growth with improved mechanical strength and stress resistance. Here, we reported two independent fragile culm mutants, fc19-1 and fc19-2, resulting from novel mutations of OsIRX10, produced by the CRISPR/Cas9 system. Compared to wild-type, the two mutants exhibited reduced contents of xylose, hemicellulose, and cellulose, and increased arabinose and lignin without significant alteration in levels of pectin and uronic acids. Despite brittleness, the mutants displayed increased breaking force, leading to improved lodging resistance. Furthermore, the altered cell wall and increased biomass porosity in fc19 largely increased biomass saccharification. Notably, the mutants showed enhanced cadmium (Cd) resistance with lower Cd accumulation in roots and shoots. The FC19 mutation impacts transcriptional levels of key genes contributing to Cd uptake, sequestration, and translocation. Moreover, transcriptome analysis revealed that the FC19 mutation resulted in alterations of genes mainly involved in carbohydrate and phenylpropanoid metabolism. Therefore, a hypothetic model was proposed to elucidate that the FC19 mutation-mediated cell wall remodeling leads to improvements in lodging resistance, biomass saccharification, and Cd resistance.
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Affiliation(s)
- Zhengjun Dang
- Rice Research Institute, Shenyang Agricultural University, Key Laboratory of Northern geng Super Rice Breeding, Ministry of Education, Shenyang 110866, China
| | - Ye Wang
- Rice Research Institute, Shenyang Agricultural University, Key Laboratory of Northern geng Super Rice Breeding, Ministry of Education, Shenyang 110866, China
| | - Meihan Wang
- Rice Research Institute, Shenyang Agricultural University, Key Laboratory of Northern geng Super Rice Breeding, Ministry of Education, Shenyang 110866, China
| | - Liyu Cao
- Rice Research Institute, Shenyang Agricultural University, Key Laboratory of Northern geng Super Rice Breeding, Ministry of Education, Shenyang 110866, China
| | - Nan Ruan
- Rice Research Institute, Shenyang Agricultural University, Key Laboratory of Northern geng Super Rice Breeding, Ministry of Education, Shenyang 110866, China
| | - Yuwei Huang
- Rice Research Institute, Shenyang Agricultural University, Key Laboratory of Northern geng Super Rice Breeding, Ministry of Education, Shenyang 110866, China
| | - Fengcheng Li
- Rice Research Institute, Shenyang Agricultural University, Key Laboratory of Northern geng Super Rice Breeding, Ministry of Education, Shenyang 110866, China.
| | - Quan Xu
- Rice Research Institute, Shenyang Agricultural University, Key Laboratory of Northern geng Super Rice Breeding, Ministry of Education, Shenyang 110866, China.
| | - Wenfu Chen
- Rice Research Institute, Shenyang Agricultural University, Key Laboratory of Northern geng Super Rice Breeding, Ministry of Education, Shenyang 110866, China
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Lv P, Wan J, Zhang C, Hina A, Al Amin GM, Begum N, Zhao T. Unraveling the Diverse Roles of Neglected Genes Containing Domains of Unknown Function (DUFs): Progress and Perspective. Int J Mol Sci 2023; 24:ijms24044187. [PMID: 36835600 PMCID: PMC9966272 DOI: 10.3390/ijms24044187] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/06/2023] [Accepted: 02/08/2023] [Indexed: 02/22/2023] Open
Abstract
Domain of unknown function (DUF) is a general term for many uncharacterized domains with two distinct features: relatively conservative amino acid sequence and unknown function of the domain. In the Pfam 35.0 database, 4795 (24%) gene families belong to the DUF type, yet, their functions remain to be explored. This review summarizes the characteristics of the DUF protein families and their functions in regulating plant growth and development, generating responses to biotic and abiotic stress, and other regulatory roles in plant life. Though very limited information is available about these proteins yet, by taking advantage of emerging omics and bioinformatic tools, functional studies of DUF proteins could be utilized in future molecular studies.
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Affiliation(s)
- Peiyun Lv
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Jinlu Wan
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Chunting Zhang
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Aiman Hina
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - G M Al Amin
- Department of Botany, Jagannath University, Dhaka 1100, Bangladesh
| | - Naheeda Begum
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
- Correspondence: (N.B.); (T.Z.)
| | - Tuanjie Zhao
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
- Correspondence: (N.B.); (T.Z.)
