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Thanapipatpong P, Vuttipongchaikij S, Chomtong T, Puangtame W, Napaumpaipond P, Gomez LD, Suttangkakul A. Alternative splicing regulates autophagy in response to environmental stresses in cucumber ( Cucumis sativus). All Life 2023. [DOI: 10.1080/26895293.2023.2195987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023] Open
Affiliation(s)
| | - Supachai Vuttipongchaikij
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand
- Center of Advanced Studies for Tropical Natural Resources, Kasetsart University, Bangkok, Thailand
- Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok, Thailand
| | - Thitikorn Chomtong
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Wilasinee Puangtame
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | | | | | - Anongpat Suttangkakul
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand
- Center of Advanced Studies for Tropical Natural Resources, Kasetsart University, Bangkok, Thailand
- Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok, Thailand
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2
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Davidson DJ, Lu F, Faas L, Dawson DM, Warren GP, Panovic I, Montgomery JRD, Ma X, Bosilkov BG, Slawin AMZ, Lebl T, Chatzifragkou A, Robinson S, Ashbrook SE, Shaw LJ, Lambert S, Van Damme I, Gomez LD, Charalampopoulos D, Westwood NJ. Organosolv Pretreatment of Cocoa Pod Husks: Isolation, Analysis, and Use of Lignin from an Abundant Waste Product. ACS Sustain Chem Eng 2023; 11:14323-14333. [PMID: 37799817 PMCID: PMC10548466 DOI: 10.1021/acssuschemeng.2c03670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 09/05/2023] [Indexed: 10/07/2023]
Abstract
Cocoa pod husks (CPHs) represent an underutilized component of the chocolate manufacturing process. While industry's current focus is understandably on the cocoa beans, the husks make up around 75 wt % of the fruit. Previous studies have been dominated by the carbohydrate polymers present in CPHs, but this work highlights the presence of the biopolymer lignin in this biomass. An optimized organosolv lignin isolation protocol was developed, delivering significant practical improvements. This new protocol may also prove to be useful for agricultural waste-derived biomasses in general. NMR analysis of the high quality lignin led to an improved structural understanding, with evidence provided to support deacetylation of the lignin occurring during the optimized pretreatment. Chemical transformation, using a tosylation, azidation, copper-catalyzed click protocol, delivered a modified lignin oligomer with an organophosphorus motif attached. Thermogravimetric analysis was used to demonstrate the oligomer's potential as a flame-retardant. Preliminary analysis of the other product streams isolated from the CPHs was also carried out.
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Affiliation(s)
- Daniel J Davidson
- School of Chemistry and Biomedical Sciences Research Complex, University of St Andrews and EaStCHEM, North Haugh, St Andrews, Fife, KY16 9ST, United Kingdom
| | - Fei Lu
- Department of Food and Nutritional Sciences, University of Reading, Reading, Berkshire, RG6 6AP, United Kingdom
| | - Laura Faas
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, North Yorkshire, YO10 5DD, United Kingdom
| | - Daniel M Dawson
- School of Chemistry and Biomedical Sciences Research Complex, University of St Andrews and EaStCHEM, North Haugh, St Andrews, Fife, KY16 9ST, United Kingdom
| | - Geoffrey P Warren
- Soil Research Centre, Department of Geography and Environmental Sciences, University of Reading, Reading, Berkshire, RG6 6AB, United Kingdom
| | - Isabella Panovic
- School of Chemistry and Biomedical Sciences Research Complex, University of St Andrews and EaStCHEM, North Haugh, St Andrews, Fife, KY16 9ST, United Kingdom
| | - James R D Montgomery
- School of Chemistry and Biomedical Sciences Research Complex, University of St Andrews and EaStCHEM, North Haugh, St Andrews, Fife, KY16 9ST, United Kingdom
| | - Xiaoyan Ma
- School of Chemistry and Biomedical Sciences Research Complex, University of St Andrews and EaStCHEM, North Haugh, St Andrews, Fife, KY16 9ST, United Kingdom
| | - Boris G Bosilkov
- School of Chemistry and Biomedical Sciences Research Complex, University of St Andrews and EaStCHEM, North Haugh, St Andrews, Fife, KY16 9ST, United Kingdom
| | - Alexandra M Z Slawin
- School of Chemistry and Biomedical Sciences Research Complex, University of St Andrews and EaStCHEM, North Haugh, St Andrews, Fife, KY16 9ST, United Kingdom
| | - Tomas Lebl
- School of Chemistry and Biomedical Sciences Research Complex, University of St Andrews and EaStCHEM, North Haugh, St Andrews, Fife, KY16 9ST, United Kingdom
| | - Afroditi Chatzifragkou
- Department of Food and Nutritional Sciences, University of Reading, Reading, Berkshire, RG6 6AP, United Kingdom
| | - Steve Robinson
- Soil Research Centre, Department of Geography and Environmental Sciences, University of Reading, Reading, Berkshire, RG6 6AB, United Kingdom
| | - Sharon E Ashbrook
- School of Chemistry and Biomedical Sciences Research Complex, University of St Andrews and EaStCHEM, North Haugh, St Andrews, Fife, KY16 9ST, United Kingdom
| | - Liz J Shaw
- Soil Research Centre, Department of Geography and Environmental Sciences, University of Reading, Reading, Berkshire, RG6 6AB, United Kingdom
| | - Smilja Lambert
- Mars Wrigley Australia, Ring Road, Wendouree, VIC 3355, Australia
| | - Isabella Van Damme
- Mars Wrigley Confectionery UK Ltd., Slough, Berkshire, SL1 4LG, United Kingdom
| | - Leonardo D Gomez
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, North Yorkshire, YO10 5DD, United Kingdom
| | - Dimitris Charalampopoulos
- Department of Food and Nutritional Sciences, University of Reading, Reading, Berkshire, RG6 6AP, United Kingdom
| | - Nicholas J Westwood
- School of Chemistry and Biomedical Sciences Research Complex, University of St Andrews and EaStCHEM, North Haugh, St Andrews, Fife, KY16 9ST, United Kingdom
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Wannitikul P, Wattana-Amorn P, Sathitnaitham S, Sakulkoo J, Suttangkakul A, Wonnapinij P, Bassel GW, Simister R, Gomez LD, Vuttipongchaikij S. Disruption of a DUF247 Containing Protein Alters Cell Wall Polysaccharides and Reduces Growth in Arabidopsis. Plants (Basel) 2023; 12:1977. [PMID: 37653894 PMCID: PMC10221614 DOI: 10.3390/plants12101977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/09/2023] [Accepted: 05/10/2023] [Indexed: 09/02/2023]
Abstract
Plant cell wall biosynthesis is a complex process that requires proteins and enzymes from glycan synthesis to wall assembly. We show that disruption of At3g50120 (DUF247-1), a member of the DUF247 multigene family containing 28 genes in Arabidopsis, results in alterations to the structure and composition of cell wall polysaccharides and reduced growth and plant size. An ELISA using cell wall antibodies shows that the mutants also exhibit ~50% reductions in xyloglucan (XyG), glucuronoxylan (GX) and heteromannan (HM) epitopes in the NaOH fraction and ~50% increases in homogalacturonan (HG) epitopes in the CDTA fraction. Furthermore, the polymer sizes of XyGs and GXs are reduced with concomitant increases in short-chain polymers, while those of HGs and mHGs are slightly increased. Complementation using 35S:DUF247-1 partially recovers the XyG and HG content, but not those of GX and HM, suggesting that DUF247-1 is more closely associated with XyGs and HGs. DUF247-1 is expressed throughout Arabidopsis, particularly in vascular and developing tissues, and its disruption affects the expression of other gene members, indicating a regulatory control role within the gene family. Our results demonstrate that DUF247-1 is required for normal cell wall composition and structure and Arabidopsis growth.
