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Tang L, Liu C, Li X, Wang H, Zhang S, Cai X, Zhang J. An aldehyde dehydrogenase gene, GhALDH7B4_A06, positively regulates fiber strength in upland cotton ( Gossypium hirsutum L.). FRONTIERS IN PLANT SCIENCE 2024; 15:1377682. [PMID: 38736450 PMCID: PMC11082362 DOI: 10.3389/fpls.2024.1377682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Accepted: 04/09/2024] [Indexed: 05/14/2024]
Abstract
High fiber strength (FS) premium cotton has significant market demand. Consequently, enhancing FS is a major objective in breeding quality cotton. However, there is a notable lack of known functionally applicable genes that can be targeted for breeding. To address this issue, our study used specific length-amplified fragment sequencing combined with bulk segregant analysis to study FS trait in an F2 population. Subsequently, we integrated these results with previous quantitative trait locus mapping results regarding fiber quality, which used simple sequence repeat markers in F2, F2:3, and recombinant inbred line populations. We identified a stable quantitative trait locus qFSA06 associated with FS located on chromosome A06 (90.74-90.83 Mb). Within this interval, we cloned a gene, GhALDH7B4_A06, which harbored a critical mutation site in coding sequences that is distinct in the two parents of the tested cotton line. In the paternal parent Ji228, the gene is normal and referred to as GhALDH7B4_A06O; however, there is a nonsense mutation in the maternal parent Ji567 that results in premature termination of protein translation, and this gene is designated as truncated GhALDH7B4_A06S. Validation using recombinant inbred lines and gene expression analysis revealed that this mutation site is correlated with cotton FS. Virus-induced gene silencing of GhALDH7B4 in cotton caused significant decreases in FS and fiber micronaire. Conversely, GhALDH7B4_A06O overexpression in Arabidopsis boosted cell wall component contents in the stem. The findings of our study provide a candidate gene for improving cotton fiber quality through molecular breeding.
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Affiliation(s)
| | | | | | | | | | | | - Jianhong Zhang
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences, Key Laboratory of Cotton Biology and Genetic Breeding in Huanghuaihai Semiarid Area, Ministry of Agriculture and Rural Affairs, Shijiazhuang, Hebei, China
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Huang H, Wei Y, Huang S, Lu S, Su H, Ma L, Huang W. Integrated metabolomic and transcriptomic analyses provide insights into regulation mechanisms during bulbous stem development in the Chinese medicinal herb plant, Stephania kwangsiensis. BMC PLANT BIOLOGY 2024; 24:276. [PMID: 38605285 PMCID: PMC11007893 DOI: 10.1186/s12870-024-04956-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Accepted: 03/27/2024] [Indexed: 04/13/2024]
Abstract
BACKGROUND Stephania kwangsiensis Lo (Menispermaceae) is a well-known Chinese herbal medicine, and its bulbous stems are used medicinally. The storage stem of S. kwangsiensis originated from the hypocotyls. To date, there are no reports on the growth and development of S. kwangsiensis storage stems. RESULTS The bulbous stem of S. kwangsiensis, the starch diameter was larger at the stable expanding stage (S3T) than at the unexpanded stage (S1T) or the rapidly expanding stage (S2T) at the three different time points. We used ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) and Illumina sequencing to identify key genes involved in bulbous stem development. A large number of differentially accumulated metabolites (DAMs) and differentially expressed genes (DEGs) were identified. Based on the differential expression profiles of the metabolites, alkaloids, lipids, and phenolic acids were the top three differentially expressed classes. Compared with S2T, significant changes in plant signal transduction and isoquinoline alkaloid biosynthesis pathways occurred at both the transcriptional and metabolic levels in S1T. In S2T compared with S3T, several metabolites involved in tyrosine metabolism were decreased. Temporal analysis of S1T to S3T indicated the downregulation of phenylpropanoid biosynthesis, including lignin biosynthesis. The annotation of key pathways showed an up-down trend for genes and metabolites involved in isoquinoline alkaloid biosynthesis, whereas phenylpropanoid biosynthesis was not completely consistent. CONCLUSIONS Downregulation of the phenylpropanoid biosynthesis pathway may be the result of carbon flow into alkaloid synthesis and storage of lipids and starch during the development of S. kwangsiensis bulbous stems. A decrease in the number of metabolites involved in tyrosine metabolism may also lead to a decrease in the upstream substrates of phenylpropane biosynthesis. Downregulation of lignin synthesis during phenylpropanoid biosynthesis may loosen restrictions on bulbous stem expansion. This study provides the first comprehensive analysis of the metabolome and transcriptome profiles of S. kwangsiensis bulbous stems. These data provide guidance for the cultivation, breeding, and harvesting of S. kwangsiensis.
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Affiliation(s)
- Hao Huang
- Guangxi Vocational University of Agriculture, Nanning, 530009, China.
| | - Ying Wei
- Guangxi Botanical Garden of Medicinal Plants, Nanning, 530023, China
| | - Shaojun Huang
- Guangxi Vocational University of Agriculture, Nanning, 530009, China
| | - Shijian Lu
- Guangxi Vocational University of Agriculture, Nanning, 530009, China
| | - Huasheng Su
- Guangxi Vocational University of Agriculture, Nanning, 530009, China
| | - Liuhui Ma
- Guangxi Vocational University of Agriculture, Nanning, 530009, China
| | - Weiping Huang
- Guangxi Vocational University of Agriculture, Nanning, 530009, China
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Mierziak J, Wojtasik W, Kulma A, Żuk M, Grajzer M, Boba A, Dymińska L, Hanuza J, Szperlik J, Szopa J. Overexpression of Bacterial Beta-Ketothiolase Improves Flax (Linum usitatissimum L.) Retting and Changes the Fibre Properties. Metabolites 2023; 13:metabo13030437. [PMID: 36984877 PMCID: PMC10052753 DOI: 10.3390/metabo13030437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/07/2023] [Accepted: 03/14/2023] [Indexed: 03/19/2023] Open
Abstract
Beta-ketothiolases are involved in the beta-oxidation of fatty acids and the metabolism of hormones, benzenoids, and hydroxybutyrate. The expression of bacterial beta-ketothiolase in flax (Linum usitatissimum L.) results in an increase in endogenous beta-ketothiolase mRNA levels and beta-hydroxybutyrate content. In the present work, the effect of overexpression of beta-ketothiolase on retting and stem and fibre composition of flax plants is presented. The content of the components was evaluated by high-performance liquid chromatography, gas chromatography–mass spectrometry, Fourier-transform infrared spectroscopy, and biochemical methods. Changes in the stem cell walls, especially in the lower lignin and pectin content, resulted in more efficient retting. The overexpression of beta-ketothiolase reduced the fatty acid and carotenoid contents in flax and affected the distribution of phenolic compounds between free and cell wall-bound components. The obtained fibres were characterized by a slightly lower content of phenolic compounds and changes in the composition of the cell wall. Based on the IR analysis, we concluded that the production of hydroxybutyrate reduced the cellulose crystallinity and led to the formation of shorter but more flexible cellulose chains, while not changing the content of the cell wall components. We speculate that the changes in chemical composition of the stems and fibres are the result of the regulatory properties of hydroxybutyrate. This provides us with a novel way to influence metabolic composition in agriculturally important crops.
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Affiliation(s)
- Justyna Mierziak
- Department of Genetic Biochemistry, Faculty of Biotechnology, Wroclaw University, Przybyszewskiego Str. 63, 51-148 Wroclaw, Poland
| | - Wioleta Wojtasik
- Department of Genetic Biochemistry, Faculty of Biotechnology, Wroclaw University, Przybyszewskiego Str. 63, 51-148 Wroclaw, Poland
- Correspondence:
| | - Anna Kulma
- Department of Genetic Biochemistry, Faculty of Biotechnology, Wroclaw University, Przybyszewskiego Str. 63, 51-148 Wroclaw, Poland
| | - Magdalena Żuk
- Department of Genetic Biochemistry, Faculty of Biotechnology, Wroclaw University, Przybyszewskiego Str. 63, 51-148 Wroclaw, Poland
| | - Magdalena Grajzer
- Department of Dietetics and Bromatology, Faculty of Pharmacy, Wroclaw Medical University, Borowska 211, 50-556 Wroclaw, Poland
| | - Aleksandra Boba
- Department of Genetics, Plant Breeding and Seed Science, Wroclaw University of Environmental and Life Sciences, Grunwaldzki Sq. 24A, 50-363 Wroclaw, Poland
| | - Lucyna Dymińska
- Department of Bioorganic Chemistry, Wroclaw University of Economics and Business, Komandorska 118/120, 53-345 Wroclaw, Poland
| | - Jerzy Hanuza
- Institute of Low Temperature and Structure Research, Polish Academy of Sciences, Okólna 2, 50-422 Wroclaw, Poland
| | - Jakub Szperlik
- Laboratory of Tissue Culture, Botanical Garden, Faculty of Biological Sciences, University of Wroclaw, Sienkiewicza 23, 50-525 Wroclaw, Poland
| | - Jan Szopa
- Department of Genetic Biochemistry, Faculty of Biotechnology, Wroclaw University, Przybyszewskiego Str. 63, 51-148 Wroclaw, Poland
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Duran Garzon C, Lequart M, Charras Q, Fournet F, Bellenger L, Sellier-Richard H, Giauffret C, Vermerris W, Domon JM, Rayon C. The maize low-lignin brown midrib3 mutant shows pleiotropic effects on photosynthetic and cell wall metabolisms in response to chilling. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 184:75-86. [PMID: 35636334 DOI: 10.1016/j.plaphy.2022.05.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 02/03/2022] [Accepted: 05/06/2022] [Indexed: 06/15/2023]
Abstract
Maize (Zea mays L.) is one of the major cereal crops in the world and is highly sensitive to low temperature. Here, changes in photosynthetic and cell wall metabolisms were investigated during a long chilling exposure in inbred line F2 and a low-lignin near-isogenic brown midrib3 mutant (F2bm3), which has a mutation in the caffeic acid O-methyltransferase (COMT) gene. Results revealed that the plant biomass was reduced, and this was more pronounced in F2bm3. Photosynthesis was altered in both lines with distinct changes in photosynthetic pigment content between F2bm3 and F2, indicating an alternative photoprotection mechanism between lines under chilling. Starch remobilization was observed in F2bm3 while concentrations of sucrose, fructose and starch increased in F2, suggesting a reduced sugar partitioning in F2. The cell wall was altered upon chilling, resulting in changes in the composition of glucuronorabinoxylan and a reduced cellulose level in F2. Chilling shifted lignin subunit composition in F2bm3 mutant to a higher proportion of p-hydroxyphenyl (H) units, whereas it resulted in lignin with a higher proportion of syringyl (S) residues in F2. On average, the total cell wall ferulic acid (FA) content increased in both genotypes, with an increase in ether-linked FA in F2bm3, suggesting a greater degree of cross-linking to lignin. The reinforcement of the cell wall with lignin enriched in H-units and a higher concentration in cell-wall-bound FA observed in F2bm3 as a response to chilling, could be a strategy to protect the photosystems.