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4
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Advanced Bioethanol Production: From Novel Raw Materials to Integrated Biorefineries. Processes (Basel) 2021. [DOI: 10.3390/pr9020206] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The production of so-called advanced bioethanol offers several advantages compared to traditional bioethanol production processes in terms of sustainability criteria. This includes, for instance, the use of nonfood crops or residual biomass as raw material and a higher potential for reducing greenhouse gas emissions. The present review focuses on the recent progress related to the production of advanced bioethanol, (i) highlighting current results from using novel biomass sources such as the organic fraction of municipal solid waste and certain industrial residues (e.g., residues from the paper, food, and beverage industries); (ii) describing new developments in pretreatment technologies for the fractionation and conversion of lignocellulosic biomass, such as the bioextrusion process or the use of novel ionic liquids; (iii) listing the use of new enzyme catalysts and microbial strains during saccharification and fermentation processes. Furthermore, the most promising biorefinery approaches that will contribute to the cost-competitiveness of advanced bioethanol production processes are also discussed, focusing on innovative technologies and applications that can contribute to achieve a more sustainable and effective utilization of all biomass fractions. Special attention is given to integrated strategies such as lignocellulose-based biorefineries for the simultaneous production of bioethanol and other high added value bioproducts.
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Bryant ND, Pu Y, Tschaplinski TJ, Tuskan GA, Muchero W, Kalluri UC, Yoo CG, Ragauskas AJ. Transgenic Poplar Designed for Biofuels. TRENDS IN PLANT SCIENCE 2020; 25:881-896. [PMID: 32482346 DOI: 10.1016/j.tplants.2020.03.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 03/19/2020] [Accepted: 03/25/2020] [Indexed: 05/12/2023]
Abstract
Members of the genus Populus (i.e., cottonwood, hybrid poplar) represent a promising source of lignocellulosic biomass for biofuels. However, one of the major factors negatively affecting poplar's efficient conversion to biofuel is the inherent recalcitrance to enzymatic saccharification due to cell wall components such as lignin. To this effect, there have been efforts to modify gene expression to reduce biomass recalcitrance by changing cell wall properties. Here, we review recent genetic modifications of poplar that led to change cell wall properties and the resulting effects on subsequent pretreatment efficacy and saccharification. Although genetic engineering's impacts on cell wall properties are not fully predictable, recent studies have shown promising improvement in the biological conversion of transgenic poplar to biofuels.
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Affiliation(s)
- Nathan D Bryant
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN 37996, USA
| | - Yunqiao Pu
- Center for Bioenergy Innovation, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; Joint Institute for Biological Science, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Timothy J Tschaplinski
- Center for Bioenergy Innovation, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Gerald A Tuskan
- Center for Bioenergy Innovation, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Wellington Muchero
- Center for Bioenergy Innovation, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Udaya C Kalluri
- Center for Bioenergy Innovation, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Chang Geun Yoo
- Department of Paper and Bioprocess Engineering, State University of New York College of Environmental Science and Forestry, Syracuse, NY 13210, USA
| | - Arthur J Ragauskas
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN 37996, USA; Center for Bioenergy Innovation, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; Joint Institute for Biological Science, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; Center for Renewable Carbon, Department of Forestry, Wildlife, and Fisheries, University of Tennessee Institute of Agriculture, Knoxville, TN 37996, USA.
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Lee S, Kim MH, Lee JH, Jeon J, Kwak JM, Kim YJ. Glycosyltransferase-Like RSE1 Negatively Regulates Leaf Senescence Through Salicylic Acid Signaling in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2020; 11:551. [PMID: 32499801 PMCID: PMC7242760 DOI: 10.3389/fpls.2020.00551] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 04/14/2020] [Indexed: 06/01/2023]
Abstract
Leaf senescence is a developmental process designed for nutrient recycling and relocation to maximize growth competence and reproductive capacity of plants. Thus, plants integrate developmental and environmental signals to precisely control senescence. To genetically dissect the complex regulatory mechanism underlying leaf senescence, we identified an early leaf senescence mutant, rse1. RSE1 encodes a putative glycosyltransferase. Loss-of-function mutations in RSE1 resulted in precocious leaf yellowing and up-regulation of senescence marker genes, indicating enhanced leaf senescence. Transcriptome analysis revealed that salicylic acid (SA) and defense signaling cascades were up-regulated in rse1 prior to the onset of leaf senescence. We found that SA accumulation was significantly increased in rse1. The rse1 phenotypes are dependent on SA-INDUCTION DEFICIENT 2 (SID2), supporting a role of SA in accelerated leaf senescence in rse1. Furthermore, RSE1 protein was localized to the cell wall, implying a possible link between the cell wall and RSE1 function. Together, we show that RSE1 negatively modulates leaf senescence through an SID2-dependent SA signaling pathway.