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Affiliation(s)
- Pitchaporn Wannitikul
- Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Road, Chattuchak, Bangkok 10900, Thailand; (P.W.); (S.S.); (J.S.); (A.S.); (P.W.)
| | - Pakorn Wattana-Amorn
- Special Research Unit for Advanced Magnetic Resonance and Center of Excellence for Innovation in Chemistry, Department of Chemistry, Faculty of Science, Kasetsart University, Ngam Wong Wan Road, Chattuchak, Bangkok 10900, Thailand;
| | - Sukhita Sathitnaitham
- Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Road, Chattuchak, Bangkok 10900, Thailand; (P.W.); (S.S.); (J.S.); (A.S.); (P.W.)
| | - Jenjira Sakulkoo
- Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Road, Chattuchak, Bangkok 10900, Thailand; (P.W.); (S.S.); (J.S.); (A.S.); (P.W.)
| | - Anongpat Suttangkakul
- Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Road, Chattuchak, Bangkok 10900, Thailand; (P.W.); (S.S.); (J.S.); (A.S.); (P.W.)
- Center of Advanced studies for Tropical Natural Resources, Kasetsart University, Ngam Wong Wan Road, Chattuchak, Bangkok 10900, Thailand
| | - Passorn Wonnapinij
- Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Road, Chattuchak, Bangkok 10900, Thailand; (P.W.); (S.S.); (J.S.); (A.S.); (P.W.)
- Center of Advanced studies for Tropical Natural Resources, Kasetsart University, Ngam Wong Wan Road, Chattuchak, Bangkok 10900, Thailand
- Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand
| | - George W. Bassel
- School of Life Sciences, The University of Warwick, Coventry CV4 7AL, UK;
| | - Rachael Simister
- CNAP, Department of Biology, University of York, Heslington, York YO10 5DD, UK; (R.S.); (L.D.G.)
| | - Leonardo D. Gomez
- CNAP, Department of Biology, University of York, Heslington, York YO10 5DD, UK; (R.S.); (L.D.G.)
| | - Supachai Vuttipongchaikij
- Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Road, Chattuchak, Bangkok 10900, Thailand; (P.W.); (S.S.); (J.S.); (A.S.); (P.W.)
- Center of Advanced studies for Tropical Natural Resources, Kasetsart University, Ngam Wong Wan Road, Chattuchak, Bangkok 10900, Thailand
- Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand
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Silva MP, Badruddin IJ, Tonon T, Rahatekar S, Gomez LD. Environmentally benign alginate extraction and fibres spinning from different European Brown algae species. Int J Biol Macromol 2023; 226:434-442. [PMID: 36502944 DOI: 10.1016/j.ijbiomac.2022.11.306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 11/28/2022] [Accepted: 11/29/2022] [Indexed: 12/13/2022]
Abstract
Applications of natural fibres are expanding, and sustainable alternatives are needed to support this growing demand. We investigated the production of fibres using alginates from Saccharina latissima (SAC), Laminaria digitata (LAM), Sacchoriza polyschides (SACC), and Himanthalia spp. (HIM). After extraction (3 % w/v biomass) using a sustainable protocol based on citric acid, crude alginate represented 61-65 % of the biomass dry weight for SAC and LAM, and 34-41 % for SACC and HIM when experiments were performed at small scale (1.5 g of starting material). Interestingly, scaling-up extraction (60 g of starting material) decreased yields to 26-30 %. SAC and LAM alginates had the highest M/G (mannuronic acid/guluronic acid) ratios and molecular weights when compared to those from SACC and HIM (M/G:1.98 and 2.23, MW: 302 and 362 kDa, vs 1.83 and 1.86, 268 and 168 kDa). When the four types of alginates were tested for spinning fibres cross-linked with CaCl2, only SAC and LAM alginates produced fibres. These fibres showed no clumps or cracks under stretching action and presented a similar Young's modulus (2.4 and 2.0 GPa). We have demonstrated that alginate extracted from S. latissima and L. digitata can be successfully spun into functional fibres cross-linked with CaCl2.
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Affiliation(s)
- Mariana P Silva
- Centre for Novel Agricultural Product, Department of Biology, University of York, Wentworth Way, York YO10 5DD, United Kingdom
| | - Ishrat Jahan Badruddin
- Enhanced Composites and Structures Centre, School of Aerospace, Transport and Manufacturing, Cranfield University, Bedfordshire MK43 0AL, United Kingdom
| | - Thierry Tonon
- Centre for Novel Agricultural Product, Department of Biology, University of York, Wentworth Way, York YO10 5DD, United Kingdom
| | - Sameer Rahatekar
- Enhanced Composites and Structures Centre, School of Aerospace, Transport and Manufacturing, Cranfield University, Bedfordshire MK43 0AL, United Kingdom
| | - Leonardo D Gomez
- Centre for Novel Agricultural Product, Department of Biology, University of York, Wentworth Way, York YO10 5DD, United Kingdom.
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da Costa RMF, Bosch M, Simister R, Gomez LD, Canhoto JM, Batista de Carvalho LAE. Valorisation Potential of Invasive Acacia dealbata, A. longifolia and A. melanoxylon from Land Clearings. Molecules 2022; 27:7006. [PMID: 36296599 PMCID: PMC9610895 DOI: 10.3390/molecules27207006] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 10/04/2022] [Accepted: 10/14/2022] [Indexed: 08/02/2023] Open
Abstract
Acacia spp. are invasive in Southern Europe, and their high propagation rates produce excessive biomass, exacerbating wildfire risk. However, lignocellulosic biomass from Acacia spp. may be utilised for diverse biorefinery applications. In this study, attenuated total reflectance Fourier transform infrared spectroscopy (FTIR-ATR), high-performance anion-exchange chromatography pulsed amperometric detection (HPAEC-PAD) and lignin content determinations were used for a comparative compositional characterisation of A. dealbata, A. longifolia and A. melanoxylon. Additionally, biomass was treated with three white-rot fungi species (Ganoderma lucidum, Pleurotus ostreatus and Trametes versicolor), which preferentially degrade lignin. Our results showed that the pre-treatments do not significantly alter neutral sugar composition while reducing lignin content. Sugar release from enzymatic saccharification was enhanced, in some cases possibly due to a synergy between white-rot fungi and mild alkali pretreatments. For example, in A. dealbata stems treated with alkali and P. ostreatus, saccharification yield was 702.3 nmol mg-1, which is higher than the samples treated only with alkali (608.1 nmol mg-1), and 2.9-fold higher than the non-pretreated controls (243.9 nmol mg-1). By characterising biomass and pretreatments, generated data creates value for unused biomass resources, contributing to the implementation of sustainable biorefining systems. In due course, the generated value will lead to economic incentives for landowners to cut back invasive Acacia spp. more frequently, thus reducing excess biomass, which exacerbates wildfire risk.