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Affiliation(s)
- Catalina Duran Garzon
- UMR-INRAE 1158 Transfrontalière BioEcoAgro, BIOlogie des Plantes et Innovation (BIOPI), Université de Picardie Jules Verne, 80039, Amiens, France
| | - Michelle Lequart
- UMR-INRAE 1158 Transfrontalière BioEcoAgro, BIOlogie des Plantes et Innovation (BIOPI), Université de Picardie Jules Verne, 80039, Amiens, France
| | - Quentin Charras
- UMR 7265 Aix Marseille Université, CEA, CNRS, BIAM, Laboratoire de Génétique et Biophysique des Plantes, 13108, Saint Paul-Lez-Durance, France
| | - Françoise Fournet
- UMR-INRAE 1158 Transfrontalière BioEcoAgro, BIOlogie des Plantes et Innovation (BIOPI), Université de Picardie Jules Verne, 80039, Amiens, France
| | - Léo Bellenger
- UMR-INRAE 1158 Transfrontalière BioEcoAgro, BIOlogie des Plantes et Innovation (BIOPI), Université de Picardie Jules Verne, 80039, Amiens, France; EA2106 Biomolécules et Biotechnologies Végétales, Faculté de Pharmacie, Université de Tours, Parc de Grandmont, 37200, Tours, France
| | - Hélène Sellier-Richard
- UMR-INRAE 1158 Transfrontalière BioEcoAgro, Unité Expérimentale Grandes Cultures Innovation et Environnement, Estrées-Mons, 80203, Péronne, France
| | - Catherine Giauffret
- UMR-INRAE 1158 Transfrontalière BioEcoAgro, AgroImpact, Estrées-Mons, 80203, Péronne, France
| | - Wilfred Vermerris
- Department of Microbiology & Cell Science, UF Genetics Institute, Florida Center for Renewable Chemicals and Fuels, University of Florida, Gainesville, FL, 32610, USA
| | - Jean-Marc Domon
- UMR-INRAE 1158 Transfrontalière BioEcoAgro, BIOlogie des Plantes et Innovation (BIOPI), Université de Picardie Jules Verne, 80039, Amiens, France
| | - Catherine Rayon
- UMR-INRAE 1158 Transfrontalière BioEcoAgro, BIOlogie des Plantes et Innovation (BIOPI), Université de Picardie Jules Verne, 80039, Amiens, France.
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Maceda-López LF, Góngora-Castillo EB, Ibarra-Laclette E, Morán-Velázquez DC, Girón Ramírez A, Bourdon M, Villalpando-Aguilar JL, Toomer G, Tang JZ, Azadi P, Santamaría JM, López-Rosas I, López MG, Simpson J, Alatorre-Cobos F. Transcriptome Mining Provides Insights into Cell Wall Metabolism and Fiber Lignification in Agave tequilana Weber. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11111496. [PMID: 35684270 PMCID: PMC9182668 DOI: 10.3390/plants11111496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/18/2022] [Accepted: 05/19/2022] [Indexed: 05/08/2023]
Abstract
Resilience of growing in arid and semiarid regions and a high capacity of accumulating sugar-rich biomass with low lignin percentages have placed Agave species as an emerging bioenergy crop. Although transcriptome sequencing of fiber-producing agave species has been explored, molecular bases that control wall cell biogenesis and metabolism in agave species are still poorly understood. Here, through RNAseq data mining, we reconstructed the cellulose biosynthesis pathway and the phenylpropanoid route producing lignin monomers in A. tequilana, and evaluated their expression patterns in silico and experimentally. Most of the orthologs retrieved showed differential expression levels when they were analyzed in different tissues with contrasting cellulose and lignin accumulation. Phylogenetic and structural motif analyses of putative CESA and CAD proteins allowed to identify those potentially involved with secondary cell wall formation. RT-qPCR assays revealed enhanced expression levels of AtqCAD5 and AtqCESA7 in parenchyma cells associated with extraxylary fibers, suggesting a mechanism of formation of sclerenchyma fibers in Agave similar to that reported for xylem cells in model eudicots. Overall, our results provide a framework for understanding molecular bases underlying cell wall biogenesis in Agave species studying mechanisms involving in leaf fiber development in monocots.
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Affiliation(s)
- Luis F. Maceda-López
- Colegio de Postgraduados, Campus Campeche, Carretera Haltunchén-Edzná km 17.5, Sihochac, Campeche 24450, Mexico; (L.F.M.-L.); (D.C.M.-V.); (J.L.V.-A.)
| | - Elsa B. Góngora-Castillo
- CONACYT-Centro de Investigación Científica de Yucatán, Unidad de Biotecnología, Calle 43 No. 130 × 32 y 34, Chuburná de Hidalgo, Mérida 97205, Mexico;
| | - Enrique Ibarra-Laclette
- Red de Estudios Moleculares Avanzados, Instituto de Ecología A. C. Carretera Antigua a Coatepec 351, El Haya, Xalapa 91070, Mexico;
| | - Dalia C. Morán-Velázquez
- Colegio de Postgraduados, Campus Campeche, Carretera Haltunchén-Edzná km 17.5, Sihochac, Campeche 24450, Mexico; (L.F.M.-L.); (D.C.M.-V.); (J.L.V.-A.)
| | - Amaranta Girón Ramírez
- Centro de Investigación Científica de Yucatán, Unidad de Biotecnología, Calle 43 No. 130 × 32 y 34, Chuburná de Hidalgo, Mérida 97205, Mexico; (A.G.R.); (J.M.S.)
| | - Matthieu Bourdon
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, UK;
| | - José L. Villalpando-Aguilar
- Colegio de Postgraduados, Campus Campeche, Carretera Haltunchén-Edzná km 17.5, Sihochac, Campeche 24450, Mexico; (L.F.M.-L.); (D.C.M.-V.); (J.L.V.-A.)
| | - Gabriela Toomer
- Division of Microbiology and Molecular Biology, IIT Research Institute, Chicago, IL 60616, USA;
| | - John Z. Tang
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA; (J.Z.T.); (P.A.)
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA; (J.Z.T.); (P.A.)
| | - Jorge M. Santamaría
- Centro de Investigación Científica de Yucatán, Unidad de Biotecnología, Calle 43 No. 130 × 32 y 34, Chuburná de Hidalgo, Mérida 97205, Mexico; (A.G.R.); (J.M.S.)
| | - Itzel López-Rosas
- CONACYT-Colegio de Postgraduados Campus Campeche, Carretera Haltunchén-Edzná km 17.5, Sihochac, Campeche 24450, Mexico;
| | - Mercedes G. López
- Departmento de Biotecnología y Bioquímica, Centro de Investigación y Estudios Avanzados del IPN, Irapuato 36824, Mexico;
| | - June Simpson
- Departmento de Ingeniería Genetica, Centro de Investigación y Estudios Avanzados del IPN, Irapuato 36824, Mexico;
| | - Fulgencio Alatorre-Cobos
- CONACYT-Colegio de Postgraduados Campus Campeche, Carretera Haltunchén-Edzná km 17.5, Sihochac, Campeche 24450, Mexico;
- Correspondence:
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de Freitas EN, Salgado JCS, Alnoch RC, Contato AG, Habermann E, Michelin M, Martínez CA, Polizeli MDLTM. Challenges of Biomass Utilization for Bioenergy in a Climate Change Scenario. BIOLOGY 2021; 10:1277. [PMID: 34943192 PMCID: PMC8698859 DOI: 10.3390/biology10121277] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 11/29/2021] [Accepted: 11/29/2021] [Indexed: 12/01/2022]
Abstract
The climate changes expected for the next decades will expose plants to increasing occurrences of combined abiotic stresses, including drought, higher temperatures, and elevated CO2 atmospheric concentrations. These abiotic stresses have significant consequences on photosynthesis and other plants' physiological processes and can lead to tolerance mechanisms that impact metabolism dynamics and limit plant productivity. Furthermore, due to the high carbohydrate content on the cell wall, plants represent a an essential source of lignocellulosic biomass for biofuels production. Thus, it is necessary to estimate their potential as feedstock for renewable energy production in future climate conditions since the synthesis of cell wall components seems to be affected by abiotic stresses. This review provides a brief overview of plant responses and the tolerance mechanisms applied in climate change scenarios that could impact its use as lignocellulosic biomass for bioenergy purposes. Important steps of biofuel production, which might influence the effects of climate change, besides biomass pretreatments and enzymatic biochemical conversions, are also discussed. We believe that this study may improve our understanding of the plant biological adaptations to combined abiotic stress and assist in the decision-making for selecting key agronomic crops that can be efficiently adapted to climate changes and applied in bioenergy production.
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Affiliation(s)
- Emanuelle Neiverth de Freitas
- Department of Biochemistry and Immunology, Faculdade de Medicina de Ribeirão Preto (FMRP), University of São Paulo, Ribeirão Preto 14049-900, São Paulo, Brazil; (E.N.d.F.); (A.G.C.)
| | - José Carlos Santos Salgado
- Department of Chemistry, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto (FFCLRP), University of São Paulo, Ribeirão Preto 14040-901, São Paulo, Brazil;
| | - Robson Carlos Alnoch
- Department of Biology, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto (FFCLRP), University of São Paulo, Ribeirão Preto 14040-901, São Paulo, Brazil; (R.C.A.); (E.H.); (C.A.M.)
| | - Alex Graça Contato
- Department of Biochemistry and Immunology, Faculdade de Medicina de Ribeirão Preto (FMRP), University of São Paulo, Ribeirão Preto 14049-900, São Paulo, Brazil; (E.N.d.F.); (A.G.C.)
| | - Eduardo Habermann
- Department of Biology, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto (FFCLRP), University of São Paulo, Ribeirão Preto 14040-901, São Paulo, Brazil; (R.C.A.); (E.H.); (C.A.M.)
| | - Michele Michelin
- Centre of Biological Engineering (CEB), Gualtar Campus, University of Minho, 4710-057 Braga, Portugal;
| | - Carlos Alberto Martínez
- Department of Biology, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto (FFCLRP), University of São Paulo, Ribeirão Preto 14040-901, São Paulo, Brazil; (R.C.A.); (E.H.); (C.A.M.)
| | - Maria de Lourdes T. M. Polizeli
- Department of Biochemistry and Immunology, Faculdade de Medicina de Ribeirão Preto (FMRP), University of São Paulo, Ribeirão Preto 14049-900, São Paulo, Brazil; (E.N.d.F.); (A.G.C.)
- Department of Biology, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto (FFCLRP), University of São Paulo, Ribeirão Preto 14040-901, São Paulo, Brazil; (R.C.A.); (E.H.); (C.A.M.)