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Affiliation(s)
- Seulbee Lee
- Center for Plant Aging Research, Institute for Basic Science, Daegu, South Korea
| | - Myung-Hee Kim
- Center for Plant Aging Research, Institute for Basic Science, Daegu, South Korea
| | - Jae Ho Lee
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology, Daegu, South Korea
| | - Jieun Jeon
- Center for Plant Aging Research, Institute for Basic Science, Daegu, South Korea
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology, Daegu, South Korea
| | - June M. Kwak
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology, Daegu, South Korea
| | - Yun Ju Kim
- Center for Plant Aging Research, Institute for Basic Science, Daegu, South Korea
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Brandon AG, Scheller HV. Engineering of Bioenergy Crops: Dominant Genetic Approaches to Improve Polysaccharide Properties and Composition in Biomass. FRONTIERS IN PLANT SCIENCE 2020; 11:282. [PMID: 32218797 PMCID: PMC7078332 DOI: 10.3389/fpls.2020.00282] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 02/25/2020] [Indexed: 05/24/2023]
Abstract
Large-scale, sustainable production of lignocellulosic bioenergy from biomass will depend on a variety of dedicated bioenergy crops. Despite their great genetic diversity, prospective bioenergy crops share many similarities in the polysaccharide composition of their cell walls, and the changes needed to optimize them for conversion are largely universal. Therefore, biomass modification strategies that do not depend on genetic background or require mutant varieties are extremely valuable. Due to their preferential fermentation and conversion by microorganisms downstream, the ideal bioenergy crop should contain a high proportion of C6-sugars in polysaccharides like cellulose, callose, galactan, and mixed-linkage glucans. In addition, the biomass should be reduced in inhibitors of fermentation like pentoses and acetate. Finally, the overall complexity of the plant cell wall should be modified to reduce its recalcitrance to enzymatic deconstruction in ways that do no compromise plant health or come at a yield penalty. This review will focus on progress in the use of a variety of genetically dominant strategies to reach these ideals. Due to the breadth and volume of research in the field of lignin bioengineering, this review will instead focus on approaches to improve polysaccharide component plant biomass. Carbohydrate content can be dramatically increased by transgenic overexpression of enzymes involved in cell wall polysaccharide biosynthesis. Additionally, the recalcitrance of the cell wall can be reduced via the overexpression of native or non-native carbohydrate active enzymes like glycosyl hydrolases or carbohydrate esterases. Some research in this area has focused on engineering plants that accumulate cell wall-degrading enzymes that are sequestered to organelles or only active at very high temperatures. The rationale being that, in order to avoid potential negative effects of cell wall modification during plant growth, the enzymes could be activated post-harvest, and post-maturation of the cell wall. A potentially significant limitation of this approach is that at harvest, the cell wall is heavily lignified, making the substrates for these enzymes inaccessible and their activity ineffective. Therefore, this review will only include research employing enzymes that are at least partially active under the ambient conditions of plant growth and cell wall development.