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Affiliation(s)
- Ricardo M. F. da Costa
- Molecular Physical-Chemistry R&D Unit, Department of Chemistry, University of Coimbra, Rua Larga, 3004-535 Coimbra, Portugal
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - Maurice Bosch
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Plas Gogerddan, Aberystwyth, Ceredigion SY23 3EE, UK
| | - Rachael Simister
- Centre for Novel Agricultural Products, Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Leonardo D. Gomez
- Centre for Novel Agricultural Products, Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Jorge M. Canhoto
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - Luís A. E. Batista de Carvalho
- Molecular Physical-Chemistry R&D Unit, Department of Chemistry, University of Coimbra, Rua Larga, 3004-535 Coimbra, Portugal
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Janthabut T, Tristianto C, Sakulkoo J, Sunvittayakul P, Suttangkakul A, Gomez LD, Vuttipongchaikij S, Sakulsingharoj C. Effects of CRISPR/Cas9 generated drooping leaf (dl) alleles on midrib and carpel formations in Oryza sativa Nipponbare. Planta 2022; 256:61. [PMID: 35994211 DOI: 10.1007/s00425-022-03973-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 06/15/2022] [Accepted: 08/12/2022] [Indexed: 06/15/2023]
Abstract
We generated drooping leaf rice mutants by CRISPR/Cas and identified two novel alleles with specific editing that allow underpinning of the function of the DL protein domain towards midrib and carpel formations. The DROOPING LEAF (DL) gene plays an essential role in regulating midrib formation and carpel specification in rice and other grass species, but the specific function of DL protein domains in different developmental processes is unclear. Analysis of different dl mutant alleles will allow dissecting the function of DL. Here, we generated Nipponbare rice dl mutants using CRISPR/Cas gene editing and identified two novel dl alleles with different effects on midrib formation and carpel development. Phenotypic and genotypic analysis of T0 and segregated T1 edited lines showed that while dl-51S allele (a 3 bp deletion and a serine deletion at position 51) reduces midrib sizes and produces normal carpels, the dl-50LS allele (a 6 bp deletion and a leucine-serine deletion at position 50-51) causes the lack of midribs and abnormal stigma. This result indicates that the 51-serine is important for midrib formation and the 50-leucine is essential for midrib and carpel development. These dl mutant alleles contribute to the DL gene functional analysis and to gain insights into possible modifications of leaf architecture of rice and other grass species.
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Affiliation(s)
- Teerapong Janthabut
- Program in Genetics, Faculty of Science, Maejo University, Chiang Mai, 50290, Thailand
| | - Christian Tristianto
- Department of Biology, Faculty of Mathematics and Natural Sciences, IPB University, Bogor, 16680, Indonesia
| | - Janejira Sakulkoo
- Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Road, Chatuchak, Bangkok, 10900, Thailand
| | - Pongsakorn Sunvittayakul
- Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Road, Chatuchak, Bangkok, 10900, Thailand
| | - Anongpat Suttangkakul
- Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Road, Chatuchak, Bangkok, 10900, Thailand
- Center of Advanced Studies for Tropical Natural Resources, Kasetsart University, 50 Ngam Wong Wan Road, Chatuchak, Bangkok, 10900, Thailand
- Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok, Thailand
| | - Leonardo D Gomez
- CNAP, Department of Biology, University of York, Heslington, York, YO10 5DD, UK
| | - Supachai Vuttipongchaikij
- Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Road, Chatuchak, Bangkok, 10900, Thailand.
- Center of Advanced Studies for Tropical Natural Resources, Kasetsart University, 50 Ngam Wong Wan Road, Chatuchak, Bangkok, 10900, Thailand.
- Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok, Thailand.
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Möller SR, Lancefield CS, Oates NC, Simister R, Dowle A, Gomez LD, McQueen-Mason SJ. CRISPR/Cas9 suppression of OsAT10, a rice BAHD acyltransferase, reduces p-coumaric acid incorporation into arabinoxylan without increasing saccharification. Front Plant Sci 2022; 13:926300. [PMID: 35937377 PMCID: PMC9355400 DOI: 10.3389/fpls.2022.926300] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 07/05/2022] [Indexed: 06/01/2023]
Abstract
Ester-linked hydroxycinnamic acids ferulic acid (FA) and para-coumaric acid (p-CA) play important roles in crosslinking within cell wall arabinoxylans (AX) and between AX and lignin in grass cell walls. The addition of hydroxycinnamates to AX, is mediated by the Mitchell clade of BAHD acyl-coenzyme A-utilizing transferases. Overexpression of OsAT10 (a Mitchell clade BAHD acyl transferase) in rice, has previously been shown to increase p-CA content in AX in leaves and stems, leading to increased cell wall digestibility, potentially associated with a concomitant decrease in FA content. To investigate the physiological role of OsAT10 we established CRISPR/Cas9 rice knock-out mutants devoid of OsAT10. Our analysis of hydroxycinnamic acid content in wild type plants revealed that AX associated p-CA is found almost exclusively in rice husks, with very little found in other tissues. Mutant plants were essentially devoid of ester-linked p-CA associated with AX, indicating that OsAT10 represents the major enzyme responsible for the addition of p-CA to arabinoxylan in rice plants. We found no change in the digestibility of rice husk lacking AX-associated p-CA, suggesting that the changes in digestibility seen in OsAT10 overexpressing plants were solely due to compensatory decreases in AX-associated FA.