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Chen C, Shi X, Zhou T, Li W, Li S, Bai G. Full-length transcriptome analysis and identification of genes involved in asarinin and aristolochic acid biosynthesis in medicinal plant Asarum sieboldii. Genome 2020; 64:639-653. [PMID: 33320770 DOI: 10.1139/gen-2020-0095] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Asarum sieboldii, a well-known traditional Chinese medicinal herb, is used for curing inflammation and ache. It contains both the bioactive ingredient asarinin and the toxic compound aristolochic acid. To address further breeding demand, genes involved in the biosynthetic pathways of asarinin and aristolochic acid should be explored. Therefore, the full-length transcriptome of A. sieboldii was sequenced using PacBio Iso-Seq to determine the candidate transcripts that encode the biosynthetic enzymes of asarinin and aristolochic acid. In this study, 63 023 full-length transcripts were generated with an average length of 1371 bp from roots, stems, and leaves, of which 49 593 transcripts (78.69%) were annotated against public databases. Furthermore, 555 alternative splicing (AS) events, 10 869 long noncoding RNAs (lncRNAs) as well as their 11 291 target genes, and 17 909 simple sequence repeats (SSRs) were identified. The data also revealed 97 candidate transcripts related to asarinin metabolism, of which six novel genes that encoded enzymes involved in asarinin biosynthesis were initially reported. In addition, 56 transcripts related to aristolochic acid biosynthesis were also identified, including CYP81B. In summary, these transcriptome data provide a useful resource to study gene function and genetic engineering in A. sieboldii.
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Affiliation(s)
- Chen Chen
- Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, Xi'an Botanical Garden of Shaanxi Province, Institute of Botany of Shaanxi Province, No. 17 Cuihua South Road, 710061, Xi'an City, Shaanxi Province, China
| | - Xinwei Shi
- Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, Xi'an Botanical Garden of Shaanxi Province, Institute of Botany of Shaanxi Province, No. 17 Cuihua South Road, 710061, Xi'an City, Shaanxi Province, China
| | - Tao Zhou
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, No. 76 Yanta West Road, 710061, Xi'an City, Shaanxi Province, China
| | - Weimin Li
- Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, Xi'an Botanical Garden of Shaanxi Province, Institute of Botany of Shaanxi Province, No. 17 Cuihua South Road, 710061, Xi'an City, Shaanxi Province, China
| | - Sifeng Li
- Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, Xi'an Botanical Garden of Shaanxi Province, Institute of Botany of Shaanxi Province, No. 17 Cuihua South Road, 710061, Xi'an City, Shaanxi Province, China
| | - Guoqing Bai
- Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, Xi'an Botanical Garden of Shaanxi Province, Institute of Botany of Shaanxi Province, No. 17 Cuihua South Road, 710061, Xi'an City, Shaanxi Province, China
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Zhang K, Cui H, Cao S, Yan L, Li M, Sun Y. Overexpression of CrCOMT from Carex rigescens increases salt stress and modulates melatonin synthesis in Arabidopsis thaliana. PLANT CELL REPORTS 2019; 38:1501-1514. [PMID: 31473792 DOI: 10.1007/s00299-019-02461-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 08/12/2019] [Indexed: 05/27/2023]
Abstract
CrCOMT, a COMT gene in Carex rigescens, was verified to enhance salt stress tolerance in transgenic Arabidopsis. High salinity severely restricts plant growth and development while melatonin can alleviate salt damage. Caffeic acid O-methyltransferase (COMT) plays an important role in regulating plant growth, development, and stress responses. COMT could also participate in melatonin biosynthesis. The objective of this study was to identify CrCOMT from Carex rigescens (Franch.) V. Krecz, a stress-tolerant grass species with a widespread distribution in north China, and to determine its physiological functions and regulatory mechanisms that impart tolerance to salt stress. The results showed that the transcription of CrCOMT exhibited different expression patterns under salt, drought, and ABA treatments. Transgenic Arabidopsis with the overexpression of CrCOMT exhibited improved growth and physiological performance under salt stress, such as higher lateral root numbers, proline level, and chlorophyll content, than in the wild type (WT). Overexpression of CrCOMT also increased dehydration tolerance in Arabidopsis. The transcription of salt response genes was more highly activated in transgenic plants than in the WT under salt stress conditions. In addition, the melatonin content in transgenic plants was higher than that in the WT after stress treatment. Taken together, our results indicated that CrCOMT may positively regulate stress responses and melatonin synthesis under salt stress.
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Affiliation(s)
- Kun Zhang
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Huiting Cui
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Shihao Cao
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Li Yan
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Mingna Li
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China.
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China.
| | - Yan Sun
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China.
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Wedow JM, Yendrek CR, Mello TR, Creste S, Martinez CA, Ainsworth EA. Metabolite and transcript profiling of Guinea grass (Panicum maximum Jacq) response to elevated [CO 2] and temperature. Metabolomics 2019; 15:51. [PMID: 30911851 PMCID: PMC6434026 DOI: 10.1007/s11306-019-1511-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 03/18/2019] [Indexed: 11/30/2022]
Abstract
INTRODUCTION By mid-century, global atmospheric carbon dioxide concentration ([CO2]) is predicted to reach 600 μmol mol-1 with global temperatures rising by 2 °C. Rising [CO2] and temperature will alter the growth and productivity of major food and forage crops across the globe. Although the impact is expected to be greatest in tropical regions, the impact of climate-change has been poorly studied in those regions. OBJECTIVES This experiment aimed to understand the effects of elevated [CO2] (600 μmol mol-1) and warming (+ 2 °C), singly and in combination, on Panicum maximum Jacq. (Guinea grass) metabolite and transcript profiles. METHODS We created a de novo assembly of the Panicum maximum transcriptome. Leaf samples were taken at two time points in the Guinea grass growing season to analyze transcriptional and metabolite profiles in plants grown at ambient and elevated [CO2] and temperature, and statistical analyses were used to integrate the data. RESULTS Elevated temperature altered the content of amino acids and secondary metabolites. The transcriptome of Guinea grass shows a clear time point separations, with the changes in the elevated temperature and [CO2] combination plots. CONCLUSION Field transcriptomics and metabolomics revealed that elevated temperature and [CO2] result in alterations in transcript and metabolite profiles associated with environmental response, secondary metabolism and stomatal function. These metabolic responses are consistent with greater growth and leaf area production under elevated temperature and [CO2]. These results show that tropical C4 grasslands may have unpredicted responses to global climate change, and that warming during a cool growing season enhances growth and alleviates stress.
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Affiliation(s)
- Jessica M Wedow
- Department of Plant Biology & Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1201 W. Gregory Drive, 147 ERML, Urbana, IL, 61801, USA
| | - Craig R Yendrek
- Department of Plant Biology & Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1201 W. Gregory Drive, 147 ERML, Urbana, IL, 61801, USA
| | - Tathyana R Mello
- Department of Biology, FFCLRP, University of Sao Paulo, Ribeirão Preto, SP, Brazil
| | - Silvana Creste
- Instituto Agronômico (IAC), Centro de Cana, Ribeirão Preto, Brazil
| | - Carlos A Martinez
- Department of Biology, FFCLRP, University of Sao Paulo, Ribeirão Preto, SP, Brazil
| | - Elizabeth A Ainsworth
- Department of Plant Biology & Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1201 W. Gregory Drive, 147 ERML, Urbana, IL, 61801, USA.
- USDA Agricultural Research Service, Global Change and Photosynthesis Research Unit, Urbana, IL, USA.
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10
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Liu S, Fu C, Gou J, Sun L, Huhman D, Zhang Y, Wang ZY. Simultaneous Downregulation of MTHFR and COMT in Switchgrass Affects Plant Performance and Induces Lesion-Mimic Cell Death. FRONTIERS IN PLANT SCIENCE 2017; 8:982. [PMID: 28676804 PMCID: PMC5476930 DOI: 10.3389/fpls.2017.00982] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 05/24/2017] [Indexed: 05/11/2023]
Abstract
Switchgrass (Panicum virgatum) has been developed into a model lignocellulosic bioenergy crop. Downregulation of caffeic acid O-methyltransferase (COMT), a key enzyme in lignin biosynthesis, has been shown to alter lignification and increase biofuel yield in switchgrass. Methylenetetrahydrofolate reductase (MTHFR) mediates C1 metabolism and provides methyl units consumed by COMT. It was predicted that co-silencing of MTHFR and COMT would impact lignification even more than either of the single genes. However, our results showed that strong downregulation of MTHFR in a COMT-deficient background led to altered plant growth and development, but no significant change in lignin content or composition was found when compared with COMT plants. Another unexpected finding was that the double MTHFR/COMT downregulated plants showed a novel lesion-mimic leaf phenotype. Molecular analyses revealed that the lesion-mimic phenotype was caused by the synergistic effect of MTHFR and COMT genes, with MTHFR playing a predominant role. Microarray analysis showed significant induction of genes related to oxidative and defense responses. The results demonstrated the lack of additive effects of MTHFR and COMT on lignification. Furthermore, this research revealed an unexpected role of the two genes in the modulation of lesion-mimic cell death as well as their synergistic effects on agronomic performance.
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Affiliation(s)
- Sijia Liu
- Department of Grassland Science, China Agricultural University, National Energy R&D Center for BiomassBeijing, China
- Forage Improvement Division, The Samuel Roberts Noble Foundation, ArdmoreOK, United States
| | - Chunxiang Fu
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of SciencesQingdao, China
| | - Jiqing Gou
- Forage Improvement Division, The Samuel Roberts Noble Foundation, ArdmoreOK, United States
- BioEnergy Science Center, Oak Ridge National Laboratory (DOE), Oak RidgeTN, United States
| | - Liang Sun
- Computing Services, The Samuel Roberts Noble Foundation, ArdmoreOK, United States
| | - David Huhman
- Plant Biology Division, The Samuel Roberts Noble Foundation, ArdmoreOK, United States
| | - Yunwei Zhang
- Department of Grassland Science, China Agricultural University, National Energy R&D Center for BiomassBeijing, China
| | - Zeng-Yu Wang
- Forage Improvement Division, The Samuel Roberts Noble Foundation, ArdmoreOK, United States
- BioEnergy Science Center, Oak Ridge National Laboratory (DOE), Oak RidgeTN, United States
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11
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Li W, Lu J, Lu K, Yuan J, Huang J, Du H, Li J. Cloning and Phylogenetic Analysis of Brassica napus L. Caffeic Acid O-Methyltransferase 1 Gene Family and Its Expression Pattern under Drought Stress. PLoS One 2016; 11:e0165975. [PMID: 27832102 PMCID: PMC5104432 DOI: 10.1371/journal.pone.0165975] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 10/20/2016] [Indexed: 01/25/2023] Open
Abstract
For many plants, regulating lignin content and composition to improve lodging resistance is a crucial issue. Caffeic acid O-methyltransferase (COMT) is a lignin monomer-specific enzyme that controls S subunit synthesis in plant vascular cell walls. Here, we identified 12 BnCOMT1 gene homologues, namely BnCOMT1-1 to BnCOMT1-12. Ten of 12 genes were composed of four highly conserved exons and three weakly conserved introns. The length of intron I, in particular, showed enormous diversification. Intron I of homologous BnCOMT1 genes showed high identity with counterpart genes in Brassica rapa and Brassica oleracea, and intron I from positional close genes in the same chromosome were relatively highly conserved. A phylogenetic analysis suggested that COMT genes experience considerable diversification and conservation in Brassicaceae species, and some COMT1 genes are unique in the Brassica genus. Our expression studies indicated that BnCOMT1 genes were differentially expressed in different tissues, with BnCOMT1-4, BnCOMT1-5, BnCOMT1-8, and BnCOMT1-10 exhibiting stem specificity. These four BnCOMT1 genes were expressed at all developmental periods (the bud, early flowering, late flowering and mature stages) and their expression level peaked in the early flowering stage in the stem. Drought stress augmented and accelerated lignin accumulation in high-lignin plants but delayed it in low-lignin plants. The expression levels of BnCOMT1s were generally reduced in water deficit condition. The desynchrony of the accumulation processes of total lignin and BnCOMT1s transcripts in most growth stages indicated that BnCOMT1s could be responsible for the synthesis of a specific subunit of lignin or that they participate in other pathways such as the melatonin biosynthesis pathway.