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Affiliation(s)
- Andrew G. Brandon
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA, United States
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Henrik V. Scheller
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA, United States
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
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Yang Y, Yoo CG, Rottmann W, Winkeler KA, Collins CM, Gunter LE, Jawdy SS, Yang X, Pu Y, Ragauskas AJ, Tuskan GA, Chen JG. PdWND3A, a wood-associated NAC domain-containing protein, affects lignin biosynthesis and composition in Populus. BMC PLANT BIOLOGY 2019; 19:486. [PMID: 31711424 PMCID: PMC6849256 DOI: 10.1186/s12870-019-2111-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 10/31/2019] [Indexed: 05/21/2023]
Abstract
BACKGROUND Plant secondary cell wall is a renewable feedstock for biofuels and biomaterials production. Arabidopsis VASCULAR-RELATED NAC DOMAIN (VND) has been demonstrated to be a key transcription factor regulating secondary cell wall biosynthesis. However, less is known about its role in the woody species. RESULTS Here we report the functional characterization of Populus deltoides WOOD-ASSOCIATED NAC DOMAIN protein 3 (PdWND3A), a sequence homolog of Arabidopsis VND4 and VND5 that are members of transcription factor networks regulating secondary cell wall biosynthesis. PdWND3A was expressed at higher level in the xylem than in other tissues. The stem tissues of transgenic P. deltoides overexpressing PdWND3A (OXPdWND3A) contained more vessel cells than that of wild-type plants. Furthermore, lignin content and lignin monomer syringyl and guaiacyl (S/G) ratio were higher in OXPdWND3A transgenic plants than in wild-type plants. Consistent with these observations, the expression of FERULATE 5-HYDROXYLASE1 (F5H1), encoding an enzyme involved in the biosynthesis of sinapyl alcohol (S unit monolignol), was elevated in OXPdWND3A transgenic plants. Saccharification analysis indicated that the rate of sugar release was reduced in the transgenic plants. In addition, OXPdWND3A transgenic plants produced lower amounts of biomass than wild-type plants. CONCLUSIONS PdWND3A affects lignin biosynthesis and composition and negatively impacts sugar release and biomass production.
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Affiliation(s)
- Yongil Yang
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Chang Geun Yoo
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- UT-ORNL Joint Institute for Biological Science, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | | | | | | | - Lee E. Gunter
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Sara S. Jawdy
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Xiaohan Yang
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Yunqiao Pu
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- UT-ORNL Joint Institute for Biological Science, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Arthur J. Ragauskas
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- UT-ORNL Joint Institute for Biological Science, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Department of Chemical and Biomolecular Engineering & Department of Forestry, Wildlife, and Fisheries, University of Tennessee, Knoxville, TN 37996 USA
| | - Gerald A. Tuskan
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Jin-Gui Chen
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
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Ke S, Liu S, Luan X, Xie XM, Hsieh TF, Zhang XQ. Mutation in a putative glycosyltransferase-like gene causes programmed cell death and early leaf senescence in rice. RICE (NEW YORK, N.Y.) 2019; 12:7. [PMID: 30758674 PMCID: PMC6374497 DOI: 10.1186/s12284-019-0266-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 02/01/2019] [Indexed: 05/19/2023]
Abstract
Leaf senescence is a genetically regulated, highly complex and ordered process. Although it has been extensively studied, the mechanism of leaf senescence is not well understood. In this study, we isolated a rice mutant, designated as premature senescence leaf (psl), which exhibits early senescence and spontaneous lesion mimic phenotype after flowering. The psl mutant displays programmed cell death with elevated accumulation of reactive oxygen species (ROS). Molecular and genetic analyses revealed that the phenotypes were caused by a phenylalanine deletion in the OsPSL (LOC_Os12g42420) that encode a putative core 2/I branching beta-1,6-N-acetylglucosaminyl transferase predicted to be involved in protein glycosylation modification. OsPSL mRNA levels increased as senescence progressed, with maximum accumulation of transcripts at late senescence stages in WT plants. Moreover, remarkedly down-regulated transcriptional levels of O-linked N-acetylglucosamine (O-GlcNAc) transferases (OGTs) genes were observed in psl mutant, supporting the occurrence of impaired O-glycosylation modification. Proteomic analysis showed that ethylene-related metabolic enzymes including S-adenosyl methionine (SAM) synthetase (SAMS) were significantly upregulated in the psl mutant compared with WT. Consistent with the proteomic results, ethylene concentration is higher in psl mutant than in wild-type plants, and transcript levels of ethylene synthesis and signal transduction genes were induced in psl mutant. The early leaf senescence of psl can be partially rescued by ethylene biosynthesis inhibitor aminoethoxyvinylglycine treatment. These results highlight the importance of protein O-glycosylation in PCD and leaf senescence, and suggest a possible role of OsPSL in ethylene signaling.