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Affiliation(s)
| | - Christopher S. Lancefield
- School of Chemistry and Biomedical Science Research Complex, University of St. Andrews, St.Andrews, United Kingdom
| | - Nicola C. Oates
- CNAP, Biology Department, University of York, York, United Kingdom
| | - Rachael Simister
- CNAP, Biology Department, University of York, York, United Kingdom
| | - Adam Dowle
- Biology Department, Bioscience Technology Facility, University of York, York, United Kingdom
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Allen H, Zeef L, Morreel K, Goeminne G, Kumar M, Gomez LD, Dean AP, Eckmann A, Casiraghi C, McQueen-Mason SJ, Boerjan W, Turner SR. Flexible and digestible wood caused by viral-induced alteration of cell wall composition. Curr Biol 2022; 32:3398-3406.e6. [PMID: 35732179 PMCID: PMC9616729 DOI: 10.1016/j.cub.2022.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/29/2022] [Accepted: 06/01/2022] [Indexed: 11/16/2022]
Abstract
Woody plant material represents a vast renewable resource that has the potential to produce biofuels and other bio-based products with favorable net CO2 emissions.1,2 Its potential has been demonstrated in a recent study that generated novel structural materials from flexible moldable wood.3 Apple rubbery wood (ARW) disease is the result of a viral infection that causes woody stems to exhibit increased flexibility.4 Although ARW disease is associated with the presence of an RNA virus5 known as apple rubbery wood virus (ARWV), how the unique symptoms develop is unknown. We demonstrate that the symptoms of ARWV infections arise from reduced lignification within the secondary cell wall of xylem fibers and result in increased wood digestibility. In contrast, the mid-lamellae region and xylem ray cells are largely unaffected by the infection. Gene expression and proteomic data from symptomatic xylem clearly show the downregulation of phenylalanine ammonia lyase (PAL), the enzyme catalyzing the first committed step in the phenylpropanoid pathway leading to lignin biosynthesis. A large increase in soluble phenolics in symptomatic xylem, including the lignin precursor phenylalanine, is also consistent with PAL downregulation. ARWV infection results in the accumulation of many host-derived virus-activated small interfering RNAs (vasiRNAs). PAL-derived vasiRNAs are among the most abundant vasiRNAs in symptomatic xylem and are likely the cause of reduced PAL activity. Apparently, the mechanism used by the virus to alter lignin exhibits similarities to the RNAi strategy used to alter lignin in genetically modified trees to generate comparable improvements in wood properties.6, 7, 8 Video abstract
Apple rubbery wood (ARW) symptoms are caused by decreased lignin in woody tissue RNA-seq, proteomics, and metabolomics suggest phenylalanine levels decrease Virus-activated small interfering RNAs (vasiRNAs) are generated in response to ARWV infection VasiRNAs cause siRNA-based downregulation of phenylalanine ammonia
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Affiliation(s)
- Holly Allen
- School of Biological Science, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Leo Zeef
- School of Biological Science, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Kris Morreel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Geert Goeminne
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium; VIB Metabolomics Core Gent, VIB, 9052 Zwijnaarde, Belgium
| | - Manoj Kumar
- School of Biological Science, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Leonardo D Gomez
- Centre for Novel Agricultural Products (CNAP), Department of Biology, University of York, York YO10 5DD, UK
| | - Andrew P Dean
- School of Biological Science, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Axel Eckmann
- Department of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Cinzia Casiraghi
- Department of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Simon J McQueen-Mason
- Centre for Novel Agricultural Products (CNAP), Department of Biology, University of York, York YO10 5DD, UK
| | - Wout Boerjan
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Simon R Turner
- School of Biological Science, University of Manchester, Oxford Road, Manchester M13 9PT, UK.
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Upton DJ, Kaushal M, Whitehead C, Faas L, Gomez LD, McQueen-Mason SJ, Srivastava S, Wood AJ. Integration of Aspergillus niger transcriptomic profile with metabolic model identifies potential targets to optimise citric acid production from lignocellulosic hydrolysate. Biotechnol Biofuels Bioprod 2022; 15:4. [PMID: 35418297 PMCID: PMC8756645 DOI: 10.1186/s13068-021-02099-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 12/24/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND Citric acid is typically produced industrially by Aspergillus niger-mediated fermentation of a sucrose-based feedstock, such as molasses. The fungus Aspergillus niger has the potential to utilise lignocellulosic biomass, such as bagasse, for industrial-scale citric acid production, but realising this potential requires strain optimisation. Systems biology can accelerate strain engineering by systematic target identification, facilitated by methods for the integration of omics data into a high-quality metabolic model. In this work, we perform transcriptomic analysis to determine the temporal expression changes during fermentation of bagasse hydrolysate and develop an evolutionary algorithm to integrate the transcriptomic data with the available metabolic model to identify potential targets for strain engineering. RESULTS The novel integrated procedure matures our understanding of suboptimal citric acid production and reveals potential targets for strain engineering, including targets consistent with the literature such as the up-regulation of citrate export and pyruvate carboxylase as well as novel targets such as the down-regulation of inorganic diphosphatase. CONCLUSIONS In this study, we demonstrate the production of citric acid from lignocellulosic hydrolysate and show how transcriptomic data across multiple timepoints can be coupled with evolutionary and metabolic modelling to identify potential targets for further engineering to maximise productivity from a chosen feedstock. The in silico strategies employed in this study can be applied to other biotechnological goals, assisting efforts to harness the potential of microorganisms for bio-based production of valuable chemicals.
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Affiliation(s)
- Daniel J Upton
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK.
| | - Mehak Kaushal
- Systems Biology for Biofuel Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), ICGEB Campus, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Caragh Whitehead
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Laura Faas
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Leonardo D Gomez
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | | | - Shireesh Srivastava
- Systems Biology for Biofuel Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), ICGEB Campus, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - A Jamie Wood
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
- Department of Mathematics, University of York, Heslington, York, YO10 5DD, UK
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10
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da Costa RMF, Winters A, Hauck B, Martín D, Bosch M, Simister R, Gomez LD, Batista de Carvalho LAE, Canhoto JM. Biorefining Potential of Wild-Grown Arundo donax, Cortaderia selloana and Phragmites australis and the Feasibility of White-Rot Fungi-Mediated Pretreatments. Front Plant Sci 2021; 12:679966. [PMID: 34276732 PMCID: PMC8283202 DOI: 10.3389/fpls.2021.679966] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 06/10/2021] [Indexed: 05/29/2023]
Abstract
Arundo donax, Cortaderia selloana and Phragmites australis are high-biomass-producing perennial Poalean species that grow abundantly and spontaneously in warm temperate regions, such as in Mediterranean-type climates, like those of Southern Europe, Western United States coastal areas, or in regions of South America, South Africa and Australia. Given their vigorous and spontaneous growth, biomass from the studied grasses often accumulates excessively in unmanaged agro-forestry areas. Nonetheless, this also creates the demand and opportunity for the valorisation of these biomass sources, particularly their cell wall polymers, for biorefining applications. By contrast, a related crop, Miscanthus × giganteus, is a perennial grass that has been extensively studied for lignocellulosic biomass production, as it can grow on low-input agricultural systems in colder climates. In this study Fourier transform mid-infrared spectroscopy (FTIR), high-performance anion-exchange chromatography (HPAEC) and lignin content determinations were used for a comparative compositional characterisation of A. donax, C. selloana and P. australis harvested from the wild, in relation to a trial field-grown M. × giganteus high-yielding genotype. A high-throughput saccharification assay showed relatively high sugar release values from the wild-grown grasses, even with a 0.1M NaOH mild alkali pretreatment. In addition to this alkaline pretreatment, biomass was treated with white-rot fungi (WRF), which preferentially degrade lignin more readily than holocellulose. Three fungal species were used: Ganoderma lucidum, Pleurotus ostreatus and Trametes versicolor. Our results showed that neutral sugar contents are not significantly altered, while some lignin is lost during the pretreatments. Furthermore, sugar release upon enzymatic saccharification was enhanced, and this was dependent on the plant biomass and fungal species used in the treatment. To maximise the potential for lignocellulose valorisation, the liquid fractions from the pretreatments were analysed by high performance liquid chromatography - photodiode array detection - electrospray ionisation tandem mass spectrometry (HPLC-PDA-ESI-MS n ). This study is one of the first to report on the composition of WRF-treated grass biomass, while assessing the potential relevance of breakdown products released during the treatments, beyond more traditional sugar-for-energy applications. Ultimately, we expect that our data will help promote the valorisation of unused biomass resources, create economic value, while contributing to the implementation of sustainable biorefining systems.