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Affiliation(s)
- Wei Li
- Chongqing Engineering Research Centre for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, PR China
| | - Junxing Lu
- Chongqing Key Laboratory of Molecular Biology of Plants Environment Adaption, College of Life Sciences, Chongqing Normal University, Chongqing, 401331, PR China
| | - Kun Lu
- Chongqing Engineering Research Centre for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, PR China
| | - Jianglian Yuan
- Chongqing Engineering Research Centre for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, PR China
| | - Jieheng Huang
- Chongqing Engineering Research Centre for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, PR China
| | - Hai Du
- Chongqing Engineering Research Centre for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, PR China
| | - Jiana Li
- Chongqing Engineering Research Centre for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, PR China
- * E-mail:
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12
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Kasirajan L, Aruchamy K, Thirugnanasambandam PP, Athiappan S. Molecular Cloning, Characterization, and Expression Analysis of Lignin Genes from Sugarcane Genotypes Varying in Lignin Content. Appl Biochem Biotechnol 2016; 181:1270-1282. [PMID: 27761796 DOI: 10.1007/s12010-016-2283-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 10/06/2016] [Indexed: 12/01/2022]
Abstract
Sugarcane (Saccharum spp.) is one of the highest biomass-producing plant and the best lignocellulosic feedstock for ethanol production. To achieve more efficient conversion of biomass to ethanol, a better understanding of the main factors affecting biomass recalcitrance is needed. Therefore, with this objective, here, we report a systematic study on lignin content, deposition, identification, and cloning of genes involved in lignin biosynthesis and their differential expression in five sugarcane clones, EC11003, EC11010, IK 76-91, IK 76-99, and Co 86032. Lignin content among the clones varied from 26.87 to 23.19 % with the highest in the clone EC11010 and the lowest in high sugar Co86032. Lignin deposition studied through phloroglucinol staining of the cell walls implied that the sclerenchyma cells of the energy canes (EC11010 and EC11003) have more lignin deposition followed by the Erianthus (IK 76-91 and IK 76-99) clones whereas Co86032 has the minimum amount of lignin deposition. We cloned partial coding regions of important genes of lignification COMT (650 bp), CCR (332 bp), and PAL (650 bp) from Erianthus, wild relative of sugarcane followed by the expression analysis through real-time PCR. Differential expression analysis showed high level of expression for the three genes in the energy cane EC11010.
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Affiliation(s)
- Lakshmi Kasirajan
- Genomics Laboratory, Division of Crop Improvement, Sugarcane Breeding Institute, Coimbatore, Tamil Nadu, 641007, India.
| | - Kalaivaani Aruchamy
- Genomics Laboratory, Division of Crop Improvement, Sugarcane Breeding Institute, Coimbatore, Tamil Nadu, 641007, India.,SRF, Centre for Plant Molecular Biology Department, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, 641007, India
| | | | - Selvi Athiappan
- Genomics Laboratory, Division of Crop Improvement, Sugarcane Breeding Institute, Coimbatore, Tamil Nadu, 641007, India
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13
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Wang Y, Fan C, Hu H, Li Y, Sun D, Wang Y, Peng L. Genetic modification of plant cell walls to enhance biomass yield and biofuel production in bioenergy crops. Biotechnol Adv 2016; 34:997-1017. [PMID: 27269671 DOI: 10.1016/j.biotechadv.2016.06.001] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 05/31/2016] [Accepted: 06/01/2016] [Indexed: 02/06/2023]
Abstract
Plant cell walls represent an enormous biomass resource for the generation of biofuels and chemicals. As lignocellulose property principally determines biomass recalcitrance, the genetic modification of plant cell walls has been posed as a powerful solution. Here, we review recent progress in understanding the effects of distinct cell wall polymers (cellulose, hemicelluloses, lignin, pectin, wall proteins) on the enzymatic digestibility of biomass under various physical and chemical pretreatments in herbaceous grasses, major agronomic crops and fast-growing trees. We also compare the main factors of wall polymer features, including cellulose crystallinity (CrI), hemicellulosic Xyl/Ara ratio, monolignol proportion and uronic acid level. Furthermore, the review presents the main gene candidates, such as CesA, GH9, GH10, GT61, GT43 etc., for potential genetic cell wall modification towards enhancing both biomass yield and enzymatic saccharification in genetic mutants and transgenic plants. Regarding cell wall modification, it proposes a novel groove-like cell wall model that highlights to increase amorphous regions (density and depth) of the native cellulose microfibrils, providing a general strategy for bioenergy crop breeding and biofuel processing technology.
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Affiliation(s)
- Yanting Wang
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan 430070, China; National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Chunfen Fan
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan 430070, China; National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Huizhen Hu
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan 430070, China; National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ying Li
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan 430070, China; National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Dan Sun
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; College of Chemistry and Chemical Engineering, Hubei University of Technology, Wuhan, Hubei 430068, China
| | - Youmei Wang
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan 430070, China; National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Liangcai Peng
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan 430070, China; National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
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14
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Santiago R, Malvar RA, Barros-Rios J, Samayoa LF, Butrón A. Hydroxycinnamate Synthesis and Association with Mediterranean Corn Borer Resistance. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2016; 64:539-51. [PMID: 26690311 DOI: 10.1021/acs.jafc.5b04862] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Previous results suggest a relationship between maize hydroxycinnamate concentration in the pith tissues and resistance to stem tunneling by Mediterranean corn borer (MCB, Sesamia nonagrioides Lef.) larvae. This study performs a more precise experiment, mapping an F2 derived from the cross between two inbreds with contrasting levels for hydroxycinnamates EP125 × PB130. We aimed to co-localize genomic regions involved in hydroxycinnamate synthesis and resistance to MCB and to highlight the particular route for each hydroxycinnamate component in relation to the better known phenylpropanoid pathway. Seven quantitative trait loci (QTLs) for p-coumarate, two QTLs for ferulate, and seven QTLs for total diferulates explained 81.7, 26.9, and 57.8% of the genotypic variance, respectively. In relation to borer resistance, alleles for increased hydroxycinnamate content (affecting one or more hydroxycinnamate compounds) could be associated with favorable effects on stem resistance to MCB, particularly the putative role of p-coumarate in borer resistance.
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Affiliation(s)
- Rogelio Santiago
- Agrobiologı́a Ambiental, Calidad de Suelos y Plantas (UVIGO), Unidad Asociada a la Misión Biológica de Galicia (CSIC); Departamento Biologı́a Vegetal y Ciencias del Suelo, Facultad de Biologı́a, Universidad de Vigo , Campus As Lagoas Marcosende, 36310 Vigo, Spain
| | - Rosa Ana Malvar
- Misión Biológica de Galicia (CSIC) , Apartado 28, 36080 Pontevedra, Spain
| | - Jaime Barros-Rios
- Department of Biological Sciences, University of North Texas , 1155 Union Circle #305220, Denton, Texas 76203, United States
| | | | - Ana Butrón
- Misión Biológica de Galicia (CSIC) , Apartado 28, 36080 Pontevedra, Spain
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15
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Fang J, Lin A, Qiu W, Cai H, Umar M, Chen R, Ming R. Transcriptome Profiling Revealed Stress-Induced and Disease Resistance Genes Up-Regulated in PRSV Resistant Transgenic Papaya. FRONTIERS IN PLANT SCIENCE 2016; 7:855. [PMID: 27379138 PMCID: PMC4909764 DOI: 10.3389/fpls.2016.00855] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 05/31/2016] [Indexed: 05/18/2023]
Abstract
Papaya is a productive and nutritious tropical fruit. Papaya Ringspot Virus (PRSV) is the most devastating pathogen threatening papaya production worldwide. Development of transgenic resistant varieties is the most effective strategy to control this disease. However, little is known about the genome-wide functional changes induced by particle bombardment transformation. We conducted transcriptome sequencing of PRSV resistant transgenic papaya SunUp and its PRSV susceptible progenitor Sunset to compare the transcriptional changes in young healthy leaves prior to infection with PRSV. In total, 20,700 transcripts were identified, and 842 differentially expressed genes (DEGs) randomly distributed among papaya chromosomes. Gene ontology (GO) category analysis revealed that microtubule-related categories were highly enriched among these DEGs. Numerous DEGs related to various transcription factors, transporters and hormone biosynthesis showed clear differences between the two cultivars, and most were up-regulated in transgenic papaya. Many known and novel stress-induced and disease-resistance genes were most highly expressed in SunUp, including MYB, WRKY, ERF, NAC, nitrate and zinc transporters, and genes involved in the abscisic acid, salicylic acid, and ethylene signaling pathways. We also identified 67,686 alternative splicing (AS) events in Sunset and 68,455 AS events in SunUp, mapping to 10,994 and 10,995 papaya annotated genes, respectively. GO enrichment for the genes displaying AS events exclusively in Sunset was significantly different from those in SunUp. Transcriptomes in Sunset and transgenic SunUp are very similar with noteworthy differences, which increased PRSV-resistance in transgenic papaya. No detrimental pathways and allergenic or toxic proteins were induced on a genome-wide scale in transgenic SunUp. Our results provide a foundation for unraveling the mechanism of PRSV resistance in transgenic papaya.
