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Guo Y, Qiu C, Long S, Chen P, Hao D, Preisner M, Wang H, Wang Y. Digital gene expression profiling of flax (Linum usitatissimum L.) stem peel identifies genes enriched in fiber-bearing phloem tissue. Gene 2017; 626:32-40. [PMID: 28479385 DOI: 10.1016/j.gene.2017.05.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 04/11/2017] [Accepted: 05/02/2017] [Indexed: 10/19/2022]
Abstract
To better understand the molecular mechanisms and gene expression characteristics associated with development of bast fiber cell within flax stem phloem, the gene expression profiling of flax stem peels and leaves were screened, using Illumina's Digital Gene Expression (DGE) analysis. Four DGE libraries (2 for stem peel and 2 for leaf), ranging from 6.7 to 9.2 million clean reads were obtained, which produced 7.0 million and 6.8 million mapped reads for flax stem peel and leave, respectively. By differential gene expression analysis, a total of 975 genes, of which 708 (73%) genes have protein-coding annotation, were identified as phloem enriched genes putatively involved in the processes of polysaccharide and cell wall metabolism. Differential expression genes (DEGs) was validated using quantitative RT-PCR, the expression pattern of all nine genes determined by qRT-PCR fitted in well with that obtained by sequencing analysis. Cluster and Gene Ontology (GO) analysis revealed that a large number of genes related to metabolic process, catalytic activity and binding category were expressed predominantly in the stem peels. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of the phloem enriched genes suggested approximately 111 biological pathways. The large number of genes and pathways produced from DGE sequencing will expand our understanding of the complex molecular and cellular events in flax bast fiber development and provide a foundation for future studies on fiber development in other bast fiber crops.
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Affiliation(s)
- Yuan Guo
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China
| | - Caisheng Qiu
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China
| | - Songhua Long
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China
| | - Ping Chen
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China
| | - Dongmei Hao
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China
| | - Marta Preisner
- Faculty of Biotechnology, University of Wrocław, Wrocław 51-148, Poland
| | - Hui Wang
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China
| | - Yufu Wang
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China.
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O'Donoghue EM, Somerfield SD, Deroles SC, Sutherland PW, Hallett IC, Erridge ZA, Brummell DA, Hunter DA. Simultaneous knock-down of six β-galactosidase genes in petunia petals prevents loss of pectic galactan but decreases petal strength. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2017; 113:208-221. [PMID: 28254702 DOI: 10.1016/j.plaphy.2017.02.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 02/05/2017] [Indexed: 05/02/2023]
Abstract
Galactose (Gal) is incorporated into cell wall polysaccharides as flowers open, but then is lost because of β-galactosidase activity as flowers mature and wilt. The significance of this for flower physiology resides in the role of galactan-containing polysaccharides in the cell wall, which is still largely unresolved. To investigate this, transcript accumulation of six cell wall-associated β-galactosidases was simultaneously knocked down in 'Mitchell' petunia (Petunia axillaris x (P. axillaris x P. hybrida)) flower petals. The multi-PhBGAL RNAi construct targeted three bud- and three senescence-associated β-galactosidase genes. The petals of the most down-regulated line (GA19) were significantly disrupted in galactose turnover during flower opening, and at the onset of senescence had retained 86% of their galactose compared with 20% in the controls. The Gal content of Na2CO3-soluble cell wall extracts and the highly insoluble polysaccharides associated with cellulose were particularly affected. Immunodetection with the antibody LM5 showed that much of the cell wall Gal in GA19 was retained as galactan, presumably the side-chains of rhamnogalacturonan-I. The flowers of GA19, despite having retained substantially more galactan, were no different from controls in their internal cell arrangement, dimensions, weight or timing of opening and senescence. However, the GA19 petals had less petal integrity (as judged by force required to cause petal fracture) after opening and showed a greater decline in this integrity with time than controls, raising the possibility that galactan loss is a mechanism for helping to maintain petal tissue cohesion after flower opening.
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Affiliation(s)
- Erin M O'Donoghue
- The New Zealand Institute for Plant & Food Research Limited, Food Industry Science Centre, Palmerston North, 4442, New Zealand.
| | - Sheryl D Somerfield
- The New Zealand Institute for Plant & Food Research Limited, Food Industry Science Centre, Palmerston North, 4442, New Zealand
| | - Simon C Deroles
- The New Zealand Institute for Plant & Food Research Limited, Food Industry Science Centre, Palmerston North, 4442, New Zealand
| | - Paul W Sutherland
- The New Zealand Institute for Plant & Food Research Limited, Mount Albert Research Centre, Auckland, 1142, New Zealand
| | - Ian C Hallett
- The New Zealand Institute for Plant & Food Research Limited, Mount Albert Research Centre, Auckland, 1142, New Zealand
| | - Zoë A Erridge
- The New Zealand Institute for Plant & Food Research Limited, Food Industry Science Centre, Palmerston North, 4442, New Zealand
| | - David A Brummell
- The New Zealand Institute for Plant & Food Research Limited, Food Industry Science Centre, Palmerston North, 4442, New Zealand
| | - Donald A Hunter
- The New Zealand Institute for Plant & Food Research Limited, Food Industry Science Centre, Palmerston North, 4442, New Zealand
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Gorshkov O, Mokshina N, Gorshkov V, Chemikosova S, Gogolev Y, Gorshkova T. Transcriptome portrait of cellulose-enriched flax fibres at advanced stage of specialization. PLANT MOLECULAR BIOLOGY 2017; 93:431-449. [PMID: 27981388 DOI: 10.1007/s11103-016-0571-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 12/02/2016] [Indexed: 05/13/2023]
Abstract
Functional specialization of cells is among the most fundamental processes of higher organism ontogenesis. The major obstacle to studying this phenomenon in plants is the difficulty of isolating certain types of cells at defined stages of in planta development for in-depth analysis. A rare opportunity is given by the developed model system of flax (Linum usitatissimum L.) phloem fibres that can be purified from the surrounding tissues at the stage of the tertiary cell wall deposition. The performed comparison of the whole transcriptome profile in isolated fibres and other portions of the flax stem, together with fibre metabolism characterization, helped to elucidate the general picture of the advanced stage of plant cell specialization and to reveal novel participants potentially involved in fibre metabolism regulation and cell wall formation. Down-regulation of all genes encoding proteins involved in xylan and lignin synthesis and up-regulation of genes for the specific set of transcription factors transcribed during tertiary cell wall formation were revealed. The increased abundance of transcripts for several glycosyltransferases indicated the enzymes that may be involved in synthesis of fibre-specific version of rhamnogalacturonan I.
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Affiliation(s)
- Oleg Gorshkov
- Kazan Institute of Biochemistry and Biophysics, Kazan Scientific Centre, Russian Academy of Science, Lobachevsky str., 2/31, Kazan, 420111, Russia
| | - Natalia Mokshina
- Kazan Institute of Biochemistry and Biophysics, Kazan Scientific Centre, Russian Academy of Science, Lobachevsky str., 2/31, Kazan, 420111, Russia
| | - Vladimir Gorshkov
- Kazan Institute of Biochemistry and Biophysics, Kazan Scientific Centre, Russian Academy of Science, Lobachevsky str., 2/31, Kazan, 420111, Russia
| | - Svetlana Chemikosova
- Kazan Institute of Biochemistry and Biophysics, Kazan Scientific Centre, Russian Academy of Science, Lobachevsky str., 2/31, Kazan, 420111, Russia
| | - Yuri Gogolev
- Kazan Institute of Biochemistry and Biophysics, Kazan Scientific Centre, Russian Academy of Science, Lobachevsky str., 2/31, Kazan, 420111, Russia
| | - Tatyana Gorshkova
- Kazan Institute of Biochemistry and Biophysics, Kazan Scientific Centre, Russian Academy of Science, Lobachevsky str., 2/31, Kazan, 420111, Russia.