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Affiliation(s)
- Ricardo M. F. da Costa
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
- Molecular Physical-Chemistry R&D Unit, Department of Chemistry, University of Coimbra, Coimbra, Portugal
| | - Ana Winters
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
| | - Barbara Hauck
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
| | - Daniel Martín
- Molecular Physical-Chemistry R&D Unit, Department of Chemistry, University of Coimbra, Coimbra, Portugal
| | - Maurice Bosch
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
| | - Rachael Simister
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, United Kingdom
| | - Leonardo D. Gomez
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, United Kingdom
| | | | - Jorge M. Canhoto
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
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11
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Mota TR, Oliveira DM, Simister R, Whitehead C, Lanot A, Dos Santos WD, Rezende CA, McQueen-Mason SJ, Gomez LD. Corrigendum to "Design of experiments driven optimization of alkaline pretreatment and saccharification for sugarcane bagasse" [Bioresour. Technol. 321 (2021) 124499]. Bioresour Technol 2021; 325:124763. [PMID: 33516595 DOI: 10.1016/j.biortech.2021.124763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Affiliation(s)
- Thatiane R Mota
- Department of Biochemistry, State University of Maringá, UEM, Maringá, Paraná 87020-900, Brazil
| | - Dyoni M Oliveira
- Department of Biochemistry, State University of Maringá, UEM, Maringá, Paraná 87020-900, Brazil
| | - Rachael Simister
- Centre for Novel Agricultural Products, Department of Biology, CNAP, University of York, York YO10 5DD, United Kingdom
| | - Caragh Whitehead
- Centre for Novel Agricultural Products, Department of Biology, CNAP, University of York, York YO10 5DD, United Kingdom
| | - Alexandra Lanot
- Centre for Novel Agricultural Products, Department of Biology, CNAP, University of York, York YO10 5DD, United Kingdom
| | - Wanderley D Dos Santos
- Department of Biochemistry, State University of Maringá, UEM, Maringá, Paraná 87020-900, Brazil
| | - Camila A Rezende
- Institute of Chemistry, University of Campinas, UNICAMP, Campinas, São Paulo 13083‑970, Brazil
| | - Simon J McQueen-Mason
- Centre for Novel Agricultural Products, Department of Biology, CNAP, University of York, York YO10 5DD, United Kingdom
| | - Leonardo D Gomez
- Centre for Novel Agricultural Products, Department of Biology, CNAP, University of York, York YO10 5DD, United Kingdom.
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12
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Calderini DF, Castillo FM, Arenas‐M A, Molero G, Reynolds MP, Craze M, Bowden S, Milner MJ, Wallington EJ, Dowle A, Gomez LD, McQueen‐Mason SJ. Overcoming the trade-off between grain weight and number in wheat by the ectopic expression of expansin in developing seeds leads to increased yield potential. New Phytol 2021; 230:629-640. [PMID: 33124693 PMCID: PMC8048851 DOI: 10.1111/nph.17048] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 10/21/2020] [Indexed: 05/19/2023]
Abstract
Wheat is the most widely grown crop globally, providing 20% of all human calories and protein. Achieving step changes in genetic yield potential is crucial to ensure food security, but efforts are thwarted by an apparent trade-off between grain size and number. Expansins are proteins that play important roles in plant growth by enhancing stress relaxation in the cell wall, which constrains cell expansion. Here, we describe how targeted overexpression of an α-expansin in early developing wheat seeds leads to a significant increase in grain size without a negative effect on grain number, resulting in a yield boost under field conditions. The best-performing transgenic line yielded 12.3% higher average grain weight than the control, and this translated to an increase in grain yield of 11.3% in field experiments using an agronomically appropriate plant density. This targeted transgenic approach provides an opportunity to overcome a common bottleneck to yield improvement across many crops.
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Affiliation(s)
- Daniel F. Calderini
- Institute of Plant Production and ProtectionUniversidad Austral de ChileCampus Isla TejaValdivia5090000Chile
| | - Francisca M. Castillo
- Institute of Plant Production and ProtectionUniversidad Austral de ChileCampus Isla TejaValdivia5090000Chile
- Institute of Biochemistry and MicrobiologyFaculty of SciencesUniversidad Austral de ChileValdivia5090000Chile
| | - Anita Arenas‐M
- Institute of Plant Production and ProtectionUniversidad Austral de ChileCampus Isla TejaValdivia5090000Chile
- Institute of Biochemistry and MicrobiologyFaculty of SciencesUniversidad Austral de ChileValdivia5090000Chile
| | - Gemma Molero
- International Maize and Wheat Improvement Center (CIMMYT)El BatánTexcocoCP 56237Mexico
| | - Matthew P. Reynolds
- International Maize and Wheat Improvement Center (CIMMYT)El BatánTexcocoCP 56237Mexico
| | | | | | | | | | - Adam Dowle
- CNAPBiology DepartmentUniversity of YorkWentworth Way, HeslingtonYorkYO10 5YWUK
| | - Leonardo D. Gomez
- CNAPBiology DepartmentUniversity of YorkWentworth Way, HeslingtonYorkYO10 5YWUK
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13
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Davis D, Simister R, Campbell S, Marston M, Bose S, McQueen-Mason SJ, Gomez LD, Gallimore WA, Tonon T. Biomass composition of the golden tide pelagic seaweeds Sargassum fluitans and S. natans (morphotypes I and VIII) to inform valorisation pathways. Sci Total Environ 2021; 762:143134. [PMID: 33148447 DOI: 10.1016/j.scitotenv.2020.143134] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [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: 06/26/2020] [Revised: 10/05/2020] [Accepted: 10/14/2020] [Indexed: 06/11/2023]
Abstract
Massive strandings of the pelagic brown algae Sargassum have occurred in the Caribbean, and to a lesser extent, in western Africa, almost every year since 2011. These events have major environmental, health, and economic impacts in the affected countries. Once on the shore, Sargassum is mechanically harvested and disposed of in landfills. Existing commercial applications of other brown algae indicate that the pelagic Sargassum could constitute a valuable feedstock for potential valorisation. However, limited data on the composition of this Sargassum biomass was available to inform on possible application through pyrolysis or enzymatic fractionation of this feedstock. To fill this gap, we conducted a detailed comparative biochemical and elemental analysis of three pelagic Sargassum morphotypes identified so far as forming Atlantic blooms: Sargassum natans I (SnI), S. fluitans III (Sf), and S. natans VIII (SnVIII). Our results showed that SnVIII accumulated a lower quantity of metals and metalloids compared to SnI and Sf, but it contained higher amounts of phenolics and non-cellulosic polysaccharides. SnVIII also had more of the carbon storage compound mannitol. No differences in the content and composition of the cell wall polysaccharide alginate were identified among the three morphotypes. In addition, enzymatic saccharification of SnI produced more sugars compared to SnVIII and Sf. Due to high content of arsenic, the use of pelagic Sargassum is not recommended for nutritional purposes. In addition, low yields of alginate extracted from this biomass, compared with brown algae used for industrial production, limit its use as viable source of commercial alginates. Further work is needed to establish routes for future valorisation of pelagic Sargassum biomass.