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Affiliation(s)
- Jingping Fang
- Key Lab of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry UniversityFuzhou, China
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Aiting Lin
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Weijing Qiu
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Hanyang Cai
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Muhammad Umar
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Rukai Chen
- Key Lab of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Ray Ming
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry UniversityFuzhou, China
- Department of Plant Biology, University of Illinois at Urbana-ChampaignUrbana, IL, USA
- *Correspondence: Ray Ming
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16
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Willis JD, Smith JA, Mazarei M, Zhang JY, Turner GB, Decker SR, Sykes RW, Poovaiah CR, Baxter HL, Mann DGJ, Davis MF, Udvardi MK, Peña MJ, Backe J, Bar-Peled M, Stewart CN. Downregulation of a UDP-Arabinomutase Gene in Switchgrass ( Panicum virgatum L.) Results in Increased Cell Wall Lignin While Reducing Arabinose-Glycans. FRONTIERS IN PLANT SCIENCE 2016; 7:1580. [PMID: 27833622 PMCID: PMC5081414 DOI: 10.3389/fpls.2016.01580] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 10/06/2016] [Indexed: 05/09/2023]
Abstract
Background: Switchgrass (Panicum virgatum L.) is a C4 perennial prairie grass and a dedicated feedstock for lignocellulosic biofuels. Saccharification and biofuel yields are inhibited by the plant cell wall's natural recalcitrance against enzymatic degradation. Plant hemicellulose polysaccharides such as arabinoxylans structurally support and cross-link other cell wall polymers. Grasses predominately have Type II cell walls that are abundant in arabinoxylan, which comprise nearly 25% of aboveground biomass. A primary component of arabinoxylan synthesis is uridine diphosphate (UDP) linked to arabinofuranose (Araf). A family of UDP-arabinopyranose mutase (UAM)/reversible glycosylated polypeptides catalyze the interconversion between UDP-arabinopyranose (UDP-Arap) and UDP-Araf. Results: The expression of a switchgrass arabinoxylan biosynthesis pathway gene, PvUAM1, was decreased via RNAi to investigate its role in cell wall recalcitrance in the feedstock. PvUAM1 encodes a switchgrass homolog of UDP-arabinose mutase, which converts UDP-Arap to UDP-Araf. Southern blot analysis revealed each transgenic line contained between one to at least seven T-DNA insertions, resulting in some cases, a 95% reduction of native PvUAM1 transcript in stem internodes. Transgenic plants had increased pigmentation in vascular tissues at nodes, but were otherwise similar in morphology to the non-transgenic control. Cell wall-associated arabinose was decreased in leaves and stems by over 50%, but there was an increase in cellulose. In addition, there was a commensurate change in arabinose side chain extension. Cell wall lignin composition was altered with a concurrent increase in lignin content and transcript abundance of lignin biosynthetic genes in mature tillers. Enzymatic saccharification efficiency was unchanged in the transgenic plants relative to the control. Conclusion: Plants with attenuated PvUAM1 transcript had increased cellulose and lignin in cell walls. A decrease in cell wall-associated arabinose was expected, which was likely caused by fewer Araf residues in the arabinoxylan. The decrease in arabinoxylan may cause a compensation response to maintain cell wall integrity by increasing cellulose and lignin biosynthesis. In cases in which increased lignin is desired, e.g., feedstocks for carbon fiber production, downregulated UAM1 coupled with altered expression of other arabinoxylan biosynthesis genes might result in even higher production of lignin in biomass.
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Affiliation(s)
- Jonathan D. Willis
- Department of Plant Sciences, University of Tennessee, KnoxvilleTN, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak RidgeTN, USA
| | - James A. Smith
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak RidgeTN, USA
- Complex Carbohydrate Research Center, University of Georgia, AthensGA, USA
| | - Mitra Mazarei
- Department of Plant Sciences, University of Tennessee, KnoxvilleTN, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak RidgeTN, USA
| | - Ji-Yi Zhang
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak RidgeTN, USA
- The Samuel Roberts Noble Foundation, ArdmoreOK, USA
| | - Geoffrey B. Turner
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak RidgeTN, USA
- The National Renewable Energy Laboratory, GoldenCO, USA
| | - Stephen R. Decker
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak RidgeTN, USA
- The National Renewable Energy Laboratory, GoldenCO, USA
| | - Robert W. Sykes
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak RidgeTN, USA
- The National Renewable Energy Laboratory, GoldenCO, USA
| | - Charleson R. Poovaiah
- Department of Plant Sciences, University of Tennessee, KnoxvilleTN, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak RidgeTN, USA
| | - Holly L. Baxter
- Department of Plant Sciences, University of Tennessee, KnoxvilleTN, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak RidgeTN, USA
| | - David G. J. Mann
- Department of Plant Sciences, University of Tennessee, KnoxvilleTN, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak RidgeTN, USA
| | - Mark F. Davis
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak RidgeTN, USA
- The National Renewable Energy Laboratory, GoldenCO, USA
| | - Michael K. Udvardi
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak RidgeTN, USA
- The Samuel Roberts Noble Foundation, ArdmoreOK, USA
| | - Maria J. Peña
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak RidgeTN, USA
- Complex Carbohydrate Research Center, University of Georgia, AthensGA, USA
| | - Jason Backe
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak RidgeTN, USA
- Complex Carbohydrate Research Center, University of Georgia, AthensGA, USA
| | - Maor Bar-Peled
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak RidgeTN, USA
- Complex Carbohydrate Research Center, University of Georgia, AthensGA, USA
- Plant Biology, University of Georgia, AthensGA, USA
- *Correspondence: Maor Bar-Peled, C. N. Stewart Jr.,
| | - C. N. Stewart
- Department of Plant Sciences, University of Tennessee, KnoxvilleTN, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak RidgeTN, USA
- *Correspondence: Maor Bar-Peled, C. N. Stewart Jr.,
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17
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Amato A, Cavallini E, Zenoni S, Finezzo L, Begheldo M, Ruperti B, Tornielli GB. A Grapevine TTG2-Like WRKY Transcription Factor Is Involved in Regulating Vacuolar Transport and Flavonoid Biosynthesis. FRONTIERS IN PLANT SCIENCE 2016; 7:1979. [PMID: 28105033 PMCID: PMC5214514 DOI: 10.3389/fpls.2016.01979] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 12/13/2016] [Indexed: 05/20/2023]
Abstract
A small set of TTG2-like homolog proteins from different species belonging to the WRKY family of transcription factors were shown to share a similar mechanism of action and to control partially conserved biochemical/developmental processes in their native species. In particular, by activating P-ATPases residing on the tonoplast, PH3 from Petunia hybrida promotes vacuolar acidification in petal epidermal cells whereas TTG2 from Arabidopsis thaliana enables the accumulation of proanthocyanidins in the seed coat. In this work we functionally characterized VvWRKY26 identified as the closest grapevine homolog of PhPH3 and AtTTG2. When constitutively expressed in petunia ph3 mutant, VvWRKY26 can fulfill the PH3 function in the regulation of vacuolar pH and restores the wild type pigmentation phenotype. By a global correlation analysis of gene expression and by transient over-expression in Vitis vinifera, we showed transcriptomic relationships of VvWRKY26 with many genes related to vacuolar acidification and transport in grapevine. Moreover, our results indicate an involvement in flavonoid pathway possibly restricted to the control of proanthocyanidin biosynthesis that is consistent with its expression pattern in grape berry tissues. Overall, the results show that, in addition to regulative mechanisms and biological roles shared with TTG2-like orthologs, VvWRKY26 can play roles in fleshy fruit development that have not been previously reported in studies from dry fruit species. This study paves the way toward the comprehension of the regulatory network controlling vacuolar acidification and flavonoid accumulation mechanisms that contribute to the final berry quality traits in grapevine.
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Affiliation(s)
| | - Erika Cavallini
- Department of Biotechnology, University of VeronaVerona, Italy
| | - Sara Zenoni
- Department of Biotechnology, University of VeronaVerona, Italy
| | - Laura Finezzo
- Department of Biotechnology, University of VeronaVerona, Italy
| | - Maura Begheldo
- Department of Agriculture, Food, Natural Resources, Animals and Environment, University of PadovaPadova, Italy
| | - Benedetto Ruperti
- Department of Agriculture, Food, Natural Resources, Animals and Environment, University of PadovaPadova, Italy
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Barrière Y, Courtial A, Chateigner-Boutin AL, Denoue D, Grima-Pettenati J. Breeding maize for silage and biofuel production, an illustration of a step forward with the genome sequence. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 242:310-329. [PMID: 26566848 DOI: 10.1016/j.plantsci.2015.08.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 08/04/2015] [Accepted: 08/13/2015] [Indexed: 05/21/2023]
Abstract
The knowledge of the gene families mostly impacting cell wall digestibility variations would significantly increase the efficiency of marker-assisted selection when breeding maize and grass varieties with improved silage feeding value and/or with better straw fermentability into alcohol or methane. The maize genome sequence of the B73 inbred line was released at the end of 2009, opening up new avenues to identify the genetic determinants of quantitative traits. Colocalizations between a large set of candidate genes putatively involved in secondary cell wall assembly and QTLs for cell wall digestibility (IVNDFD) were then investigated, considering physical positions of both genes and QTLs. Based on available data from six RIL progenies, 59 QTLs corresponding to 38 non-overlapping positions were matched up with a list of 442 genes distributed all over the genome. Altogether, 176 genes colocalized with IVNDFD QTLs and most often, several candidate genes colocalized at each QTL position. Frequent QTL colocalizations were found firstly with genes encoding ZmMYB and ZmNAC transcription factors, and secondly with genes encoding zinc finger, bHLH, and xylogen regulation factors. In contrast, close colocalizations were less frequent with genes involved in monolignol biosynthesis, and found only with the C4H2, CCoAOMT5, and CCR1 genes. Close colocalizations were also infrequent with genes involved in cell wall feruloylation and cross-linkages. Altogether, investigated colocalizations between candidate genes and cell wall digestibility QTLs suggested a prevalent role of regulation factors over constitutive cell wall genes on digestibility variations.
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Affiliation(s)
- Yves Barrière
- INRA, UR889, Unité de Génétique et d'Amélioration des Plantes Fourragères, 86600 Lusignan, France.
| | - Audrey Courtial
- LRSV, Laboratoire de Recherche en Sciences Végétales, UMR5546, Université Paul Sabatier Toulouse III / CNRS, Auzeville, BP 42617, 31326 Castanet-Tolosan, France; INRA, US1258, Centre National de Ressources Génomiques Végétales, CS 52627, 31326 Castanet-Tolosan, France
| | | | - Dominique Denoue
- INRA, UR889, Unité de Génétique et d'Amélioration des Plantes Fourragères, 86600 Lusignan, France
| | - Jacqueline Grima-Pettenati
- LRSV, Laboratoire de Recherche en Sciences Végétales, UMR5546, Université Paul Sabatier Toulouse III / CNRS, Auzeville, BP 42617, 31326 Castanet-Tolosan, France
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Leonardi GDA, Carlos NA, Mazzafera P, Balbuena TS. Eucalyptus urograndis stem proteome is responsive to short-term cold stress. Genet Mol Biol 2015; 38:191-8. [PMID: 26273222 PMCID: PMC4530643 DOI: 10.1590/s1415-475738220140235] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Accepted: 11/07/2014] [Indexed: 01/03/2023] Open
Abstract
Eucalyptus urograndis is a hybrid eucalyptus of major economic importance to the Brazilian pulp and paper industry. Although widely used in forest nurseries around the country, little is known about the biochemical changes imposed by environmental stress in this species. In this study, we evaluated the changes in the stem proteome after short-term stimulation by exposure to low temperature. Using two-dimensional gel electrophoresis coupled to high-resolution mass spectrometry-based protein identification, 12 proteins were found to be differentially regulated and successfully identified after stringent database searches against a protein database from a closely related species (Eucalyptus grandis). The identification of these proteins indicated that the E. urograndis stem proteome responded quickly to low temperature, mostly by down-regulating specific proteins involved in energy metabolism, protein synthesis and signaling. The results of this study represent the first step in understanding the molecular and biochemical responses of E. urograndis to thermal stress.