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Ibragimova NN, Ageeva MV, Gorshkova TA. Development of gravitropic response: unusual behavior of flax phloem G-fibers. PROTOPLASMA 2017; 254:749-762. [PMID: 27263083 DOI: 10.1007/s00709-016-0985-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 05/13/2016] [Indexed: 05/25/2023]
Abstract
The major mechanism of gravitropism that is discussed for herbal plants is based on the nonuniform elongation of cells located on the opposite stem sides, occurring in the growing zone of an organ. However, gravitropic response of flax (Linum usitatissimum L.) is well-pronounced in the lower half of developing stem, which has ceased elongation long in advance of plant inclination. We have analyzed the stem curvature region by various approaches of microscopy and found the undescribed earlier significant modifications in primary phloem fibers that have constitutively developed G-layer. In fibers on the pulling stem side, cell portions were widened with formation of "bottlenecks" between them, leading to the "sausage-like" shape of a cell. Lumen diameter in fiber widening increased, while cell wall thickness decreased. Callose was deposited in proximity to bottlenecks and sometimes totally occluded their lumen. Structure of fiber cell wall changed considerably, with formation of breaks between G- and S-layers. Thick fibrillar structures that were revealed in fiber cell wall by light microscopy got oblique orientation instead of parallel to the fiber axis one in control plants. The described changes occurred at various combinations of gravitational and mechanical stimuli. Thus, phloem fibers with constitutively formed gelatinous cell wall, located in nonelongating parts of herbal plant, are involved in gravitropism and may become an important element in general understanding of the gravity effects on plants. We suggest flax phloem fibers as the model system to study the mechanism of plant position correction, including signal perception and transduction.
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Affiliation(s)
- Nadezda N Ibragimova
- Kazan Institute of Biochemistry and Biophysics, Kazan Scientific Center, Russian Academy of Sciences, Lobachevsky Str. 2/31, Kazan, 420111, Russia.
| | - Marina V Ageeva
- Kazan Institute of Biochemistry and Biophysics, Kazan Scientific Center, Russian Academy of Sciences, Lobachevsky Str. 2/31, Kazan, 420111, Russia
| | - Tatyana A Gorshkova
- Kazan Institute of Biochemistry and Biophysics, Kazan Scientific Center, Russian Academy of Sciences, Lobachevsky Str. 2/31, Kazan, 420111, Russia
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Yin Z, Balmant K, Geng S, Zhu N, Zhang T, Dufresne C, Dai S, Chen S. Bicarbonate Induced Redox Proteome Changes in Arabidopsis Suspension Cells. FRONTIERS IN PLANT SCIENCE 2017; 8:58. [PMID: 28184230 PMCID: PMC5266719 DOI: 10.3389/fpls.2017.00058] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 01/10/2017] [Indexed: 05/12/2023]
Abstract
Climate change as a result of increasing atmospheric CO2 affects plant growth and productivity. CO2 is not only a carbon donor for photosynthesis but also an environmental signal that can perturb cellular redox homeostasis and lead to modifications of redox-sensitive proteins. Although redox regulation of protein functions has emerged as an important mechanism in several biological processes, protein redox modifications and how they function in plant CO2 response remain unclear. Here a new iodoTMTRAQ proteomics technology was employed to analyze changes in protein redox modifications in Arabidopsis thaliana suspension cells in response to bicarbonate (mimic of elevated CO2) in a time-course study. A total of 47 potential redox-regulated proteins were identified with functions in carbohydrate and energy metabolism, transport, ROS scavenging, cell structure modulation and protein turnover. This inventory of previously unknown redox responsive proteins in Arabidopsis bicarbonate responses lays a foundation for future research toward understanding the molecular mechanisms underlying plant CO2 responses.
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Affiliation(s)
- Zepeng Yin
- Plant Molecular and Cellular Biology Program, Department of Biology, Genetics Institute, University of FloridaGainesville, FL, USA
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field, Alkali Soil Natural Environmental Science Center, Ministry of Education, Northeast Forestry UniversityHarbin, China
| | - Kelly Balmant
- Plant Molecular and Cellular Biology Program, Department of Biology, Genetics Institute, University of FloridaGainesville, FL, USA
| | - Sisi Geng
- Plant Molecular and Cellular Biology Program, Department of Biology, Genetics Institute, University of FloridaGainesville, FL, USA
| | - Ning Zhu
- Plant Molecular and Cellular Biology Program, Department of Biology, Genetics Institute, University of FloridaGainesville, FL, USA
- Interdisciplinary Center for Biotechnology Research, University of FloridaGainesville, FL, USA
| | - Tong Zhang
- Plant Molecular and Cellular Biology Program, Department of Biology, Genetics Institute, University of FloridaGainesville, FL, USA
| | | | - Shaojun Dai
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field, Alkali Soil Natural Environmental Science Center, Ministry of Education, Northeast Forestry UniversityHarbin, China
- *Correspondence: Shaojun Dai
| | - Sixue Chen
- Plant Molecular and Cellular Biology Program, Department of Biology, Genetics Institute, University of FloridaGainesville, FL, USA
- Interdisciplinary Center for Biotechnology Research, University of FloridaGainesville, FL, USA
- Sixue Chen
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Badhan A, Wang Y, McAllister TA. Analysis of Complex Carbohydrate Composition in Plant Cell Wall Using Fourier Transformed Mid-Infrared Spectroscopy (FT-IR). Methods Mol Biol 2017; 1588:209-214. [PMID: 28417371 DOI: 10.1007/978-1-4939-6899-2_16] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Fourier transformed mid-infrared spectroscopy (FTIR) is a powerful tool for compositional analysis of plant cell walls (Acebes et al., Front Plant Sci 5:303, 2014; Badhan et al., Biotechnol Biofuels 7:1-15, 2014; Badhan et al., BioMed Res Int 2015: 562952, 2015; Roach et al., Plant Physiol 156:1351-1363, 2011). The infrared spectrum generates a fingerprint of a sample with absorption peaks corresponding to the frequency of vibrations between the bonds of the atoms making up the material. Here, we describe a method focused on the use of FTIR in combination with principal component analysis (PCA) to characterize the composition of the plant cell wall. This method has been successfully used to study complex enzyme saccharification processes like rumen digestion to identify recalcitrant moieties in low-quality forage which resist rumen digestion (Badhan et al., BioMed Res Int 2015: 562952, 2015), as well as to characterize cell wall mutant lines or transgenic lines expressing exogenous hydrolases (Badhan et al., Biotechnol Biofuels 7:1-15, 2014; Roach et al., Plant Physiol 156:1351-1363, 2011). The FTIR method described here facilitates high-throughput identification of the major compositional differences across a large set of samples in a low cost and nondestructive manner.
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Affiliation(s)
- Ajay Badhan
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403 1st Ave South, Lethbridge, AB, Canada, T1J 4B1
| | - Yuxi Wang
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403 1st Ave South, Lethbridge, AB, Canada, T1J 4B1
| | - Tim A McAllister
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403 1st Ave South, Lethbridge, AB, Canada, T1J 4B1.
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Behr M, Legay S, Žižková E, Motyka V, Dobrev PI, Hausman JF, Lutts S, Guerriero G. Studying Secondary Growth and Bast Fiber Development: The Hemp Hypocotyl Peeks behind the Wall. FRONTIERS IN PLANT SCIENCE 2016; 7:1733. [PMID: 27917184 PMCID: PMC5114303 DOI: 10.3389/fpls.2016.01733] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 11/03/2016] [Indexed: 05/24/2023]
Abstract
Cannabis sativa L. is an annual herbaceous crop grown for the production of long extraxylary fibers, the bast fibers, rich in cellulose and used both in the textile and biocomposite sectors. Despite being herbaceous, hemp undergoes secondary growth and this is well exemplified by the hypocotyl. The hypocotyl was already shown to be a suitable model to study secondary growth in other herbaceous species, namely Arabidopsis thaliana and it shows an important practical advantage, i.e., elongation and radial thickening are temporally separated. This study focuses on the mechanisms marking the transition from primary to secondary growth in the hemp hypocotyl by analysing the suite of events accompanying vascular tissue and bast fiber development. Transcriptomics, imaging and quantification of phytohormones were carried out on four representative developmental stages (i.e., 6-9-15-20 days after sowing) to provide a comprehensive overview of the events associated with primary and secondary growth in hemp. This multidisciplinary approach provides cell wall-related snapshots of the growing hemp hypocotyl and identifies marker genes associated with the young (expansins, β-galactosidases, and transcription factors involved in light-related processes) and the older hypocotyl (secondary cell wall biosynthetic genes and transcription factors).