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Affiliation(s)
- Shanwen Ke
- Guangdong Engineering Research Center of Grassland Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642 China
| | - Shuchun Liu
- Guangdong Engineering Research Center of Grassland Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642 China
| | - Xin Luan
- Guangdong Engineering Research Center of Grassland Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642 China
| | - Xin-Ming Xie
- Guangdong Engineering Research Center of Grassland Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642 China
| | - Tzung-Fu Hsieh
- Plants for Human Health Institute, North Carolina State University, North Carolina Research Campus, Kannapolis, NC 28081 USA
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695 USA
| | - Xiang-Qian Zhang
- Guangdong Engineering Research Center of Grassland Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642 China
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Li K, Chen Y, Luo Y, Huang F, Zhao C, Cheng F, Xiang X, Pan G. A 22-bp deletion in OsPLS3 gene encoding a DUF266-containing protein is implicated in rice leaf senescence. PLANT MOLECULAR BIOLOGY 2018; 98:19-32. [PMID: 30117035 DOI: 10.1007/s11103-018-0758-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 07/18/2018] [Indexed: 05/04/2023]
Abstract
Key message The OsPLS3 locus was isolated by map-based cloning that encodes a DUF266-containing protein. OsPLS3 regulates the onset of leaf senescence in rice. Glycosyltransferases (GTs) are one of the most important enzyme groups required for the modification of plant secondary metabolites and play a crucial role in plant growth and development, however the biological functions of most GTs remain elusive. We reported here the identification and characterization of a novel Oryza sativa premature leaf senescence mutant (ospls3). Through map-based cloning strategy, we determined that 22-bp deletion in the OsPLS3 gene encoding a domain of unknown function 266 (DUF266)-containing protein, a member of GT14-like, underlies the premature leaf senescence phenotype in the ospls3 mutant. The OsPLS3 mRNA levels progressively declined with the age-dependent leaf senescence in wild-type rice, implying a negative role of OsPLS3 in regulating leaf senescence. Physiological analysis, and histochemical staining and transmission electron microscopy assays indicated that the ospls3 mutant accumulated higher levels of ethylene and reactive oxygen species than its wild type. Furthermore, the ospls3 mutant showed hypersensitivity to exogenous 1-aminocyclopropane-1-carboxylic acid, H2O2 and high level of cytokinins. Our results indicated that the DUF266-containing gene OsPLS3 plays an important role in the onset of leaf senescence, in part through cytokinin and ethylene signaling in rice.
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Affiliation(s)
- Kunyu Li
- Department of Agronomy, Zijingang Campus, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Yaodong Chen
- Department of Agronomy, Zijingang Campus, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Yanmin Luo
- Department of Agronomy, Zijingang Campus, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Fudeng Huang
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, People's Republic of China
| | - Chaoyue Zhao
- Department of Agronomy, Zijingang Campus, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Fangmin Cheng
- Department of Agronomy, Zijingang Campus, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Xun Xiang
- Experimental Teaching Center, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Gang Pan
- Department of Agronomy, Zijingang Campus, Zhejiang University, Hangzhou, 310058, People's Republic of China.
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Macaya-Sanz D, Chen J, Kalluri UC, Muchero W, Tschaplinski TJ, Gunter LE, Simon SJ, Biswal AK, Bryan AC, Payyavula R, Xie M, Yang Y, Zhang J, Mohnen D, Tuskan GA, DiFazio SP. Agronomic performance of Populus deltoides trees engineered for biofuel production. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:253. [PMID: 29213313 PMCID: PMC5707814 DOI: 10.1186/s13068-017-0934-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 10/19/2017] [Indexed: 05/02/2023]
Abstract
BACKGROUND One of the major barriers to the development of lignocellulosic feedstocks is the recalcitrance of plant cell walls to deconstruction and saccharification. Recalcitrance can be reduced by targeting genes involved in cell wall biosynthesis, but this can have unintended consequences that compromise the agronomic performance of the trees under field conditions. Here we report the results of a field trial of fourteen distinct transgenic Populus deltoides lines that had previously demonstrated reduced recalcitrance without yield penalties under greenhouse conditions. RESULTS Survival and productivity of the trial were excellent in the first year, and there was little evidence for reduced performance of the transgenic lines with modified target gene expression. Surprisingly, the most striking phenotypic effects in this trial were for two empty-vector control lines that had modified bud set and bud flush. This is most likely due to somaclonal variation or insertional mutagenesis. Traits related to yield, crown architecture, herbivory, pathogen response, and frost damage showed few significant differences between target gene transgenics and empty vector controls. However, there were a few interesting exceptions. Lines overexpressing the DUF231 gene, a putative O-acetyltransferase, showed early bud flush and marginally increased height growth. Lines overexpressing the DUF266 gene, a putative glycosyltransferase, had significantly decreased stem internode length and slightly higher volume index. Finally, lines overexpressing the PFD2 gene, a putative member of the prefoldin complex, had a slightly reduced volume index. CONCLUSIONS This field trial demonstrates that these cell wall modifications, which decreased cell wall recalcitrance under laboratory conditions, did not seriously compromise first-year performance in the field, despite substantial challenges, including an outbreak of a stem boring insect (Gypsonoma haimbachiana), attack by a leaf rust pathogen (Melampsora spp.), and a late frost event. This bodes well for the potential utility of these lines as advanced biofuels feedstocks.