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Affiliation(s)
- Gabriela de Almeida Leonardi
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista "Júlio de Mesquita Filho", Jaboticabal, SP, Brazil
| | - Natália Aparecida Carlos
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista "Júlio de Mesquita Filho", Jaboticabal, SP, Brazil
| | - Paulo Mazzafera
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Tiago Santana Balbuena
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista "Júlio de Mesquita Filho", Jaboticabal, SP, Brazil
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20
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Tian FX, Zang JL, Wang T, Xie YL, Zhang J, Hu JJ. Aldehyde Dehydrogenase Gene Superfamily in Populus: Organization and Expression Divergence between Paralogous Gene Pairs. PLoS One 2015; 10:e0124669. [PMID: 25909656 PMCID: PMC4409362 DOI: 10.1371/journal.pone.0124669] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 03/16/2015] [Indexed: 11/18/2022] Open
Abstract
Aldehyde dehydrogenases (ALDHs) constitute a superfamily of NAD(P)+-dependent enzymes that catalyze the irreversible oxidation of a wide range of reactive aldehydes to their corresponding nontoxic carboxylic acids. ALDHs have been studied in many organisms from bacteria to mammals; however, no systematic analyses incorporating genome organization, gene structure, expression profiles, and cis-acting elements have been conducted in the model tree species Populus trichocarpa thus far. In this study, a comprehensive analysis of the Populus ALDH gene superfamily was performed. A total of 26 Populus ALDH genes were found to be distributed across 12 chromosomes. Genomic organization analysis indicated that purifying selection may have played a pivotal role in the retention and maintenance of PtALDH gene families. The exon-intron organizations of PtALDHs were highly conserved within the same family, suggesting that the members of the same family also may have conserved functionalities. Microarray data and qRT-PCR analysis indicated that most PtALDHs had distinct tissue-specific expression patterns. The specificity of cis-acting elements in the promoter regions of the PtALDHs and the divergence of expression patterns between nine paralogous PtALDH gene pairs suggested that gene duplications may have freed the duplicate genes from the functional constraints. The expression levels of some ALDHs were up- or down-regulated by various abiotic stresses, implying that the products of these genes may be involved in the adaptation of Populus to abiotic stresses. Overall, the data obtained from our investigation contribute to a better understanding of the complexity of the Populus ALDH gene superfamily and provide insights into the function and evolution of ALDH gene families in vascular plants.
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Affiliation(s)
- Feng-Xia Tian
- College of Life Science and Technology, Nanyang Normal University, Nanyang, Henan, 473061, China
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Jian-Lei Zang
- College of Life Science and Technology, Nanyang Normal University, Nanyang, Henan, 473061, China
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Tan Wang
- College of Life Science and Technology, Nanyang Normal University, Nanyang, Henan, 473061, China
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Yu-Li Xie
- College of Life Science and Technology, Nanyang Normal University, Nanyang, Henan, 473061, China
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Jin Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Research Institute of Wood Industry, Chinese Academy of Forestry, Beijing, 100091, China
- * E-mail: (JZ); (JJH)
| | - Jian-Jun Hu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- * E-mail: (JZ); (JJH)
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Li L, Hill-Skinner S, Liu S, Beuchle D, Tang HM, Yeh CT, Nettleton D, Schnable PS. The maize brown midrib4 (bm4) gene encodes a functional folylpolyglutamate synthase. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 81:493-504. [PMID: 25495051 PMCID: PMC4329605 DOI: 10.1111/tpj.12745] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 12/03/2014] [Accepted: 12/08/2014] [Indexed: 05/02/2023]
Abstract
Mutations in the brown midrib4 (bm4) gene affect the accumulation and composition of lignin in maize. Fine-mapping analysis of bm4 narrowed the candidate region to an approximately 105 kb interval on chromosome 9 containing six genes. Only one of these six genes, GRMZM2G393334, showed decreased expression in mutants. At least four of 10 Mu-induced bm4 mutant alleles contain a Mu insertion in the GRMZM2G393334 gene. Based on these results, we concluded that GRMZM2G393334 is the bm4 gene. GRMZM2G393334 encodes a putative folylpolyglutamate synthase (FPGS), which functions in one-carbon (C1) metabolism to polyglutamylate substrates of folate-dependent enzymes. Yeast complementation experiments demonstrated that expression of the maize bm4 gene in FPGS-deficient met7 yeast is able to rescue the yeast mutant phenotype, thus demonstrating that bm4 encodes a functional FPGS. Consistent with earlier studies, bm4 mutants exhibit a modest decrease in lignin concentration and an overall increase in the S:G lignin ratio relative to wild-type. Orthologs of bm4 include at least one paralogous gene in maize and various homologs in other grasses and dicots. Discovery of the gene underlying the bm4 maize phenotype illustrates a role for FPGS in lignin biosynthesis.
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Affiliation(s)
- Li Li
- Department of Agronomy, Iowa State University2035 Roy J. Carver Co-Lab, Ames, IA, 50011-3650, USA
- College of Agronomy, Northwest Agriculture and Forestry University#3, Taicheng road, Yangling, Shaanxi, 712100, China
| | - Sarah Hill-Skinner
- Department of Agronomy, Iowa State University2035 Roy J. Carver Co-Lab, Ames, IA, 50011-3650, USA
| | - Sanzhen Liu
- Department of Agronomy, Iowa State University2035 Roy J. Carver Co-Lab, Ames, IA, 50011-3650, USA
| | - Danielle Beuchle
- Department of Genetics, Development and Cell Biology, Iowa State University1210 Molecular Biology Building, Ames, IA 50011-3260, USA
| | - Ho Man Tang
- Department of Genetics, Development and Cell Biology, Iowa State University1210 Molecular Biology Building, Ames, IA 50011-3260, USA
| | - Cheng-Ting Yeh
- Department of Agronomy, Iowa State University2035 Roy J. Carver Co-Lab, Ames, IA, 50011-3650, USA
| | - Dan Nettleton
- Center for Plant Genomics, Iowa State University2035 Roy J. Carver Co-Lab, Ames, IA, 50011-3650, USA
- Department of Statistics, Iowa State University2115 Snedecor, Ames, IA, 50011, USA
| | - Patrick S Schnable
- Department of Agronomy, Iowa State University2035 Roy J. Carver Co-Lab, Ames, IA, 50011-3650, USA
- Department of Genetics, Development and Cell Biology, Iowa State University1210 Molecular Biology Building, Ames, IA 50011-3260, USA
- Center for Plant Genomics, Iowa State University2035 Roy J. Carver Co-Lab, Ames, IA, 50011-3650, USA
- *
For correspondence (e-mail )
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22
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Giordano A, Liu Z, Panter SN, Dimech AM, Shang Y, Wijesinghe H, Fulgueras K, Ran Y, Mouradov A, Rochfort S, Patron NJ, Spangenberg GC. Reduced lignin content and altered lignin composition in the warm season forage grass Paspalum dilatatum by down-regulation of a Cinnamoyl CoA reductase gene. Transgenic Res 2014; 23:503-17. [PMID: 24504635 PMCID: PMC4010725 DOI: 10.1007/s11248-014-9784-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 01/29/2014] [Indexed: 11/13/2022]
Abstract
C4 grasses are favoured as forage crops in warm, humid climates. The use of C4 grasses in pastures is expected to increase because the tropical belt is widening due to global climate change. While the forage quality of Paspalum dilatatum (dallisgrass) is higher than that of other C4 forage grass species, digestibility of warm-season grasses is, in general, poor compared with most temperate grasses. The presence of thick-walled parenchyma bundle-sheath cells around the vascular bundles found in the C4 forage grasses are associated with the deposition of lignin polymers in cell walls. High lignin content correlates negatively with digestibility, which is further reduced by a high ratio of syringyl (S) to guaiacyl (G) lignin subunits. Cinnamoyl-CoA reductase (CCR) catalyses the conversion of cinnamoyl CoA to cinnemaldehyde in the monolignol biosynthetic pathway and is considered to be the first step in the lignin-specific branch of the phenylpropanoid pathway. We have isolated three putative CCR1 cDNAs from P. dilatatum and demonstrated that their spatio-temporal expression pattern correlates with the developmental profile of lignin deposition. Further, transgenic P. dilatatum plants were produced in which a sense-suppression gene cassette, delivered free of vector backbone and integrated separately to the selectable marker, reduced CCR1 transcript levels. This resulted in the reduction of lignin, largely attributable to a decrease in G lignin.
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Affiliation(s)
- Andrea Giordano
- Department of Environment and Primary Industries, AgriBio Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC 3083 Australia
- La Trobe University, Kingsbury Drive, Bundoora, VIC 3086 Australia
- Present Address: Plant Biology Department, Federal University of Viçosa, Av. PH Rolfs s/n, Viçosa, MG Brazil
| | - Zhiqian Liu
- Department of Environment and Primary Industries, AgriBio Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC 3083 Australia
| | - Stephen N. Panter
- Department of Environment and Primary Industries, AgriBio Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC 3083 Australia
| | - Adam M. Dimech
- Department of Environment and Primary Industries, AgriBio Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC 3083 Australia
| | - Yongjin Shang
- Department of Environment and Primary Industries, AgriBio Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC 3083 Australia
| | - Hewage Wijesinghe
- Department of Environment and Primary Industries, AgriBio Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC 3083 Australia
| | - Karen Fulgueras
- Department of Environment and Primary Industries, AgriBio Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC 3083 Australia
| | - Yidong Ran
- Department of Environment and Primary Industries, AgriBio Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC 3083 Australia
| | - Aidyn Mouradov
- Department of Environment and Primary Industries, AgriBio Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC 3083 Australia
- Present Address: School of Applied Sciences, RMIT University, Plenty Road, Bundoora, VIC 3083 Australia
| | - Simone Rochfort
- Department of Environment and Primary Industries, AgriBio Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC 3083 Australia
- La Trobe University, Kingsbury Drive, Bundoora, VIC 3086 Australia
| | - Nicola J. Patron
- Department of Environment and Primary Industries, AgriBio Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC 3083 Australia
- Present Address: The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH UK
| | - German C. Spangenberg
- Department of Environment and Primary Industries, AgriBio Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC 3083 Australia
- La Trobe University, Kingsbury Drive, Bundoora, VIC 3086 Australia
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23
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Seong ES, Yoo JH, Lee JG, Kim HY, Hwang IS, Heo K, Kim JK, Lim JD, Sacks EJ, Yu CY. Antisense-overexpression of the MsCOMT gene induces changes in lignin and total phenol contents in transgenic tobacco plants. Mol Biol Rep 2013; 40:1979-86. [PMID: 23160900 DOI: 10.1007/s11033-012-2255-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Accepted: 10/10/2012] [Indexed: 10/27/2022]
Abstract
Initially, we isolated the caffeic acid O-methyltransferase (COMT) gene from Miscanthus sinensis (accession number HM062766.1). Next, we produced transgenic tobacco plants with down-regulated COMT gene expression to study its control of total phenol and lignin content and to perform morphological analysis. These transgenic plants were found to have reduced PAL and ascorbate peroxidases expression, which are related to the phenylpropanoid pathway and antioxidant activity. The MsCOMT-down-regulated plants had decreased total lignin in the leaves and stem compared with control plants. Reduced flavonol concentrations were confirmed in MsCOMT-down-regulated transgenic plants. We also observed a morphological difference, with reduced plant cell number in transgenic plants harboring antisense MsCOMT. The transgenic tobacco plants with down-regulated COMT gene expression demonstrate that COMT plays a crucial role related to controlling lignin and phenol content in plants. Also, COMT activity may be related to flavonoid production in the plant lignin pathway.
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Affiliation(s)
- Eun Soo Seong
- Bioherb Research Institute, Kangwon National University, Chuncheon, 200-701, South Korea.