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Affiliation(s)
- Marc Behr
- Environmental Research and Innovation Department, Luxembourg Institute of Science and TechnologyEsch-sur-Alzette, Luxembourg
- Groupe de Recherche en Physiologie Végétale, Earth and Life Institute-Agronomy, Université catholique de LouvainLouvain-la-Neuve, Belgium
| | - Sylvain Legay
- Environmental Research and Innovation Department, Luxembourg Institute of Science and TechnologyEsch-sur-Alzette, Luxembourg
| | - Eva Žižková
- Institute of Experimental Botany, The Czech Academy of SciencesPrague, Czechia
| | - Václav Motyka
- Institute of Experimental Botany, The Czech Academy of SciencesPrague, Czechia
| | - Petre I. Dobrev
- Institute of Experimental Botany, The Czech Academy of SciencesPrague, Czechia
| | - Jean-Francois Hausman
- Environmental Research and Innovation Department, Luxembourg Institute of Science and TechnologyEsch-sur-Alzette, Luxembourg
| | - Stanley Lutts
- Groupe de Recherche en Physiologie Végétale, Earth and Life Institute-Agronomy, Université catholique de LouvainLouvain-la-Neuve, Belgium
| | - Gea Guerriero
- Environmental Research and Innovation Department, Luxembourg Institute of Science and TechnologyEsch-sur-Alzette, Luxembourg
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Gorshkova T, Mokshina N, Chernova T, Ibragimova N, Salnikov V, Mikshina P, Tryfona T, Banasiak A, Immerzeel P, Dupree P, Mellerowicz EJ. Aspen Tension Wood Fibers Contain β-(1---> 4)-Galactans and Acidic Arabinogalactans Retained by Cellulose Microfibrils in Gelatinous Walls. PLANT PHYSIOLOGY 2015; 169:2048-63. [PMID: 26378099 PMCID: PMC4634055 DOI: 10.1104/pp.15.00690] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 09/12/2015] [Indexed: 05/04/2023]
Abstract
Contractile cell walls are found in various plant organs and tissues such as tendrils, contractile roots, and tension wood. The tension-generating mechanism is not known but is thought to involve special cell wall architecture. We previously postulated that tension could result from the entrapment of certain matrix polymers within cellulose microfibrils. As reported here, this hypothesis was corroborated by sequential extraction and analysis of cell wall polymers that are retained by cellulose microfibrils in tension wood and normal wood of hybrid aspen (Populus tremula × Populus tremuloides). β-(1→4)-Galactan and type II arabinogalactan were the main large matrix polymers retained by cellulose microfibrils that were specifically found in tension wood. Xyloglucan was detected mostly in oligomeric form in the alkali-labile fraction and was enriched in tension wood. β-(1→4)-Galactan and rhamnogalacturonan I backbone epitopes were localized in the gelatinous cell wall layer. Type II arabinogalactans retained by cellulose microfibrils had a higher content of (methyl)glucuronic acid and galactose in tension wood than in normal wood. Thus, β-(1→4)-galactan and a specialized form of type II arabinogalactan are trapped by cellulose microfibrils specifically in tension wood and, thus, are the main candidate polymers for the generation of tensional stresses by the entrapment mechanism. We also found high β-galactosidase activity accompanying tension wood differentiation and propose a testable hypothesis that such activity might regulate galactan entrapment and, thus, mechanical properties of cell walls in tension wood.
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Affiliation(s)
- Tatyana Gorshkova
- Kazan Institute of Biochemistry and Biophysics, Kazan Scientific Centre, Russian Academy of Sciences, 420111 Kazan, Russia (T.G., N.M., T.C., N.I., V.S., P.M.);Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom (T.T., P.D.);Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umea Plant Science Centre, 90183 Umea, Sweden (A.B., P.I., E.J.M.); andInstitute of Experimental Biology, University of Wroclaw, 50-328 Wroclaw, Poland (A.B.)
| | - Natalia Mokshina
- Kazan Institute of Biochemistry and Biophysics, Kazan Scientific Centre, Russian Academy of Sciences, 420111 Kazan, Russia (T.G., N.M., T.C., N.I., V.S., P.M.);Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom (T.T., P.D.);Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umea Plant Science Centre, 90183 Umea, Sweden (A.B., P.I., E.J.M.); andInstitute of Experimental Biology, University of Wroclaw, 50-328 Wroclaw, Poland (A.B.)
| | - Tatyana Chernova
- Kazan Institute of Biochemistry and Biophysics, Kazan Scientific Centre, Russian Academy of Sciences, 420111 Kazan, Russia (T.G., N.M., T.C., N.I., V.S., P.M.);Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom (T.T., P.D.);Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umea Plant Science Centre, 90183 Umea, Sweden (A.B., P.I., E.J.M.); andInstitute of Experimental Biology, University of Wroclaw, 50-328 Wroclaw, Poland (A.B.)
| | - Nadezhda Ibragimova
- Kazan Institute of Biochemistry and Biophysics, Kazan Scientific Centre, Russian Academy of Sciences, 420111 Kazan, Russia (T.G., N.M., T.C., N.I., V.S., P.M.);Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom (T.T., P.D.);Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umea Plant Science Centre, 90183 Umea, Sweden (A.B., P.I., E.J.M.); andInstitute of Experimental Biology, University of Wroclaw, 50-328 Wroclaw, Poland (A.B.)
| | - Vadim Salnikov
- Kazan Institute of Biochemistry and Biophysics, Kazan Scientific Centre, Russian Academy of Sciences, 420111 Kazan, Russia (T.G., N.M., T.C., N.I., V.S., P.M.);Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom (T.T., P.D.);Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umea Plant Science Centre, 90183 Umea, Sweden (A.B., P.I., E.J.M.); andInstitute of Experimental Biology, University of Wroclaw, 50-328 Wroclaw, Poland (A.B.)
| | - Polina Mikshina
- Kazan Institute of Biochemistry and Biophysics, Kazan Scientific Centre, Russian Academy of Sciences, 420111 Kazan, Russia (T.G., N.M., T.C., N.I., V.S., P.M.);Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom (T.T., P.D.);Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umea Plant Science Centre, 90183 Umea, Sweden (A.B., P.I., E.J.M.); andInstitute of Experimental Biology, University of Wroclaw, 50-328 Wroclaw, Poland (A.B.)
| | - Theodora Tryfona
- Kazan Institute of Biochemistry and Biophysics, Kazan Scientific Centre, Russian Academy of Sciences, 420111 Kazan, Russia (T.G., N.M., T.C., N.I., V.S., P.M.);Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom (T.T., P.D.);Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umea Plant Science Centre, 90183 Umea, Sweden (A.B., P.I., E.J.M.); andInstitute of Experimental Biology, University of Wroclaw, 50-328 Wroclaw, Poland (A.B.)
| | - Alicja Banasiak
- Kazan Institute of Biochemistry and Biophysics, Kazan Scientific Centre, Russian Academy of Sciences, 420111 Kazan, Russia (T.G., N.M., T.C., N.I., V.S., P.M.);Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom (T.T., P.D.);Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umea Plant Science Centre, 90183 Umea, Sweden (A.B., P.I., E.J.M.); andInstitute of Experimental Biology, University of Wroclaw, 50-328 Wroclaw, Poland (A.B.)
| | - Peter Immerzeel
- Kazan Institute of Biochemistry and Biophysics, Kazan Scientific Centre, Russian Academy of Sciences, 420111 Kazan, Russia (T.G., N.M., T.C., N.I., V.S., P.M.);Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom (T.T., P.D.);Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umea Plant Science Centre, 90183 Umea, Sweden (A.B., P.I., E.J.M.); andInstitute of Experimental Biology, University of Wroclaw, 50-328 Wroclaw, Poland (A.B.)
| | - Paul Dupree
- Kazan Institute of Biochemistry and Biophysics, Kazan Scientific Centre, Russian Academy of Sciences, 420111 Kazan, Russia (T.G., N.M., T.C., N.I., V.S., P.M.);Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom (T.T., P.D.);Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umea Plant Science Centre, 90183 Umea, Sweden (A.B., P.I., E.J.M.); andInstitute of Experimental Biology, University of Wroclaw, 50-328 Wroclaw, Poland (A.B.)
| | - Ewa J Mellerowicz
- Kazan Institute of Biochemistry and Biophysics, Kazan Scientific Centre, Russian Academy of Sciences, 420111 Kazan, Russia (T.G., N.M., T.C., N.I., V.S., P.M.);Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom (T.T., P.D.);Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umea Plant Science Centre, 90183 Umea, Sweden (A.B., P.I., E.J.M.); andInstitute of Experimental Biology, University of Wroclaw, 50-328 Wroclaw, Poland (A.B.)