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Affiliation(s)
- Doleasha Davis
- Department of Chemistry, University of the West Indies, Mona Campus, Mona, Kingston 7, Jamaica; Department of Biology, Centre for Novel Agricultural Products, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Rachael Simister
- Department of Biology, Centre for Novel Agricultural Products, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Sanjay Campbell
- Department of Chemistry, University of the West Indies, Mona Campus, Mona, Kingston 7, Jamaica; Department of Biology, Centre for Novel Agricultural Products, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Melissa Marston
- Department of Chemistry, University of the West Indies, Mona Campus, Mona, Kingston 7, Jamaica
| | - Suranjana Bose
- Green Chemistry Centre of Excellence, Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Simon J McQueen-Mason
- Department of Biology, Centre for Novel Agricultural Products, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Leonardo D Gomez
- Department of Biology, Centre for Novel Agricultural Products, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Winklet A Gallimore
- Department of Chemistry, University of the West Indies, Mona Campus, Mona, Kingston 7, Jamaica
| | - Thierry Tonon
- Department of Biology, Centre for Novel Agricultural Products, University of York, Heslington, York YO10 5DD, United Kingdom.
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14
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Mota TR, Oliveira DM, Simister R, Whitehead C, Lanot A, Dos Santos WD, Rezende CA, McQueen-Mason SJ, Gomez LD. Design of experiments driven optimization of alkaline pretreatment and saccharification for sugarcane bagasse. Bioresour Technol 2021; 321:124499. [PMID: 33310387 DOI: 10.1016/j.biortech.2020.124499] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 10/23/2020] [Revised: 11/28/2020] [Accepted: 11/30/2020] [Indexed: 06/12/2023]
Abstract
To maximize the sugar release from sugarcane bagasse, a high-resolution Fractional Factorial Design (FFD) was combined with a Central Composite Orthogonal (CCO) design to simultaneously evaluate a wide range of variables for alkaline pretreatment (NaOH: 0.1-1 mol/L, temperature: 100-220 °C, and time: 20-80 min) and enzymatic saccharification (enzyme loading: 2.5-17.5%, and reaction volume: 550-850 µL). A total of 46 experimental conditions were evaluated and the maximum sugar yield (423 mg/g) was obtained after 18 h enzymatic hydrolysis under optimized conditions (0.25 mol/L NaOH at 202 °C for 40 min, with 12.5% of enzyme loading). Biomass compositional analyses showed that the pretreatments strongly removed lignin (up to 70%), silica (up to 80%) and promoted cellulose enrichment (25-110%). This robust design of experiments resulted in maximizing enzymatic hydrolysis efficiency of sugarcane bagasse and further indicated that this combined approach is versatile for other lignocellulosic biomasses.
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Affiliation(s)
- Thatiane R Mota
- Department of Biochemistry, State University of Maringá, UEM, Maringá, Paraná, 87020-900, Brazil
| | - Dyoni M Oliveira
- Department of Biochemistry, State University of Maringá, UEM, Maringá, Paraná, 87020-900, Brazil
| | - Rachael Simister
- Centre for Novel Agricultural Products, Department of Biology, CNAP, University of York, York YO10 5DD, United Kingdom
| | - Caragh Whitehead
- Centre for Novel Agricultural Products, Department of Biology, CNAP, University of York, York YO10 5DD, United Kingdom
| | - Alexandra Lanot
- Centre for Novel Agricultural Products, Department of Biology, CNAP, University of York, York YO10 5DD, United Kingdom
| | - Wanderley D Dos Santos
- Department of Biochemistry, State University of Maringá, UEM, Maringá, Paraná, 87020-900, Brazil
| | - Camila A Rezende
- Institute of Chemistry, University of Campinas, UNICAMP, Campinas, São Paulo 13083‑970, Brazil
| | - Simon J McQueen-Mason
- Centre for Novel Agricultural Products, Department of Biology, CNAP, University of York, York YO10 5DD, United Kingdom.
| | - Leonardo D Gomez
- Centre for Novel Agricultural Products, Department of Biology, CNAP, University of York, York YO10 5DD, United Kingdom.
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15
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Nguyen DT, Gomez LD, Harper A, Halpin C, Waugh R, Simister R, Whitehead C, Oakey H, Nguyen HT, Nguyen TV, Duong TX, McQueen-Mason SJ. Association mapping identifies quantitative trait loci (QTL) for digestibility in rice straw. Biotechnol Biofuels 2020; 13:165. [PMID: 33062051 PMCID: PMC7545568 DOI: 10.1186/s13068-020-01807-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 09/27/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND The conversion of lignocellulosic biomass from agricultural waste into biofuels and chemicals is considered a promising way to provide sustainable low carbon products without compromising food security. However, the use of lignocellulosic biomass for biofuel and chemical production is limited by the cost-effectiveness of the production process due to its recalcitrance to enzymatic hydrolysis and fermentable sugar release (i.e., saccharification). Rice straw is a particularly attractive feedstock because millions of tons are currently burned in the field each year for disposal. The aim of this study was to explore the underlying natural genetic variation that impacts the recalcitrance of rice (Oryza sativa) straw to enzymatic saccharification. Ultimately, we wanted to investigate whether we could identify genetic markers that could be used in rice breeding to improve commercial cultivars for this trait. Here, we describe the development and characterization of a Vietnamese rice genome-wide association panel, high-throughput analysis of rice straw saccharification and lignin content, and the results from preliminary genome-wide association studies (GWAS) of the combined data sets. We identify both QTL and plausible candidate genes that may have an impact on the saccharification of rice straw. RESULTS We assembled a diversity panel comprising 151 rice genotypes (Indica and Japonica types) from commercial, historical elite cultivars, and traditional landraces grown in Vietnam. The diversity panel was genotyped using genotype by sequencing (GBS) methods yielding a total of 328,915 single nucleotide polymorphisms (SNPs). We collected phenotypic data from stems of these 151 genotypes for biomass saccharification and lignin content. Using GWAS on the indica genotypes over 2 years we identified ten significant QTL for saccharification (digestibility) and seven significant QTL for lignin. One QTL on chromosome 11 occurred in both GWAS for digestibility and for lignin. Seven QTL for digestibility, on CH2, CH6, CH7, CH8, and CH11, were observed in both years of the study. The QTL regions for saccharification include three potential candidate genes that have been previously reported to influence digestibility: OsAT10; OsIRX9; and OsMYB58/63-L. CONCLUSIONS Despite the difficulties associated with multi-phasic analysis of complex traits in novel germplasm, a moderate resolution GWAS successfully identified genetic associations encompassing both known and/or novel genes involved in determining the saccharification potential and lignin content of rice straw. Plausible candidates within QTL regions, in particular those with roles in cell wall biosynthesis, were identified but will require validation to confirm their value for application in rice breeding.