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Wu X, Wu J, Luo Y, Bragg J, Anderson O, Vogel J, Gu YQ. Phylogenetic, Molecular, and Biochemical Characterization of Caffeic Acid o-Methyltransferase Gene Family in Brachypodium distachyon. INTERNATIONAL JOURNAL OF PLANT GENOMICS 2013; 2013:423189. [PMID: 23431288 PMCID: PMC3562662 DOI: 10.1155/2013/423189] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Revised: 12/03/2012] [Accepted: 12/07/2012] [Indexed: 05/02/2023]
Abstract
Caffeic acid o-methyltransferase (COMT) is one of the important enzymes controlling lignin monomer production in plant cell wall synthesis. Analysis of the genome sequence of the new grass model Brachypodium distachyon identified four COMT gene homologs, designated as BdCOMT1, BdCOMT2, BdCOMT3, and BdCOMT4. Phylogenetic analysis suggested that they belong to the COMT gene family, whereas syntenic analysis through comparisons with rice and sorghum revealed that BdCOMT4 on Chromosome 3 is the orthologous copy of the COMT genes well characterized in other grass species. The other three COMT genes are unique to Brachypodium since orthologous copies are not found in the collinear regions of rice and sorghum genomes. Expression studies indicated that all four Brachypodium COMT genes are transcribed but with distinct patterns of tissue specificity. Full-length cDNAs were cloned in frame into the pQE-T7 expression vector for the purification of recombinant Brachypodium COMT proteins. Biochemical characterization of enzyme activity and substrate specificity showed that BdCOMT4 has significant effect on a broad range of substrates with the highest preference for caffeic acid. The other three COMTs had low or no effect on these substrates, suggesting that a diversified evolution occurred on these duplicate genes that not only impacted their pattern of expression, but also altered their biochemical properties.
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Affiliation(s)
- Xianting Wu
- Western Regional Research Center, USDA-ARS, 800 Buchanan Street, Albany, CA 94710, USA
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Jiajie Wu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, 61 Daizong Avenue, Tai'an, Shandong 271018, China
| | - Yangfan Luo
- Western Regional Research Center, USDA-ARS, 800 Buchanan Street, Albany, CA 94710, USA
| | - Jennifer Bragg
- Western Regional Research Center, USDA-ARS, 800 Buchanan Street, Albany, CA 94710, USA
| | - Olin Anderson
- Western Regional Research Center, USDA-ARS, 800 Buchanan Street, Albany, CA 94710, USA
| | - John Vogel
- Western Regional Research Center, USDA-ARS, 800 Buchanan Street, Albany, CA 94710, USA
| | - Yong Q. Gu
- Western Regional Research Center, USDA-ARS, 800 Buchanan Street, Albany, CA 94710, USA
- *Yong Q. Gu:
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Kaur H, Shaker K, Heinzel N, Ralph J, Gális I, Baldwin IT. Environmental stresses of field growth allow cinnamyl alcohol dehydrogenase-deficient Nicotiana attenuata plants to compensate for their structural deficiencies. PLANT PHYSIOLOGY 2012; 159:1545-70. [PMID: 22645069 PMCID: PMC3425196 DOI: 10.1104/pp.112.196717] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2012] [Accepted: 05/03/2012] [Indexed: 05/02/2023]
Abstract
The organized lignocellulosic assemblies of cell walls provide the structural integrity required for the large statures of terrestrial plants. Silencing two CINNAMYL ALCOHOL DEHYDROGENASE (CAD) genes in Nicotiana attenuata produced plants (ir-CAD) with thin, red-pigmented stems, low CAD and sinapyl alcohol dehydrogenase activity, low lignin contents, and rubbery, structurally unstable stems when grown in the glasshouse (GH). However, when planted into their native desert habitat, ir-CAD plants produced robust stems that survived wind storms as well as the wild-type plants. Despite efficient silencing of NaCAD transcripts and enzymatic activity, field-grown ir-CAD plants had delayed and restricted spread of red stem pigmentation, a color change reflecting blocked lignification by CAD silencing, and attained wild-type-comparable total lignin contents. The rubbery GH phenotype was largely restored when field-grown ir-CAD plants were protected from wind, herbivore attack, and ultraviolet B exposure and grown in restricted rooting volumes; conversely, it was lost when ir-CAD plants were experimentally exposed to wind, ultraviolet B, and grown in large pots in growth chambers. Transcript and liquid chromatography-electrospray ionization-time-of-flight analysis revealed that these environmental stresses enhanced the accumulation of various phenylpropanoids in stems of field-grown plants; gas chromatography-mass spectrometry and nuclear magnetic resonance analysis revealed that the lignin of field-grown ir-CAD plants had GH-grown comparable levels of sinapaldehyde and syringaldehyde cross-linked into their lignins. Additionally, field-grown ir-CAD plants had short, thick stems with normal xylem element traits, which collectively enabled field-grown ir-CAD plants to compensate for the structural deficiencies associated with CAD silencing. Environmental stresses play an essential role in regulating lignin biosynthesis in lignin-deficient plants.
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Affiliation(s)
| | | | | | - John Ralph
- Department of Molecular Ecology (H.K., N.H., I.G., I.T.B.) and Department of Biosynthesis/Nuclear Magnetic Resonance (K.S.), Max-Planck Institute for Chemical Ecology, Jena 07745, Germany; Department of Biochemistry and Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin 53706 (J.R.); and Institute of Plant Science and Resources, Okayama University, Okayama 710–0046, Japan (I.G.)
| | - Ivan Gális
- Department of Molecular Ecology (H.K., N.H., I.G., I.T.B.) and Department of Biosynthesis/Nuclear Magnetic Resonance (K.S.), Max-Planck Institute for Chemical Ecology, Jena 07745, Germany; Department of Biochemistry and Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin 53706 (J.R.); and Institute of Plant Science and Resources, Okayama University, Okayama 710–0046, Japan (I.G.)
| | - Ian T. Baldwin
- Department of Molecular Ecology (H.K., N.H., I.G., I.T.B.) and Department of Biosynthesis/Nuclear Magnetic Resonance (K.S.), Max-Planck Institute for Chemical Ecology, Jena 07745, Germany; Department of Biochemistry and Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin 53706 (J.R.); and Institute of Plant Science and Resources, Okayama University, Okayama 710–0046, Japan (I.G.)
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Brenner WG, Schmülling T. Transcript profiling of cytokinin action in Arabidopsis roots and shoots discovers largely similar but also organ-specific responses. BMC PLANT BIOLOGY 2012; 12:112. [PMID: 22824128 PMCID: PMC3519560 DOI: 10.1186/1471-2229-12-112] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Accepted: 06/13/2012] [Indexed: 05/17/2023]
Abstract
BACKGROUND The plant hormone cytokinin regulates growth and development of roots and shoots in opposite ways. In shoots it is a positive growth regulator whereas it inhibits growth in roots. It may be assumed that organ-specific regulation of gene expression is involved in these differential activities, but little is known about it. To get more insight into the transcriptional events triggered by cytokinin in roots and shoots, we studied genome-wide gene expression in cytokinin-treated and cytokinin-deficient roots and shoots. RESULTS It was found by principal component analysis of the transcriptomic data that the immediate-early response to a cytokinin stimulus differs from the later response, and that the transcriptome of cytokinin-deficient plants is different from both the early and the late cytokinin induction response. A higher cytokinin status in the roots activated the expression of numerous genes normally expressed predominantly in the shoot, while a lower cytokinin status in the shoot reduced the expression of genes normally more active in the shoot to a more root-like level. This shift predominantly affected nuclear genes encoding plastid proteins. An organ-specific regulation was assigned to a number of genes previously known to react to a cytokinin signal, including root-specificity for the cytokinin hydroxylase gene CYP735A2 and shoot specificity for the cell cycle regulator gene CDKA;1. Numerous cytokinin-regulated genes were newly discovered or confirmed, including the meristem regulator genes SHEPHERD and CLAVATA1, auxin-related genes (IAA7, IAA13, AXR1, PIN2, PID), several genes involved in brassinosteroid (CYP710A1, CYP710A2, DIM/DWF) and flavonol (MYB12, CHS, FLS1) synthesis, various transporter genes (e.g. HKT1), numerous members of the AP2/ERF transcription factor gene family, genes involved in light signalling (PhyA, COP1, SPA1), and more than 80 ribosomal genes. However, contrasting with the fundamental difference of the growth response of roots and shoots to the hormone, the vast majority of the cytokinin-regulated transcriptome showed similar response patterns in roots and shoots. CONCLUSIONS The shift of the root and shoot transcriptomes towards the respective other organ depending on the cytokinin status indicated that the hormone determines part of the organ-specific transcriptome pattern independent of morphological organ identity. Numerous novel cytokinin-regulated genes were discovered which had escaped earlier discovery, most probably due to unspecific sampling. These offer novel insights into the diverse activities of cytokinin, including crosstalk with other hormones and different environmental cues, identify the AP2/ERF class of transcriptions factors as particularly cytokinin sensitive, and also suggest translational control of cytokinin-induced changes.
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Affiliation(s)
- Wolfram G Brenner
- Institute of Biology/Applied Genetics, Dahlem Centre of Plant Sciences (DCPS), Freie Universität Berlin, Albrecht-Thaer-Weg 6, D-14195, Berlin, Germany
| | - Thomas Schmülling
- Institute of Biology/Applied Genetics, Dahlem Centre of Plant Sciences (DCPS), Freie Universität Berlin, Albrecht-Thaer-Weg 6, D-14195, Berlin, Germany
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Jung HJG, Samac DA, Sarath G. Modifying crops to increase cell wall digestibility. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2012; 185-186:65-77. [PMID: 22325867 DOI: 10.1016/j.plantsci.2011.10.014] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Revised: 10/18/2011] [Accepted: 10/20/2011] [Indexed: 05/18/2023]
Abstract
Improving digestibility of roughage cell walls will improve ruminant animal performance and reduce loss of nutrients to the environment. The main digestibility impediment for dicotyledonous plants is highly lignified secondary cell walls, notably in stem secondary xylem, which become almost non-digestible. Digestibility of grasses is slowed severely by lignification of most tissues, but these cell walls remain largely digestible. Cell wall lignification creates an access barrier to potentially digestible wall material by rumen bacteria if cells have not been physically ruptured. Traditional breeding has focused on increasing total dry matter digestibility rather than cell wall digestibility, which has resulted in minimal reductions in cell wall lignification. Brown midrib mutants in some annual grasses exhibit small reductions in lignin concentration and improved cell wall digestibility. Similarly, transgenic approaches down-regulating genes in monolignol synthesis have produced plants with reduced lignin content and improved cell wall digestibility. While major reductions in lignin concentration have been associated with poor plant fitness, smaller reductions in lignin provided measurable improvements in digestibility without significantly impacting agronomic fitness. Additional targets for genetic modification to enhance digestibility and improve roughages for use as biofuel feedstocks are discussed; including manipulating cell wall polysaccharide composition, novel lignin structures, reduced lignin/polysaccharide cross-linking, smaller lignin polymers, enhanced development of non-lignified tissues, and targeting specific cell types. Greater tissue specificity of transgene expression will be needed to maximize benefits while avoiding negative impacts on plant fitness.cauliflower mosiac virus (CaMV) 35S promoter.