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Gritsch C, Wan Y, Mitchell RAC, Shewry PR, Hanley SJ, Karp A. G-fibre cell wall development in willow stems during tension wood induction. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:6447-59. [PMID: 26220085 PMCID: PMC4588891 DOI: 10.1093/jxb/erv358] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Willows (Salix spp.) are important as a potential feedstock for bioenergy and biofuels. Previous work suggested that reaction wood (RW) formation could be a desirable trait for biofuel production in willows as it is associated with increased glucose yields, but willow RW has not been characterized for cell wall components. Fasciclin-like arabinogalactan (FLA) proteins are highly up-regulated in RW of poplars and are considered to be involved in cell adhesion and cellulose biosynthesis. COBRA genes are involved in anisotropic cell expansion by modulating the orientation of cellulose microfibril deposition. This study determined the temporal and spatial deposition of non-cellulosic polysaccharides in cell walls of the tension wood (TW) component of willow RW and compared it with opposite wood (OW) and normal wood (NW) using specific antibodies and confocal laser scanning microscopy and transmission electron microscopy. In addition, the expression patterns of an FLA gene (SxFLA12) and a COBRA-like gene (SxCOBL4) were compared using RNA in situ hybridization. Deposition of the non-cellulosic polysaccharides (1-4)-β-D-galactan, mannan and de-esterified homogalacturonan was found to be highly associated with TW, often with the G-layer itself. Of particular interest was that the G-layer itself can be highly enriched in (1-4)-β-D-galactan, especially in G-fibres where the G-layer is still thickening, which contrasts with previous studies in poplar. Only xylan showed a similar distribution in TW, OW, and NW, being restricted to the secondary cell wall layers. SxFLA12 and SxCOBL4 transcripts were specifically expressed in developing TW, confirming their importance. A model of polysaccharides distribution in developing willow G-fibre cells is presented.
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Affiliation(s)
- Cristina Gritsch
- Rothamsted Research, West Common, Harpenden, Hertfordshire AL5 2JQ, UK
| | - Yongfang Wan
- Rothamsted Research, West Common, Harpenden, Hertfordshire AL5 2JQ, UK
| | | | - Peter R Shewry
- Rothamsted Research, West Common, Harpenden, Hertfordshire AL5 2JQ, UK
| | - Steven J Hanley
- Rothamsted Research, West Common, Harpenden, Hertfordshire AL5 2JQ, UK
| | - Angela Karp
- Rothamsted Research, West Common, Harpenden, Hertfordshire AL5 2JQ, UK
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Mizrachi E, Maloney VJ, Silberbauer J, Hefer CA, Berger DK, Mansfield SD, Myburg AA. Investigating the molecular underpinnings underlying morphology and changes in carbon partitioning during tension wood formation in Eucalyptus. THE NEW PHYTOLOGIST 2015; 206:1351-63. [PMID: 25388807 DOI: 10.1111/nph.13152] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 09/25/2014] [Indexed: 05/13/2023]
Abstract
Tension wood has distinct physical and chemical properties, including altered fibre properties, cell wall composition and ultrastructure. It serves as a good system for investigating the genetic regulation of secondary cell wall biosynthesis and wood formation. The reference genome sequence for Eucalyptus grandis allows investigation of the global transcriptional reprogramming that accompanies tension wood formation in this global wood fibre crop. We report the first comprehensive analysis of physicochemical wood property changes in tension wood of Eucalyptus measured in a hybrid (E. grandis × Eucalyptus urophylla) clone, as well as genome-wide gene expression changes in xylem tissues 3 wk post-induction using RNA sequencing. We found that Eucalyptus tension wood in field-grown trees is characterized by an increase in cellulose, a reduction in lignin, xylose and mannose, and a marked increase in galactose. Gene expression profiling in tension wood-forming tissue showed corresponding down-regulation of monolignol biosynthetic genes, and differential expression of several carbohydrate active enzymes. We conclude that alterations of cell wall traits induced by tension wood formation in Eucalyptus are a consequence of a combination of down-regulation of lignin biosynthesis and hemicellulose remodelling, rather than the often proposed up-regulation of the cellulose biosynthetic pathway.
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Affiliation(s)
- Eshchar Mizrachi
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Pretoria, 0028, South Africa
| | - Victoria J Maloney
- Department of Wood Science, University of British Columbia, 4030-2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Janine Silberbauer
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Pretoria, 0028, South Africa
| | - Charles A Hefer
- Bioinformatics and Computational Biology Unit, Department of Biochemistry, University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa
| | - Dave K Berger
- Department of Plant Science, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa
| | - Shawn D Mansfield
- Department of Wood Science, University of British Columbia, 4030-2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Alexander A Myburg
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Pretoria, 0028, South Africa
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Chakraborty A, Sarkar D, Satya P, Karmakar PG, Singh NK. Pathways associated with lignin biosynthesis in lignomaniac jute fibres. Mol Genet Genomics 2015; 290:1523-42. [PMID: 25724692 DOI: 10.1007/s00438-015-1013-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 02/15/2015] [Indexed: 01/09/2023]
Abstract
We generated the bast transcriptomes of a deficient lignified phloem fibre mutant and its wild-type jute (Corchorus capsularis) using Illumina paired-end sequencing. A total of 34,163 wild-type and 29,463 mutant unigenes, with average lengths of 1442 and 1136 bp, respectively, were assembled de novo, ~77-79 % of which were functionally annotated. These annotated unigenes were assigned to COG (~37-40 %) and GO (~22-28 %) classifications and mapped to 189 KEGG pathways (~19-21 %). We discovered 38 and 43 isoforms of 16 and 10 genes of the upstream shikimate-aromatic amino acid and downstream monolignol biosynthetic pathways, respectively, rendered their sequence similarities, confirmed the identities of 22 of these candidate gene families by phylogenetic analyses and reconstructed the pathway leading to lignin biosynthesis in jute fibres. We also identified major genes and bast-related transcription factors involved in secondary cell wall (SCW) formation. The quantitative RT-PCRs revealed that phenylalanine ammonia-lyase 1 (CcPAL1) was co-down-regulated with several genes of the upstream shikimate pathway in mutant bast tissues at an early growth stage, although its expression relapsed to the normal level at the later growth stage. However, cinnamyl alcohol dehydrogenase 7 (CcCAD7) was strongly down-regulated in mutant bast tissues irrespective of growth stages. CcCAD7 disruption at an early growth stage was accompanied by co-up-regulation of SCW-specific genes cellulose synthase A7 (CcCesA7) and fasciclin-like arabinogalactan 6 (CcFLA6), which was predicted to be involved in coordinating the S-layers' deposition in the xylan-type jute fibres. Our results identified CAD as a promising target for developing low-lignin jute fibres using genomics-assisted molecular approaches.
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Affiliation(s)
- Avrajit Chakraborty
- Biotechnology Unit, Division of Crop Improvement, ICAR-Central Research Institute for Jute and Allied Fibres (CRIJAF), Barrackpore, Kolkata, 700 120, West Bengal, India
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Banasiak A, Ibatullin FM, Brumer H, Mellerowicz EJ. Glycoside Hydrolase Activities in Cell Walls of Sclerenchyma Cells in the Inflorescence Stems of Arabidopsis thaliana Visualized in Situ. PLANTS (BASEL, SWITZERLAND) 2014; 3:513-25. [PMID: 27135517 PMCID: PMC4844284 DOI: 10.3390/plants3040513] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 10/29/2014] [Accepted: 10/30/2014] [Indexed: 11/16/2022]
Abstract
Techniques for in situ localization of gene products provide indispensable information for understanding biological function. In the case of enzymes, biological function is directly related to activity, and therefore, knowledge of activity patterns is central to understanding the molecular controls of plant development. We have previously developed a novel type of fluorogenic substrate for revealing glycoside hydrolase activity in planta, based on resorufin β-glycosides Here, we explore a wider range of such substrates to visualize glycoside hydrolase activities in Arabidopsis inflorescence stems in real time, especially highlighting distinct distribution patterns of these activities in the secondary cell walls of sclerenchyma cells. The results demonstrate that β-1,4-glucosidase, β-1,4-glucanase and β-1,4-galactosidase activities accompany secondary wall deposition. In contrast, xyloglucanase activity follows a different pattern, with the highest signal observed in mature cells, concentrated in the middle lamella. These data further the understanding of the process of cell wall deposition and function in sclerenchymatic tissues of plants.