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Affiliation(s)
- Duong T. Nguyen
- Plant Biotechnology Division,, Field Crops Research Institute (FCRI), Hai Duong, Vietnam
- School of Agriculture and Environment, University of Western Australia (UWA), Crawley, WA Australia
| | - Leonardo D. Gomez
- Centre for Novel Agricultural Products (CNAP), University of York (UoY), Wentworth Way, York, UK
| | - Andrea Harper
- Centre for Novel Agricultural Products (CNAP), University of York (UoY), Wentworth Way, York, UK
| | - Claire Halpin
- Division of Plant Sciences, School of Life Sciences, University of Dundee (UoD), Dundee, UK
| | - Robbie Waugh
- Division of Plant Sciences, School of Life Sciences, University of Dundee (UoD), Dundee, UK
- Cell, and Molecular Genetics, The James Hutton Institute (JHI), Invergowrie Dundee, UK
- School of Agriculture Food and Wine, University of Adelaide, Waite Campus, Adelaide, SA Australia
| | - Rachael Simister
- Centre for Novel Agricultural Products (CNAP), University of York (UoY), Wentworth Way, York, UK
| | - Caragh Whitehead
- Centre for Novel Agricultural Products (CNAP), University of York (UoY), Wentworth Way, York, UK
| | - Helena Oakey
- Division of Plant Sciences, School of Life Sciences, University of Dundee (UoD), Dundee, UK
- School of Agriculture Food and Wine, University of Adelaide, Waite Campus, Adelaide, SA Australia
| | - Huong T. Nguyen
- Plant Biotechnology Division,, Field Crops Research Institute (FCRI), Hai Duong, Vietnam
| | - Tuat V. Nguyen
- Vietnam Academy of Agricultural Sciences, Hanoi, Vietnam
| | - Tu X. Duong
- Plant Biotechnology Division,, Field Crops Research Institute (FCRI), Hai Duong, Vietnam
| | - Simon J. McQueen-Mason
- Centre for Novel Agricultural Products (CNAP), University of York (UoY), Wentworth Way, York, UK
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16
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Oliveira DM, Mota TR, Salatta FV, Sinzker RC, Končitíková R, Kopečný D, Simister R, Silva M, Goeminne G, Morreel K, Rencoret J, Gutiérrez A, Tryfona T, Marchiosi R, Dupree P, Del Río JC, Boerjan W, McQueen-Mason SJ, Gomez LD, Ferrarese-Filho O, Dos Santos WD. Cell wall remodeling under salt stress: Insights into changes in polysaccharides, feruloylation, lignification, and phenolic metabolism in maize. Plant Cell Environ 2020; 43:2172-2191. [PMID: 32441772 DOI: 10.1111/pce.13805] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [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: 03/21/2020] [Revised: 04/27/2020] [Accepted: 05/14/2020] [Indexed: 05/15/2023]
Abstract
Although cell wall polymers play important roles in the tolerance of plants to abiotic stress, the effects of salinity on cell wall composition and metabolism in grasses remain largely unexplored. Here, we conducted an in-depth study of changes in cell wall composition and phenolic metabolism induced upon salinity in maize seedlings and plants. Cell wall characterization revealed that salt stress modulated the deposition of cellulose, matrix polysaccharides and lignin in seedling roots, plant roots and stems. The extraction and analysis of arabinoxylans by size-exclusion chromatography, 2D-NMR spectroscopy and carbohydrate gel electrophoresis showed a reduction of arabinoxylan content in salt-stressed roots. Saponification and mild acid hydrolysis revealed that salinity also reduced the feruloylation of arabinoxylans in roots of seedlings and plants. Determination of lignin content and composition by nitrobenzene oxidation and 2D-NMR confirmed the increased incorporation of syringyl units in lignin of maize roots. Salt stress also induced the expression of genes and the activity of enzymes enrolled in phenylpropanoid biosynthesis. The UHPLC-MS-based metabolite profiling confirmed the modulation of phenolic profiling by salinity and the accumulation of ferulate and its derivatives 3- and 4-O-feruloyl quinate. In conclusion, we present a model for explaining cell wall remodeling in response to salinity.
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Affiliation(s)
- Dyoni M Oliveira
- Department of Biochemistry, State University of Maringá, Maringá, Brazil
| | - Thatiane R Mota
- Department of Biochemistry, State University of Maringá, Maringá, Brazil
| | - Fábio V Salatta
- Department of Biochemistry, State University of Maringá, Maringá, Brazil
| | - Renata C Sinzker
- Department of Biochemistry, State University of Maringá, Maringá, Brazil
| | - Radka Končitíková
- Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - David Kopečný
- Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Rachael Simister
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, UK
| | - Mariana Silva
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, UK
| | - Geert Goeminne
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Kris Morreel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Jorge Rencoret
- Instituto de Recursos Naturales y Agrobiología de Sevilla, CSIC, Seville, Spain
| | - Ana Gutiérrez
- Instituto de Recursos Naturales y Agrobiología de Sevilla, CSIC, Seville, Spain
| | - Theodora Tryfona
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Rogério Marchiosi
- Department of Biochemistry, State University of Maringá, Maringá, Brazil
| | - Paul Dupree
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - José C Del Río
- Instituto de Recursos Naturales y Agrobiología de Sevilla, CSIC, Seville, Spain
| | - Wout Boerjan
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Simon J McQueen-Mason
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, UK
| | - Leonardo D Gomez
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, UK
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17
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Lueangwattanapong K, Ammam F, Mason PM, Whitehead C, McQueen-Mason SJ, Gomez LD, Smith JAC, Thompson IP. Anaerobic digestion of Crassulacean Acid Metabolism plants: Exploring alternative feedstocks for semi-arid lands. Bioresour Technol 2020; 297:122262. [PMID: 31711909 DOI: 10.1016/j.biortech.2019.122262] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 08/30/2019] [Revised: 10/09/2019] [Accepted: 10/11/2019] [Indexed: 06/10/2023]
Abstract
In this work, five Crassulacean Acid Metabolism (CAM) species from the five different genera (Agave, Ananas, Euphorbia, Kalanchoe, and Opuntia) were selected as alternative feedstocks and their biochemical methane potentials (BMP) were investigated. Batch assays were performed using sludge and rumen fluid as inocula under uncontrolled pH and at mesophilic temperature (39 °C). Mean methane yields from the CAM plants inoculated with AD sludge ranged from 281 to 382 ml/gVS. These values were not significantly different from the methane yield obtained from maize, a feedstock for biomethane and volatile fatty acid (VFA), suggesting that CAM plants may be viable as bioenergy crops on poor-quality soils in areas with low rainfall that are unsuitable for cultivation of food crops.