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Affiliation(s)
- Hans-Joachim G Jung
- USDA-Agricultural Research Service, Plant Science Research Unit, St. Paul, MN 55108, USA.
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Chavigneau H, Goué N, Delaunay S, Courtial A, Jouanin L, Reymond M, Méchin V, Barrière Y. QTL for floral stem lignin content and degradability in three recombinant inbred line (RIL) progenies of <i>Arabidopsis thaliana</i> and search for candidate genes involved in cell wall biosynthesis and degradability. ACTA ACUST UNITED AC 2012. [DOI: 10.4236/ojgen.2012.21002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Comparative genomics and evolutionary analyses of the O-methyltransferase gene family in Populus. Gene 2011; 479:37-46. [PMID: 21338660 DOI: 10.1016/j.gene.2011.02.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2011] [Revised: 02/07/2011] [Accepted: 02/13/2011] [Indexed: 11/22/2022]
Abstract
S-adenosyl-l-methionine (SAM) dependent O-methyltransferases (OMTs) proteins are involved in the methylation of various secondary metabolites. The OMT genes have been studied in various plants, but these studies focused either on a single or a small set of genes. Moreover, no comprehensive study was published yet on the OMT gene family in a tree species. To investigate the evolutionary history of this gene family and the functional diversification of its members, phylogenetic and several comparative genomics analyses were performed. Phylogeny across land plant lineages showed that OMT genes were distributed in two main classes deeply rooted in the phylogeny of land plants, suggesting that they have evolved by a gene duplication that had happen in the ancestor of land plants. COMT and COMT-like genes were clustering with few flavonoid and multifunctional OMT genes in class II. Class I included flavonoid, simple phenol, and multifunctional OMT genes. All 26 Populus OMT genes were located in segmental duplication blocks and two third of them were tandem duplicated, indicating the role of duplication processes in the expansion of this gene family. Expression profiling of OMT genes in Populus showed that only PoptrOMT25 was differentially expressed in xylem. The other genes were differentially expressed in leaves, bark, or both. Some OMT genes showed differential expression patterns under various biotic and abiotic stresses. The divergence of protein sequences, the phylogenetic distribution, and the expression of COMT and COMT-like genes suggest that they have evolved different functions or tissue specificities following duplications.
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Louie GV, Bowman ME, Tu Y, Mouradov A, Spangenberg G, Noel JP. Structure-function analyses of a caffeic acid O-methyltransferase from perennial ryegrass reveal the molecular basis for substrate preference. THE PLANT CELL 2010; 22:4114-27. [PMID: 21177481 PMCID: PMC3027180 DOI: 10.1105/tpc.110.077578] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2010] [Revised: 10/20/2010] [Accepted: 11/19/2010] [Indexed: 05/02/2023]
Abstract
Lignin forms from the polymerization of phenylpropanoid-derived building blocks (the monolignols), whose modification through hydroxylation and O-methylation modulates the chemical and physical properties of the lignin polymer. The enzyme caffeic acid O-methyltransferase (COMT) is central to lignin biosynthesis. It is often targeted in attempts to engineer the lignin composition of transgenic plants for improved forage digestibility, pulping efficiency, or utility in biofuel production. Despite intensive investigation, the structural determinants of the regiospecificity and substrate selectivity of COMT remain poorly defined. Reported here are x-ray crystallographic structures of perennial ryegrass (Lolium perenne) COMT (Lp OMT1) in open conformational state, apo- and holoenzyme forms and, most significantly, in a closed conformational state complexed with the products S-adenosyl-L-homocysteine and sinapaldehyde. The product-bound complex reveals the post-methyl-transfer organization of COMT's catalytic groups with reactant molecules and the fully formed phenolic-ligand binding site. The core scaffold of the phenolic ligand forges a hydrogen-bonding network involving the 4-hydroxy group that anchors the aromatic ring and thereby permits only metahydroxyl groups to be positioned for transmethylation. While distal from the site of transmethylation, the propanoid tail substituent governs the kinetic preference of ryegrass COMT for aldehydes over alcohols and acids due to a single hydrogen bond donor for the C9 oxygenated moiety dictating the preference for an aldehyde.
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Affiliation(s)
- Gordon V. Louie
- The Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, California 92037
| | - Marianne E. Bowman
- The Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, California 92037
| | - Yi Tu
- Department of Primary Industries, Biosciences Research Division, Victorian AgriBiosciences Centre, Bundoora, Victoria 3083, Australia
- Molecular Plant Breeding Cooperative Research Centre, Bundoora, Victoria 3083, Australia
- La Trobe University, Bundoora, Victoria 3083, Australia
| | - Aidyn Mouradov
- Department of Primary Industries, Biosciences Research Division, Victorian AgriBiosciences Centre, Bundoora, Victoria 3083, Australia
- Molecular Plant Breeding Cooperative Research Centre, Bundoora, Victoria 3083, Australia
- La Trobe University, Bundoora, Victoria 3083, Australia
| | - German Spangenberg
- Department of Primary Industries, Biosciences Research Division, Victorian AgriBiosciences Centre, Bundoora, Victoria 3083, Australia
- Molecular Plant Breeding Cooperative Research Centre, Bundoora, Victoria 3083, Australia
- La Trobe University, Bundoora, Victoria 3083, Australia
| | - Joseph P. Noel
- The Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, California 92037
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Truntzler M, Barrière Y, Sawkins MC, Lespinasse D, Betran J, Charcosset A, Moreau L. Meta-analysis of QTL involved in silage quality of maize and comparison with the position of candidate genes. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2010; 121:1465-82. [PMID: 20658277 DOI: 10.1007/s00122-010-1402-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2009] [Accepted: 07/05/2010] [Indexed: 05/17/2023]
Abstract
A meta-analysis of quantitative trait loci (QTL) associated with plant digestibility and cell wall composition in maize was carried out using results from 11 different mapping experiments. Statistical methods implemented in "MetaQTL" software were used to build a consensus map, project QTL positions and perform meta-analysis. Fifty-nine QTL for traits associated with digestibility and 150 QTL for traits associated with cell wall composition were included in the analysis. We identified 26 and 42 metaQTL for digestibility and cell wall composition traits, respectively. Fifteen metaQTL with confidence interval (CI) smaller than 10 cM were identified. As expected from trait correlations, 42% of metaQTL for digestibility displayed overlapping CIs with metaQTL for cell wall composition traits. Coincidences were particularly strong on chromosomes 1 and 3. In a second step, 356 genes selected from the MAIZEWALL database as candidates for the cell wall biosynthesis pathway were positioned on our consensus map. Colocalizations between candidate genes and metaQTL positions appeared globally significant based on χ(2) tests. This study contributed in identifying key chromosomal regions involved in silage quality and potentially associated genes for most of these regions. These genes deserve further investigation, in particular through association mapping.
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Affiliation(s)
- M Truntzler
- INRA, UMR de Genetique Vegetale INRA/Univ. Paris XI/CNRS/INA PG, Paris, France.
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Tu Y, Rochfort S, Liu Z, Ran Y, Griffith M, Badenhorst P, Louie GV, Bowman ME, Smith KF, Noel JP, Mouradov A, Spangenberg G. Functional analyses of caffeic acid O-Methyltransferase and Cinnamoyl-CoA-reductase genes from perennial ryegrass (Lolium perenne). THE PLANT CELL 2010; 22:3357-73. [PMID: 20952635 PMCID: PMC2990129 DOI: 10.1105/tpc.109.072827] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2009] [Revised: 09/07/2010] [Accepted: 09/27/2010] [Indexed: 05/02/2023]
Abstract
Cinnamoyl CoA-reductase (CCR) and caffeic acid O-methyltransferase (COMT) catalyze key steps in the biosynthesis of monolignols, which serve as building blocks in the formation of plant lignin. We identified candidate genes encoding these two enzymes in perennial ryegrass (Lolium perenne) and show that the spatio-temporal expression patterns of these genes in planta correlate well with the developmental profile of lignin deposition. Downregulation of CCR1 and caffeic acid O-methyltransferase 1 (OMT1) using an RNA interference-mediated silencing strategy caused dramatic changes in lignin level and composition in transgenic perennial ryegrass plants grown under both glasshouse and field conditions. In CCR1-deficient perennial ryegrass plants, metabolic profiling indicates the redirection of intermediates both within and beyond the core phenylpropanoid pathway. The combined results strongly support a key role for the OMT1 gene product in the biosynthesis of both syringyl- and guaiacyl-lignin subunits in perennial ryegrass. Both field-grown OMT1-deficient and CCR1-deficient perennial ryegrass plants showed enhanced digestibility without obvious detrimental effects on either plant fitness or biomass production. This highlights the potential of metabolic engineering not only to enhance the forage quality of grasses but also to produce optimal feedstock plants for biofuel production.
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Affiliation(s)
- Yi Tu
- Department of Primary Industries, Biosciences Research Division, Victorian AgriBiosciences Centre, Bundoora, Victoria, 3083, Australia
- Molecular Plant Breeding Cooperative Research Centre, Bundoora, Victoria, 3083, Australia
- La Trobe University, Bundoora, Victoria, 3083, Australia
| | - Simone Rochfort
- Department of Primary Industries, Biosciences Research Division, Victorian AgriBiosciences Centre, Bundoora, Victoria, 3083, Australia
- La Trobe University, Bundoora, Victoria, 3083, Australia
| | - Zhiqian Liu
- Department of Primary Industries, Biosciences Research Division, Victorian AgriBiosciences Centre, Bundoora, Victoria, 3083, Australia
| | - Yidong Ran
- Department of Primary Industries, Biosciences Research Division, Victorian AgriBiosciences Centre, Bundoora, Victoria, 3083, Australia
| | - Megan Griffith
- Department of Primary Industries, Biosciences Research Division, Victorian AgriBiosciences Centre, Bundoora, Victoria, 3083, Australia
- Molecular Plant Breeding Cooperative Research Centre, Bundoora, Victoria, 3083, Australia
| | - Pieter Badenhorst
- Department of Primary Industries, Biosciences Research Division, Victorian AgriBiosciences Centre, Bundoora, Victoria, 3083, Australia
| | - Gordon V. Louie
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, California 92037
| | - Marianne E. Bowman
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, California 92037
| | - Kevin F. Smith
- Department of Primary Industries, Biosciences Research Division, Victorian AgriBiosciences Centre, Bundoora, Victoria, 3083, Australia
- Molecular Plant Breeding Cooperative Research Centre, Bundoora, Victoria, 3083, Australia
- La Trobe University, Bundoora, Victoria, 3083, Australia
| | - Joseph P. Noel
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, California 92037
| | - Aidyn Mouradov
- Department of Primary Industries, Biosciences Research Division, Victorian AgriBiosciences Centre, Bundoora, Victoria, 3083, Australia
- Molecular Plant Breeding Cooperative Research Centre, Bundoora, Victoria, 3083, Australia
- La Trobe University, Bundoora, Victoria, 3083, Australia
| | - German Spangenberg
- Department of Primary Industries, Biosciences Research Division, Victorian AgriBiosciences Centre, Bundoora, Victoria, 3083, Australia
- Molecular Plant Breeding Cooperative Research Centre, Bundoora, Victoria, 3083, Australia
- La Trobe University, Bundoora, Victoria, 3083, Australia
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