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Affiliation(s)
- Alicja Banasiak
- Institute of Experimental Biology, University of Wroclaw, 50-328 Wroclaw, Poland.
| | - Farid M Ibatullin
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, 106 91 Stockholm, Sweden.
- Biophysics Division, Petersburg Nuclear Physics Institute, National Research Center Kurchatov Institute, Gatchina 188300, Russia.
| | - Harry Brumer
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, 106 91 Stockholm, Sweden.
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC V6T 1Z1, Canada.
- Department of Chemistry, University of British Columbia, 2185 East Mall, Vancouver, BC V6T 1Z1, Canada.
| | - Ewa J Mellerowicz
- Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umea Plant Science Centre, 90183 Umea, Sweden.
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Renouard S, Tribalatc MA, Lamblin F, Mongelard G, Fliniaux O, Corbin C, Marosevic D, Pilard S, Demailly H, Gutierrez L, Hano C, Mesnard F, Lainé E. RNAi-mediated pinoresinol lariciresinol reductase gene silencing in flax (Linum usitatissimum L.) seed coat: consequences on lignans and neolignans accumulation. JOURNAL OF PLANT PHYSIOLOGY 2014; 171:1372-7. [PMID: 25046758 DOI: 10.1016/j.jplph.2014.06.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Revised: 06/12/2014] [Accepted: 06/13/2014] [Indexed: 05/24/2023]
Abstract
RNAi technology was applied to down regulate LuPLR1 gene expression in flax (Linum usitatissimum L.) seeds. This gene encodes a pinoresinol lariciresinol reductase responsible for the synthesis of (+)-secoisolariciresinol diglucoside (SDG), the major lignan accumulated in the seed coat. If flax lignans biological properties and health benefits are well documented their roles in planta remain unclear. This loss of function strategy was developed to better understand the implication of the PLR1 enzyme in the lignan biosynthetic pathway and to provide new insights on the functions of these compounds. RNAi plants generated exhibited LuPLR1 gene silencing as demonstrated by quantitative RT-PCR experiments and the failed to accumulate SDG. The accumulation of pinoresinol the substrate of the PLR1 enzyme under its diglucosylated form (PDG) was increased in transgenic seeds but did not compensate the overall loss of SDG. The monolignol flux was also deviated through the synthesis of 8-5' linked neolignans dehydrodiconiferyl alcohol glucoside (DCG) and dihydro-dehydrodiconiferyl alcohol glucoside (DDCG) which were observed for the first time in flax seeds.
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Affiliation(s)
- Sullivan Renouard
- Laboratoire LBLGC EA 1207, Antenne Scientifique Universitaire de Chartres Univ Orleans, 21 rue de Loigny la Bataille, 28000 Chartres, France.
| | - Marie-Aude Tribalatc
- Laboratoire BIOPI EA 3900, UFR de Pharmacie, 1 rue des Louvels 80037 Amiens, France
| | - Frederic Lamblin
- Laboratoire LBLGC EA 1207, Antenne Scientifique Universitaire de Chartres Univ Orleans, 21 rue de Loigny la Bataille, 28000 Chartres, France
| | - Gaëlle Mongelard
- CRRBM, Univ Picardie Jules Verne, 33 rue Saint-Leu, 80039 Amiens, France
| | - Ophélie Fliniaux
- Laboratoire BIOPI EA 3900, UFR de Pharmacie, 1 rue des Louvels 80037 Amiens, France
| | - Cyrielle Corbin
- Laboratoire LBLGC EA 1207, Antenne Scientifique Universitaire de Chartres Univ Orleans, 21 rue de Loigny la Bataille, 28000 Chartres, France
| | - Djurdjica Marosevic
- Laboratoire LBLGC EA 1207, Antenne Scientifique Universitaire de Chartres Univ Orleans, 21 rue de Loigny la Bataille, 28000 Chartres, France
| | - Serge Pilard
- Plateforme analytique, UFR Sciences, 80039 Amiens, France
| | - Hervé Demailly
- CRRBM, Univ Picardie Jules Verne, 33 rue Saint-Leu, 80039 Amiens, France
| | - Laurent Gutierrez
- CRRBM, Univ Picardie Jules Verne, 33 rue Saint-Leu, 80039 Amiens, France
| | - Christophe Hano
- Laboratoire LBLGC EA 1207, Antenne Scientifique Universitaire de Chartres Univ Orleans, 21 rue de Loigny la Bataille, 28000 Chartres, France
| | - François Mesnard
- Laboratoire BIOPI EA 3900, UFR de Pharmacie, 1 rue des Louvels 80037 Amiens, France
| | - Eric Lainé
- Laboratoire LBLGC EA 1207, Antenne Scientifique Universitaire de Chartres Univ Orleans, 21 rue de Loigny la Bataille, 28000 Chartres, France
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Mokshina N, Gorshkova T, Deyholos MK. Chitinase-like (CTL) and cellulose synthase (CESA) gene expression in gelatinous-type cellulosic walls of flax (Linum usitatissimum L.) bast fibers. PLoS One 2014; 9:e97949. [PMID: 24918577 PMCID: PMC4053336 DOI: 10.1371/journal.pone.0097949] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 04/26/2014] [Indexed: 11/19/2022] Open
Abstract
Plant chitinases (EC 3.2.1.14) and chitinase-like (CTL) proteins have diverse functions including cell wall biosynthesis and disease resistance. We analyzed the expression of 34 chitinase and chitinase-like genes of flax (collectively referred to as LusCTLs), belonging to glycoside hydrolase family 19 (GH19). Analysis of the transcript expression patterns of LusCTLs in the stem and other tissues identified three transcripts (LusCTL19, LusCTL20, LusCTL21) that were highly enriched in developing bast fibers, which form cellulose-rich gelatinous-type cell walls. The same three genes had low relative expression in tissues with primary cell walls and in xylem, which forms a xylan type of secondary cell wall. Phylogenetic analysis of the LusCTLs identified a flax-specific sub-group that was not represented in any of other genomes queried. To provide further context for the gene expression analysis, we also conducted phylogenetic and expression analysis of the cellulose synthase (CESA) family genes of flax, and found that expression of secondary wall-type LusCESAs (LusCESA4, LusCESA7 and LusCESA8) was correlated with the expression of two LusCTLs (LusCTL1, LusCTL2) that were the most highly enriched in xylem. The expression of LusCTL19, LusCTL20, and LusCTL21 was not correlated with that of any CESA subgroup. These results defined a distinct type of CTLs that may have novel functions specific to the development of the gelatinous (G-type) cellulosic walls.