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Affiliation(s)
- David Macaya-Sanz
- Department of Biology, West Virginia University, Morgantown, WV 26506 USA
| | - Jin‐Gui Chen
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Udaya C. Kalluri
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Wellington Muchero
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Timothy J. Tschaplinski
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Lee E. Gunter
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Sandra J. Simon
- Department of Biology, West Virginia University, Morgantown, WV 26506 USA
| | - Ajaya K. Biswal
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602 USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602 USA
| | - Anthony C. Bryan
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Raja Payyavula
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Meng Xie
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Yongil Yang
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Jin Zhang
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Debra Mohnen
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602 USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602 USA
| | - Gerald A. Tuskan
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Stephen P. DiFazio
- Department of Biology, West Virginia University, Morgantown, WV 26506 USA
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Yang Y, Yoo CG, Winkeler KA, Collins CM, Hinchee MAW, Jawdy SS, Gunter LE, Engle NL, Pu Y, Yang X, Tschaplinski TJ, Ragauskas AJ, Tuskan GA, Chen JG. Overexpression of a Domain of Unknown Function 231-containing protein increases O-xylan acetylation and cellulose biosynthesis in Populus. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:311. [PMID: 29299061 PMCID: PMC5744390 DOI: 10.1186/s13068-017-0998-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 12/14/2017] [Indexed: 05/02/2023]
Abstract
BACKGROUND Domain of Unknown Function 231-containing proteins (DUF231) are plant specific and their function is largely unknown. Studies in the model plants Arabidopsis and rice suggested that some DUF231 proteins act in the process of O-acetyl substitution of hemicellulose and esterification of pectin. However, little is known about the function of DUF231 proteins in woody plant species. RESULTS This study provides evidence supporting that one member of DUF231 family proteins in the woody perennial plant Populus deltoides (genotype WV94), PdDUF231A, has a role in the acetylation of xylan and affects cellulose biosynthesis. A total of 52 DUF231-containing proteins were identified in the Populus genome. In P. deltoides transgenic lines overexpressing PdDUF231A (OXPdDUF231A), glucose and cellulose contents were increased. Consistent with these results, the transcript levels of cellulose biosynthesis-related genes were increased in the OXPdDUF231A transgenic lines. Furthermore, the relative content of total acetylated xylan was increased in the OXPdDUF231A transgenic lines. Enzymatic saccharification assays revealed that the rate of glucose release increased in OXPdDUF231A transgenic lines. Plant biomass productivity was also increased in OXPdDUF231A transgenic lines. CONCLUSIONS These results suggest that PdDUF231A affects cellulose biosynthesis and plays a role in the acetylation of xylan. PdDUF231A is a promising target for genetic modification for biofuel production because biomass productivity and compositional quality can be simultaneously improved through overexpression.
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Affiliation(s)
- Yongil Yang
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Chang Geun Yoo
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- UT-ORNL Joint Institute for Biological Science, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | | | | | | | - Sara S. Jawdy
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Lee E. Gunter
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Nancy L. Engle
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Yunqiao Pu
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- UT-ORNL Joint Institute for Biological Science, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Xiaohan Yang
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Timothy J. Tschaplinski
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Arthur J. Ragauskas
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- UT-ORNL Joint Institute for Biological Science, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN 37996 USA
- Department of Forestry, Wildlife, and Fisheries, University of Tennessee, Knoxville, TN 37996 USA
| | - Gerald A. Tuskan
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Jin-Gui Chen
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
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