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MacMillan CP, Birke H, Chuah A, Brill E, Tsuji Y, Ralph J, Dennis ES, Llewellyn D, Pettolino FA. Tissue and cell-specific transcriptomes in cotton reveal the subtleties of gene regulation underlying the diversity of plant secondary cell walls. BMC Genomics 2017; 18:539. [PMID: 28720072 PMCID: PMC5516393 DOI: 10.1186/s12864-017-3902-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 06/22/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Knowledge of plant secondary cell wall (SCW) regulation and deposition is mainly based on the Arabidopsis model of a 'typical' lignocellulosic SCW. However, SCWs in other plants can vary from this. The SCW of mature cotton seed fibres is highly cellulosic and lacks lignification whereas xylem SCWs are lignocellulosic. We used cotton as a model to study different SCWs and the expression of the genes involved in their formation via RNA deep sequencing and chemical analysis of stem and seed fibre. RESULTS Transcriptome comparisons from cotton xylem and pith as well as from a developmental series of seed fibres revealed tissue-specific and developmentally regulated expression of several NAC transcription factors some of which are likely to be important as top tier regulators of SCW formation in xylem and/or seed fibre. A so far undescribed hierarchy was identified between the top tier NAC transcription factors SND1-like and NST1/2 in cotton. Key SCW MYB transcription factors, homologs of Arabidopsis MYB46/83, were practically absent in cotton stem xylem. Lack of expression of other lignin-specific MYBs in seed fibre relative to xylem could account for the lack of lignin deposition in seed fibre. Expression of a MYB103 homolog correlated with temporal expression of SCW CesAs and cellulose synthesis in seed fibres. FLAs were highly expressed and may be important structural components of seed fibre SCWs. Finally, we made the unexpected observation that cell walls in the pith of cotton stems contained lignin and had a higher S:G ratio than in xylem, despite that tissue's lacking many of the gene transcripts normally associated with lignin biosynthesis. CONCLUSIONS Our study in cotton confirmed some features of the currently accepted gene regulatory cascade for 'typical' plant SCWs, but also revealed substantial differences, especially with key downstream NACs and MYBs. The lignocellulosic SCW of cotton xylem appears to be achieved differently from that in Arabidopsis. Pith cell walls in cotton stems are compositionally very different from that reported for other plant species, including Arabidopsis. The current definition of a 'typical' primary or secondary cell wall might not be applicable to all cell types in all plant species.
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Affiliation(s)
| | - Hannah Birke
- CSIRO Agriculture and Food, PO Box 1700, Canberra, ACT, 2601, Australia.,Present address: Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Aaron Chuah
- John Curtin School of Medical Research, The Australian National University, ACT, Canberra, 2601, Australia
| | - Elizabeth Brill
- CSIRO Agriculture and Food, PO Box 1700, Canberra, ACT, 2601, Australia
| | - Yukiko Tsuji
- Department of Biochemistry and the Department of Energy's Great Lakes BioEnergy Research Center, The Wisconsin Energy Institute, 1552 University Avenue, Madison, WI, 53726-4084, USA
| | - John Ralph
- Department of Biochemistry and the Department of Energy's Great Lakes BioEnergy Research Center, The Wisconsin Energy Institute, 1552 University Avenue, Madison, WI, 53726-4084, USA
| | | | - Danny Llewellyn
- CSIRO Agriculture and Food, PO Box 1700, Canberra, ACT, 2601, Australia
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Dumitrache A, Akinosho H, Rodriguez M, Meng X, Yoo CG, Natzke J, Engle NL, Sykes RW, Tschaplinski TJ, Muchero W, Ragauskas AJ, Davison BH, Brown SD. Consolidated bioprocessing of Populus using Clostridium (Ruminiclostridium) thermocellum: a case study on the impact of lignin composition and structure. Biotechnol Biofuels 2016; 9:31. [PMID: 26855670 PMCID: PMC4743434 DOI: 10.1186/s13068-016-0445-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 01/20/2016] [Indexed: 05/04/2023]
Abstract
BACKGROUND Higher ratios of syringyl-to-guaiacyl (S/G) lignin components of Populus were shown to improve sugar release by enzymatic hydrolysis using commercial blends. Cellulolytic microbes are often robust biomass hydrolyzers and may offer cost advantages; however, it is unknown whether their activity can also be significantly influenced by the ratio of different monolignol types in Populus biomass. Hydrolysis and fermentation of autoclaved, but otherwise not pretreated Populus trichocarpa by Clostridium thermocellum ATCC 27405 was compared using feedstocks that had similar carbohydrate and total lignin contents but differed in S/G ratios. RESULTS Populus with an S/G ratio of 2.1 was converted more rapidly and to a greater extent compared to similar biomass that had a ratio of 1.2. For either microbes or commercial enzymes, an approximate 50 % relative difference in total solids solubilization was measured for both biomasses, which suggests that the differences and limitations in the microbial breakdown of lignocellulose may be largely from the enzymatic hydrolytic process. Surprisingly, the reduction in glucan content per gram solid in the residual microbially processed biomass was similar (17-18 %) irrespective of S/G ratio, pointing to a similar mechanism of solubilization that proceeded at different rates. Fermentation metabolome testing did not reveal the release of known biomass-derived alcohol and aldehyde inhibitors that could explain observed differences in microbial hydrolytic activity. Biomass-derived p-hydroxybenzoic acid was up to nine-fold higher in low S/G ratio biomass fermentations, but was not found to be inhibitory in subsequent test fermentations. Cellulose crystallinity and degree of polymerization did not vary between Populus lines and had minor changes after fermentation. However, lignin molecular weights and cellulose accessibility determined by Simons' staining were positively correlated to the S/G content. CONCLUSIONS Higher S/G ratios in Populus biomass lead to longer and more linear lignin chains and greater access to surface cellulosic content by microbe-bound enzymatic complexes. Substrate access limitation is suggested as a primary bottleneck in solubilization of minimally processed Populus, which has important implications for microbial deconstruction of lignocellulose biomass. Our findings will allow others to examine different Populus lines and to test if similar observations are possible for other plant species.