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Affiliation(s)
- Natalia Mokshina
- Kazan Institute of Biochemistry and Biophysics, Russian Academy of Sciences, Kazan, Russia
| | - Tatyana Gorshkova
- Kazan Institute of Biochemistry and Biophysics, Russian Academy of Sciences, Kazan, Russia
| | - Michael K. Deyholos
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
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Badhan A, Jin L, Wang Y, Han S, Kowalczys K, Brown DCW, Ayala CJ, Latoszek-Green M, Miki B, Tsang A, McAllister T. Expression of a fungal ferulic acid esterase in alfalfa modifies cell wall digestibility. BIOTECHNOLOGY FOR BIOFUELS 2014; 7:39. [PMID: 24650274 PMCID: PMC3999942 DOI: 10.1186/1754-6834-7-39] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2013] [Accepted: 02/21/2014] [Indexed: 05/17/2023]
Abstract
BACKGROUND Alfalfa (Medicago sativa) is an important forage crop in North America owing to its high biomass production, perennial nature and ability to fix nitrogen. Feruloyl esterase (EC 3.1.1.73) hydrolyzes ester linkages in plant cell walls and has the potential to further improve alfalfa as biomass for biofuel production. RESULTS In this study, faeB [GenBank:AJ309807] was synthesized at GenScript and sub-cloned into a novel pEACH vector containing different signaling peptides to target type B ferulic acid esterase (FAEB) proteins to the apoplast, chloroplast, endoplasmic reticulum and vacuole. Four constructs harboring faeB were transiently expressed in Nicotiana leaves, with FAEB accumulating at high levels in all target sites, except chloroplast. Stable transformed lines of alfalfa were subsequently obtained using Agrobacterium tumefaciens (LBA4404). Out of 136 transgenic plants regenerated, 18 independent lines exhibited FAEB activity. Subsequent in vitro digestibility and Fourier transformed infrared spectroscopy (FTIR) analysis of FAEB-expressing lines showed that they possessed modified cell wall morphology and composition with a reduction in ester linkages and elevated lignin content. Consequently, they were more recalcitrant to digestion by mixed ruminal microorganisms. Interestingly, delignification by alkaline peroxide treatment followed by exposure to a commercial cellulase mixture resulted in higher glucose release from transgenic lines as compared to the control line. CONCLUSION Modifying cell wall crosslinking has the potential to lower recalcitrance of holocellulose, but also exhibited unintended consequences on alfalfa cell wall digestibility due to elevated lignin content. The combination of efficient delignification treatment (alkaline peroxide) and transgenic esterase activity complement each other towards efficient and effective digestion of transgenic lines.
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Affiliation(s)
- Ajay Badhan
- Agriculture and Agri-Food Canada, Lethbridge Research Centre, 5403 1st Avenue South, Lethbridge, AB T1J 4B1, Canada
| | - Long Jin
- Agriculture and Agri-Food Canada, Lethbridge Research Centre, 5403 1st Avenue South, Lethbridge, AB T1J 4B1, Canada
| | - Yuxi Wang
- Agriculture and Agri-Food Canada, Lethbridge Research Centre, 5403 1st Avenue South, Lethbridge, AB T1J 4B1, Canada
| | - Shuyou Han
- Agriculture and Agri-Food Canada, Southern Crop Protection and Food Research Centre, London, ON N5V 4T3, Canada
| | - Katarzyna Kowalczys
- Canadian Centre for Agri-Food Research in Health and Medicine, St Boniface Hospital Research Centre, Winnipeg, MB R2H 2A6, Canada
| | - Daniel CW Brown
- Agriculture and Agri-Food Canada, Southern Crop Protection and Food Research Centre, London, ON N5V 4T3, Canada
- Canadian Centre for Agri-Food Research in Health and Medicine, St Boniface Hospital Research Centre, Winnipeg, MB R2H 2A6, Canada
| | - Carlos Juarez Ayala
- Agriculture and Agri-Food Canada, Southern Crop Protection and Food Research Centre, London, ON N5V 4T3, Canada
| | - Marysia Latoszek-Green
- Agriculture and Agri-Food Canada, Southern Crop Protection and Food Research Centre, London, ON N5V 4T3, Canada
| | - Brian Miki
- Agriculture and Agri-Food Canada, Southern Crop Protection and Food Research Centre, London, ON N5V 4T3, Canada
| | - Adrian Tsang
- Biology Department, Concordia University, Montreal, QC H4B 1R6, Canada
| | - Tim McAllister
- Agriculture and Agri-Food Canada, Lethbridge Research Centre, 5403 1st Avenue South, Lethbridge, AB T1J 4B1, Canada
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Gorshkova TA, Kozlova LV, Mikshina PV. Spatial structure of plant cell wall polysaccharides and its functional significance. BIOCHEMISTRY (MOSCOW) 2014; 78:836-53. [PMID: 24010845 DOI: 10.1134/s0006297913070146] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Plant polysaccharides comprise the major portion of organic matter in the biosphere. The cell wall built on the basis of polysaccharides is the key feature of a plant organism largely determining its biology. All together, around 10 types of polysaccharide backbones, which can be decorated by different substituents giving rise to endless diversity of carbohydrate structures, are present in cell walls of higher plants. Each of the numerous cell types present in plants has cell wall with specific parameters, the features of which mostly arise from the structure of polymeric components. The structure of polysaccharides is not directly encoded by the genome and has variability in many parameters (molecular weight, length, and location of side chains, presence of modifying groups, etc.). The extent of such variability is limited by the "functional fitting" of the polymer, which is largely based on spatial organization of the polysaccharide and its ability to form supramolecular complexes of an appropriate type. Consequently, the carrier of the functional specificity is not the certain molecular structure but the certain type of the molecules having a certain degree of heterogeneity. This review summarizes the data on structural features of plant cell wall polysaccharides, considers formation of supramolecular complexes, gives examples of tissue- and stage-specific polysaccharides and functionally significant carbohydrate-carbohydrate interactions in plant cell wall, and presents approaches to analyze the spatial structure of polysaccharides and their complexes.
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Affiliation(s)
- T A Gorshkova
- Kazan Institute of Biochemistry and Biophysics, Kazan Scientific Center, Russian Academy of Sciences, 420111 Kazan, Russia.
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Deyholos MK, Potter S. Engineering bast fiber feedstocks for use in composite materials. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2014. [DOI: 10.1016/j.bcab.2013.09.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Chantreau M, Grec S, Gutierrez L, Dalmais M, Pineau C, Demailly H, Paysant-Leroux C, Tavernier R, Trouvé JP, Chatterjee M, Guillot X, Brunaud V, Chabbert B, van Wuytswinkel O, Bendahmane A, Thomasset B, Hawkins S. PT-Flax (phenotyping and TILLinG of flax): development of a flax (Linum usitatissimum L.) mutant population and TILLinG platform for forward and reverse genetics. BMC PLANT BIOLOGY 2013; 13:159. [PMID: 24128060 PMCID: PMC3853753 DOI: 10.1186/1471-2229-13-159] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 10/09/2013] [Indexed: 05/04/2023]
Abstract
BACKGROUND Flax (Linum usitatissimum L.) is an economically important fiber and oil crop that has been grown for thousands of years. The genome has been recently sequenced and transcriptomics are providing information on candidate genes potentially related to agronomically-important traits. In order to accelerate functional characterization of these genes we have generated a flax EMS mutant population that can be used as a TILLinG (Targeting Induced Local Lesions in Genomes) platform for forward and reverse genetics. RESULTS A population of 4,894 M2 mutant seed families was generated using 3 different EMS concentrations (0.3%, 0.6% and 0.75%) and used to produce M2 plants for subsequent phenotyping and DNA extraction. 10,839 viable M2 plants (4,033 families) were obtained and 1,552 families (38.5%) showed a visual developmental phenotype (stem size and diameter, plant architecture, flower-related). The majority of these families showed more than one phenotype. Mutant phenotype data are organised in a database and can be accessed and searched at UTILLdb (http://urgv.evry.inra.fr/UTILLdb). Preliminary screens were also performed for atypical fiber and seed phenotypes. Genomic DNA was extracted from 3,515 M2 families and eight-fold pooled for subsequent mutant detection by ENDO1 nuclease mis-match cleavage. In order to validate the collection for reverse genetics, DNA pools were screened for two genes coding enzymes of the lignin biosynthesis pathway: Coumarate-3-Hydroxylase (C3H) and Cinnamyl Alcohol Dehydrogenase (CAD). We identified 79 and 76 mutations in the C3H and CAD genes, respectively. The average mutation rate was calculated as 1/41 Kb giving rise to approximately 9,000 mutations per genome. Thirty-five out of the 52 flax cad mutant families containing missense or codon stop mutations showed the typical orange-brown xylem phenotype observed in CAD down-regulated/mutant plants in other species. CONCLUSIONS We have developed a flax mutant population that can be used as an efficient forward and reverse genetics tool. The collection has an extremely high mutation rate that enables the detection of large numbers of independant mutant families by screening a comparatively low number of M2 families. The population will prove to be a valuable resource for both fundamental research and the identification of agronomically-important genes for crop improvement in flax.
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Affiliation(s)
- Maxime Chantreau
- Université Lille Nord de France, Lille 1 UMR 1281, Villeneuve d'Ascq cedex F-59650, France
- INRA UMR, 281 Stress Abiotiques et Différenciation des Végétaux Cultivés, Villeneuve d’Ascq F-59650, France
| | - Sébastien Grec
- Université Lille Nord de France, Lille 1 UMR 1281, Villeneuve d'Ascq cedex F-59650, France
- INRA UMR, 281 Stress Abiotiques et Différenciation des Végétaux Cultivés, Villeneuve d’Ascq F-59650, France
| | - Laurent Gutierrez
- CRRBM, UFR des Sciences, UPJV, 33 rue Saint Leu, Amiens cedex 80039, France
| | - Marion Dalmais
- URGV, Unité de Recherche en Génomique Végétale, Université d'Evry Val d'Essonne, INRA, 2 rue Gaston Crémieux CP 5708, Evry cedex 91057, France
| | | | - Hervé Demailly
- CRRBM, UFR des Sciences, UPJV, 33 rue Saint Leu, Amiens cedex 80039, France
| | | | | | - Jean-Paul Trouvé
- Terre de Lin, société cooperative agricole, Saint-Pierre-Le-Viger, 76 740, France
| | - Manash Chatterjee
- Bench Bio Pvt Ltd., c/o Jai Research Foundation, Vapi, Gujarat 396195, India
- National University of Ireland Galway (NUIG), University Road, Galway, Ireland
| | | | - Véronique Brunaud
- URGV, Unité de Recherche en Génomique Végétale, Université d'Evry Val d'Essonne, INRA, 2 rue Gaston Crémieux CP 5708, Evry cedex 91057, France
| | - Brigitte Chabbert
- INRA, UMR614 Fractionnement des AgroRessources et Environnement, Reims F-51100, France
- Université de Reims Champagne-Ardenne, UMR614 Fractionnement des AgroRessources et Environnement, Reims F-51100, France
| | | | - Abdelhafid Bendahmane
- URGV, Unité de Recherche en Génomique Végétale, Université d'Evry Val d'Essonne, INRA, 2 rue Gaston Crémieux CP 5708, Evry cedex 91057, France
| | - Brigitte Thomasset
- CNRS-FRE 3580, GEC, Université de Technologie de Compiègne, CS 60319, Compiègnecedex 60203, France
| | - Simon Hawkins
- Université Lille Nord de France, Lille 1 UMR 1281, Villeneuve d'Ascq cedex F-59650, France
- INRA UMR, 281 Stress Abiotiques et Différenciation des Végétaux Cultivés, Villeneuve d’Ascq F-59650, France
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Genomic and expression analysis of the flax (Linum usitatissimum) family of glycosyl hydrolase 35 genes. BMC Genomics 2013; 14:344. [PMID: 23701735 PMCID: PMC3673811 DOI: 10.1186/1471-2164-14-344] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Accepted: 04/15/2013] [Indexed: 11/10/2022] Open
Abstract
Background Several β-galactosidases of the Glycosyl Hydrolase 35 (GH35) family have been characterized, and many of these modify cell wall components, including pectins, xyloglucans, and arabinogalactan proteins. The phloem fibres of flax (Linum usitatissimum) have gelatinous-type cell walls that are rich in crystalline cellulose and depend on β-galactosidase activity for their normal development. In this study, we investigate the transcript expression patterns and inferred evolutionary relationships of the complete set of flax GH35 genes, to better understand the functions of these genes in flax and other species. Results Using the recently published flax genome assembly, we identified 43 β-galactosidase-like (BGAL) genes, based on the presence of a GH35 domain. Phylogenetic analyses of their protein sequences clustered them into eight sub-families. Sub-family B, whose members in other species were known to be expressed in developing flowers and pollen, was greatly under represented in flax (p-value < 0.01). Sub-family A5, whose sole member from arabidopsis has been described as its primary xyloglucan BGAL, was greatly expanded in flax (p-value < 0.01). A number of flax BGALs were also observed to contain non-consensus GH35 active sites. Expression patterns of the flax BGALs were investigated using qRT-PCR and publicly available microarray data. All predicted flax BGALs showed evidence of expression in at least one tissue. Conclusion Flax has a large number of BGAL genes, which display a distinct distribution among the BGAL sub-families, in comparison to other closely related species with available whole genome assemblies. Almost every flax BGAL was expressed in fibres, the majority of which expressed predominately in fibres as compared to other tissues, suggesting an important role for the expansion of this gene family in the development of this species as a fibre crop. Variations displayed in the canonical GH35 active site suggest a variety of roles unique to flax, which will require further characterization.
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72
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Martín I, Hernández-Nistal J, Albornos L, Labrador E, Dopico B. βIII-Gal is Involved in Galactan Reduction During Phloem Element Differentiation in Chickpea Stems. ACTA ACUST UNITED AC 2013; 54:960-70. [DOI: 10.1093/pcp/pct050] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Hobson N, Deyholos MK. LuFLA1PRO and LuBGAL1PRO promote gene expression in the phloem fibres of flax (Linum usitatissimum). PLANT CELL REPORTS 2013; 32:517-528. [PMID: 23328964 DOI: 10.1007/s00299-013-1383-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Revised: 12/12/2012] [Accepted: 01/02/2013] [Indexed: 06/01/2023]
Abstract
Cell type-specific promoters were identified that drive gene expression in an industrially important product. To identify flax (Linum usitatissimum) gene promoters, we analyzed the genomic regions upstream of a fasciclin-like arabinogalactan protein (LuFLA1) and a beta-galactosidase (LuBGAL1). Both of these genes encode transcripts that have been found to be highly enriched in tissues bearing phloem fibres. Using a beta-glucuronidase (GUS) reporter construct, we found that a 908-bp genomic sequence upstream of LuFLA1 (LuFLA1PRO) directed GUS expression with high specificity to phloem fibres undergoing secondary cell wall development. The DNA sequence upstream of LuBGAL1 (LuBGAL1PRO) likewise produced GUS staining in phloem fibres with developing secondary walls, as well as in tissues of developing flowers and seed bolls. These data provide further evidence of a specific role for LuFLA1 in phloem fibre development, and demonstrate the utility of LuFLA1PRO and LuBGAL1PRO as tools for biotechnology and further investigations of phloem fibre development.
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Affiliation(s)
- Neil Hobson
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada.
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74
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Fenart S, Chabi M, Gallina S, Huis R, Neutelings G, Riviere N, Thomasset B, Hawkins S, Lucau-Danila A. Intra-platform comparison of 25-mer and 60-mer oligonucleotide Nimblegen DNA microarrays. BMC Res Notes 2013; 6:43. [PMID: 23375116 PMCID: PMC3608165 DOI: 10.1186/1756-0500-6-43] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Accepted: 01/30/2013] [Indexed: 01/02/2023] Open
Abstract
Background We performed a Nimblegen intra-platform microarray comparison by assessing two categories of flax target probes (short 25-mers oligonucleotides and long 60-mers oligonucleotides) in identical conditions of target production, design, labelling, hybridization, image analyses, and data filtering. We compared technical parameters of array hybridizations, precision and accuracy as well as specific gene expression profiles. Results Comparison of the hybridization quality, precision and accuracy of expression measurements, as well as an interpretation of differential gene expression in flax tissues were performed. Both array types yielded reproducible, accurate and comparable data that are coherent for expression measurements and identification of differentially expressed genes. 60-mers arrays gave higher hybridization efficiencies and therefore were more sensitive allowing the detection of a higher number of unigenes involved in the same biological process and/or belonging to the same multigene family. Conclusion The two flax arrays provide a good resolution of expressed functions; however the 60-mers arrays are more sensitive and provide a more in-depth coverage of candidate genes potentially involved in different biological processes.