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Affiliation(s)
- Alexandru Dumitrache
- />Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- />BioEnergy Sciences Center, Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
| | - Hannah Akinosho
- />Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- />BioEnergy Sciences Center, Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
- />Renewable Bioproducts Institute, Georgia Institute of Technology, Atlanta, GA 30332 USA
- />UT-ORNL Joint Institute for Biological Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Miguel Rodriguez
- />Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- />BioEnergy Sciences Center, Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
| | - Xianzhi Meng
- />BioEnergy Sciences Center, Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
- />Renewable Bioproducts Institute, Georgia Institute of Technology, Atlanta, GA 30332 USA
- />School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332 USA
| | - Chang Geun Yoo
- />Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- />BioEnergy Sciences Center, Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
- />UT-ORNL Joint Institute for Biological Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Jace Natzke
- />Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- />BioEnergy Sciences Center, Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
| | - Nancy L. Engle
- />Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- />BioEnergy Sciences Center, Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
| | - Robert W. Sykes
- />National Renewable Energy Laboratory, US Department of Energy, Golden, CO 80401 USA
| | - Timothy J. Tschaplinski
- />Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- />BioEnergy Sciences Center, Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
| | - Wellington Muchero
- />Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- />BioEnergy Sciences Center, Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
| | - Arthur J. Ragauskas
- />Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- />BioEnergy Sciences Center, Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
- />UT-ORNL Joint Institute for Biological Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- />Department of Chemical and Biomolecular Engineering, Department of Forestry, Wildlife, and Fisheries, University of Tennessee, Knoxville, TN 37996 USA
| | - Brian H. Davison
- />Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- />BioEnergy Sciences Center, Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
| | - Steven D. Brown
- />Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- />BioEnergy Sciences Center, Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
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Fernández-Pérez F, Vivar T, Pomar F, Pedreño MA, Novo-Uzal E. Peroxidase 4 is involved in syringyl lignin formation in Arabidopsis thaliana. J Plant Physiol 2015; 175:86-94. [PMID: 25506770 DOI: 10.1016/j.jplph.2014.11.006] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2014] [Revised: 11/19/2014] [Accepted: 11/20/2014] [Indexed: 05/11/2023]
Abstract
Syringyl lignins result from the oxidative polymerization of sinapyl alcohol in a reaction mediated by syringyl (basic) peroxidases. Several peroxidases have been identified in the genome of Arabidopsis thaliana as close homologues to ZePrx, the best characterized basic peroxidase so far, but none of these has been directly involved in lignification. We have used a knock-out mutant of AtPrx4, the closest homologue to ZePrx, to study the involvement of this basic peroxidase in the physiology of the plant under both long- and short-day light conditions. Our results suggest that AtPrx4 is involved in cell wall lignification, especially in syringyl monomer formation. The disruption of AtPrx4 causes a decrease in syringyl units proportion, but only when light conditions are optimal. Moreover, the effect of AtPrx4 disruption is age-dependent, and it is only significant when the elongation process of the stem has ceased and lignification becomes active. In conclusion, AtPrx4 emerges as a basic peroxidase regulated by day length with an important role in lignification.
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Affiliation(s)
| | - Tamara Vivar
- Department of Plant Biology, University of Murcia, Murcia 30100, Spain
| | - Federico Pomar
- Deparment of Animal Biology, Plant Biology and Ecology, University of A Coruña, A Coruña 15071, Spain
| | - María A Pedreño
- Department of Plant Biology, University of Murcia, Murcia 30100, Spain
| | - Esther Novo-Uzal
- Department of Plant Biology, University of Murcia, Murcia 30100, Spain.
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