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Affiliation(s)
- Stephane Fenart
- Université Lille Nord de France, Lille 1, UMR INRA 1281, SADV, F- 59650 Villeneuve d'Ascq cedex, France
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75
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Abstract
Recent progress in the identification and characterization of pectin biosynthetic proteins and the discovery of pectin domain-containing proteoglycans are changing our view of how pectin, the most complex family of plant cell wall polysaccharides, is synthesized. The functional confirmation of four types of pectin biosynthetic glycosyltransferases, the identification of multiple putative pectin glycosyl- and methyltransferases, and the characteristics of the GAUT1:GAUT7 homogalacturonan biosynthetic complex with its novel mechanism for retaining catalytic subunits in the Golgi apparatus and its 12 putative interacting proteins are beginning to provide a framework for the pectin biosynthetic process. We propose two partially overlapping hypothetical and testable models for pectin synthesis: the consecutive glycosyltransferase model and the domain synthesis model.
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Affiliation(s)
- Melani A Atmodjo
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602-4712, USA.
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76
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Liwanag AJM, Ebert B, Verhertbruggen Y, Rennie EA, Rautengarten C, Oikawa A, Andersen MC, Clausen MH, Scheller HV. Pectin biosynthesis: GALS1 in Arabidopsis thaliana is a β-1,4-galactan β-1,4-galactosyltransferase. THE PLANT CELL 2012; 24:5024-36. [PMID: 23243126 PMCID: PMC3556973 DOI: 10.1105/tpc.112.106625] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Revised: 10/22/2012] [Accepted: 11/28/2012] [Indexed: 05/17/2023]
Abstract
β-1,4-Galactans are abundant polysaccharides in plant cell walls, which are generally found as side chains of rhamnogalacturonan I. Rhamnogalacturonan I is a major component of pectin with a backbone of alternating rhamnose and galacturonic acid residues and side chains that include α-1,5-arabinans, β-1,4-galactans, and arabinogalactans. Many enzymes are required to synthesize pectin, but few have been identified. Pectin is most abundant in primary walls of expanding cells, but β-1,4-galactan is relatively abundant in secondary walls, especially in tension wood that forms in response to mechanical stress. We investigated enzymes in glycosyltransferase family GT92, which has three members in Arabidopsis thaliana, which we designated GALACTAN SYNTHASE1, (GALS1), GALS2 and GALS3. Loss-of-function mutants in the corresponding genes had a decreased β-1,4-galactan content, and overexpression of GALS1 resulted in plants with 50% higher β-1,4-galactan content. The plants did not have an obvious growth phenotype. Heterologously expressed and affinity-purified GALS1 could transfer Gal residues from UDP-Gal onto β-1,4-galactopentaose. GALS1 specifically formed β-1,4-galactosyl linkages and could add successive β-1,4-galactosyl residues to the acceptor. These observations confirm the identity of the GT92 enzyme as β-1,4-galactan synthase. The identification of this enzyme could provide an important tool for engineering plants with improved bioenergy properties.
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Affiliation(s)
- April Jennifer Madrid Liwanag
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, California 94608
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Berit Ebert
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, California 94608
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Yves Verhertbruggen
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, California 94608
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Emilie A. Rennie
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, California 94608
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
| | - Carsten Rautengarten
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, California 94608
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Ai Oikawa
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, California 94608
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Mathias C.F. Andersen
- Department of Chemistry, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Mads H. Clausen
- Department of Chemistry, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Henrik Vibe Scheller
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, California 94608
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
- Address correspondence to
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Wang Z, Hobson N, Galindo L, Zhu S, Shi D, McDill J, Yang L, Hawkins S, Neutelings G, Datla R, Lambert G, Galbraith DW, Grassa CJ, Geraldes A, Cronk QC, Cullis C, Dash PK, Kumar PA, Cloutier S, Sharpe AG, Wong GKS, Wang J, Deyholos MK. The genome of flax (Linum usitatissimum) assembled de novo from short shotgun sequence reads. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 72:461-73. [PMID: 22757964 DOI: 10.1111/j.1365-313x.2012.05093.x] [Citation(s) in RCA: 252] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Flax (Linum usitatissimum) is an ancient crop that is widely cultivated as a source of fiber, oil and medicinally relevant compounds. To accelerate crop improvement, we performed whole-genome shotgun sequencing of the nuclear genome of flax. Seven paired-end libraries ranging in size from 300 bp to 10 kb were sequenced using an Illumina genome analyzer. A de novo assembly, comprised exclusively of deep-coverage (approximately 94× raw, approximately 69× filtered) short-sequence reads (44-100 bp), produced a set of scaffolds with N(50) =694 kb, including contigs with N(50)=20.1 kb. The contig assembly contained 302 Mb of non-redundant sequence representing an estimated 81% genome coverage. Up to 96% of published flax ESTs aligned to the whole-genome shotgun scaffolds. However, comparisons with independently sequenced BACs and fosmids showed some mis-assembly of regions at the genome scale. A total of 43384 protein-coding genes were predicted in the whole-genome shotgun assembly, and up to 93% of published flax ESTs, and 86% of A. thaliana genes aligned to these predicted genes, indicating excellent coverage and accuracy at the gene level. Analysis of the synonymous substitution rates (K(s) ) observed within duplicate gene pairs was consistent with a recent (5-9 MYA) whole-genome duplication in flax. Within the predicted proteome, we observed enrichment of many conserved domains (Pfam-A) that may contribute to the unique properties of this crop, including agglutinin proteins. Together these results show that de novo assembly, based solely on whole-genome shotgun short-sequence reads, is an efficient means of obtaining nearly complete genome sequence information for some plant species.
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Affiliation(s)
- Zhiwen Wang
- BGI-Shenzen, Bei Shan Industrial Zone, Yantian District, Shenzhen 518083, China
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Mellerowicz EJ, Gorshkova TA. Tensional stress generation in gelatinous fibres: a review and possible mechanism based on cell-wall structure and composition. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:551-65. [PMID: 22090441 DOI: 10.1093/jxb/err339] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Gelatinous fibres are specialized fibres, distinguished by the presence of an inner, gelatinous cell-wall layer. In recent years, they have attracted increasing interest since their walls have a desirable chemical composition (low lignin, low pentosan, and high cellulose contents) for applications such as saccharification and biofuel production, and they have interesting mechanical properties, being capable of generating high tensional stress. However, the unique character of gelatinous layer has not yet been widely recognized. The first part of this review presents a model of gelatinous-fibre organization and stresses the unique character of the gelatinous layer as a separate type of cell-wall layer, different from either primary or secondary wall layers. The second part discusses major current models of tensional stress generation by these fibres and presents a novel unifying model based on recent advances in knowledge of gelatinous wall structure. Understanding this mechanism could potentially lead to novel biomimetic developments in material sciences.
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Affiliation(s)
- Ewa J Mellerowicz
- Umeå Plant Science Center, Department of Forest Genetics and Plant Physiology, SE-90183 Umeå, Sweden.
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Wang YH, Poudel DD, Hasenstein KH. Identification of SSR markers associated with saccharification yield using pool-based genome-wide association mapping in sorghum. Genome 2011; 54:883-9. [PMID: 21999235 DOI: 10.1139/g11-055] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Saccharification describes the conversion of plant biomass by cellulase into glucose. Because plants have never been selected for high saccharification yield, cellulosic ethanol production faces a significant bottleneck. To improve saccharification yield, it is critical to identify the genes that affect this process. In this study, we used pool-based genome-wide association mapping to identify simple sequence repeat (SSR) markers associated with saccharification yield. Screening of 703 SSR markers against the low and high saccharification pools identified two markers on the sorghum chromosomes 2 (23-1062) and 4 (74-508c) associated with saccharification yield. The association was significant at 1% using either general or mixed linear models. Localization of these markers based on the whole genome sequence indicates that 23-1062 is 223 kb from a β-glucanase (Bg) gene and 74-508c is 81 kb from a steroid-binding protein (Sbp) gene. Bg is critical for cell wall assembly and degradation, but Sbp can suppress the expression of Bg as demonstrated in Arabidopsis (Yang et al. 2005). These markers are found physically close to genes encoding plant cell wall synthesis enzymes such as xyloglucan fucosyltransferase (149 kb from 74-508c) and UDP-D-glucose 4-epimerase (46 kb from 23-1062). Genetic transformation of selected candidate genes is in progress to examine their effect on saccharification yield in plants.
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Affiliation(s)
- Yi-Hong Wang
- Department of Biology, University of Louisiana at Lafayette, Lafayette, LA 70504, USA.
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