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Affiliation(s)
| | - Fariza Ammam
- Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, United Kingdom
| | - P Michael Mason
- Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, United Kingdom
| | - Caragh Whitehead
- Department of Biology, Centre for Novel Agricultural Products, University of York, Wentworth Way, Heslington, York YO10 5DD, United Kingdom
| | - Simon J McQueen-Mason
- Department of Biology, Centre for Novel Agricultural Products, University of York, Wentworth Way, Heslington, York YO10 5DD, United Kingdom
| | - Leonardo D Gomez
- Department of Biology, Centre for Novel Agricultural Products, University of York, Wentworth Way, Heslington, York YO10 5DD, United Kingdom
| | - J Andrew C Smith
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, United Kingdom
| | - Ian P Thompson
- Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, United Kingdom.
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18
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Oliveira DM, Mota TR, Salatta FV, Marchiosi R, Gomez LD, McQueen‐Mason SJ, Ferrarese‐Filho O, dos Santos WD. Designing xylan for improved sustainable biofuel production. Plant Biotechnol J 2019; 17:2225-2227. [PMID: 31077637 PMCID: PMC6835121 DOI: 10.1111/pbi.13150] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 04/17/2019] [Accepted: 05/05/2019] [Indexed: 05/25/2023]
Affiliation(s)
- Dyoni M. Oliveira
- Laboratory of Plant BiochemistryDepartment of BiochemistryState University of MaringáMaringáParanáBrazil
| | - Thatiane R. Mota
- Laboratory of Plant BiochemistryDepartment of BiochemistryState University of MaringáMaringáParanáBrazil
| | - Fábio V. Salatta
- Laboratory of Plant BiochemistryDepartment of BiochemistryState University of MaringáMaringáParanáBrazil
| | - Rogério Marchiosi
- Laboratory of Plant BiochemistryDepartment of BiochemistryState University of MaringáMaringáParanáBrazil
| | - Leonardo D. Gomez
- Centre for Novel Agricultural ProductsDepartment of BiologyUniversity of YorkYorkUK
| | | | - Osvaldo Ferrarese‐Filho
- Laboratory of Plant BiochemistryDepartment of BiochemistryState University of MaringáMaringáParanáBrazil
| | - Wanderley D. dos Santos
- Laboratory of Plant BiochemistryDepartment of BiochemistryState University of MaringáMaringáParanáBrazil
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19
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Grandis A, Leite DCC, Tavares EQP, Arenque-Musa BC, Gaiarsa JW, Martins MCM, De Souza AP, Gomez LD, Fabbri C, Mattei B, Buckeridge MS. Cell wall hydrolases act in concert during aerenchyma development in sugarcane roots. Ann Bot 2019; 124:1067-1089. [PMID: 31190078 PMCID: PMC6881219 DOI: 10.1093/aob/mcz099] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [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: 02/11/2019] [Accepted: 06/07/2019] [Indexed: 05/09/2023]
Abstract
BACKGROUND AND AIMS Cell wall disassembly occurs naturally in plants by the action of several glycosyl-hydrolases during different developmental processes such as lysigenous and constitutive aerenchyma formation in sugarcane roots. Wall degradation has been reported in aerenchyma development in different species, but little is known about the action of glycosyl-hydrolases in this process. METHODS In this work, gene expression, protein levels and enzymatic activity of cell wall hydrolases were assessed. Since aerenchyma formation is constitutive in sugarcane roots, they were assessed in segments corresponding to the first 5 cm from the root tip where aerenchyma develops. KEY RESULTS Our results indicate that the wall degradation starts with a partial attack on pectins (by acetyl esterases, endopolygalacturonases, β-galactosidases and α-arabinofuranosidases) followed by the action of β-glucan-/callose-hydrolysing enzymes. At the same time, there are modifications in arabinoxylan (by α-arabinofuranosidases), xyloglucan (by XTH), xyloglucan-cellulose interactions (by expansins) and partial hydrolysis of cellulose. Saccharification revealed that access to the cell wall varies among segments, consistent with an increase in recalcitrance and composite formation during aerenchyma development. CONCLUSION Our findings corroborate the hypothesis that hydrolases are synchronically synthesized, leading to cell wall modifications that are modulated by the fine structure of cell wall polymers during aerenchyma formation in the cortex of sugarcane roots.
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Affiliation(s)
- Adriana Grandis
- Laboratory of Plant Physiological Ecology (LAFIECO), Department of Botany, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Débora C C Leite
- Laboratory of Plant Physiological Ecology (LAFIECO), Department of Botany, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Eveline Q P Tavares
- Laboratory of Plant Physiological Ecology (LAFIECO), Department of Botany, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Bruna C Arenque-Musa
- Laboratory of Plant Physiological Ecology (LAFIECO), Department of Botany, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Jonas W Gaiarsa
- GaTE Lab, Department of Botany, Institute of Bioscience, University of São Paulo, São Paulo, Brazil
| | - Marina C M Martins
- Laboratory of Plant Physiological Ecology (LAFIECO), Department of Botany, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Amanda P De Souza
- Laboratory of Plant Physiological Ecology (LAFIECO), Department of Botany, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Leonardo D Gomez
- Centre for Novel Agricultural Products, Department of Biology, University of York, UK
| | - Claudia Fabbri
- Department of Biology and Biotechnology ‘C. Darwin’, University of Rome – Sapienza, Italy
| | - Benedetta Mattei
- Department of Biology and Biotechnology ‘C. Darwin’, University of Rome – Sapienza, Italy
- Department of Life, Health and Environmental Sciences, University of L’Aquila, Italy
| | - Marcos S Buckeridge
- Laboratory of Plant Physiological Ecology (LAFIECO), Department of Botany, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
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20
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da Costa RMF, Simister R, Roberts LA, Timms-Taravella E, Cambler AB, Corke FMK, Han J, Ward RJ, Buckeridge MS, Gomez LD, Bosch M. Nutrient and drought stress: implications for phenology and biomass quality in miscanthus. Ann Bot 2019; 124:553-566. [PMID: 30137291 PMCID: PMC6821376 DOI: 10.1093/aob/mcy155] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 07/25/2018] [Indexed: 05/23/2023]
Abstract
BACKGROUND AND AIMS The cultivation of dedicated biomass crops, including miscanthus, on marginal land provides a promising approach to the reduction of dependency on fossil fuels. However, little is known about the impact of environmental stresses often experienced on lower-grade agricultural land on cell-wall quality traits in miscanthus biomass crops. In this study, three different miscanthus genotypes were exposed to drought stress and nutrient stress, both separately and in combination, with the aim of evaluating their impact on plant growth and cell-wall properties. METHODS Automated imaging facilities at the National Plant Phenomics Centre (NPPC-Aberystwyth) were used for dynamic phenotyping to identify plant responses to separate and combinatorial stresses. Harvested leaf and stem samples of the three miscanthus genotypes (Miscanthus sinensis, Miscanthus sacchariflorus and Miscanthus × giganteus) were separately subjected to saccharification assays, to measure sugar release, and cell-wall composition analyses. KEY RESULTS Phenotyping showed that the M. sacchariflorus genotype Sac-5 and particularly the M. sinensis genotype Sin-11 coped better than the M. × giganteus genotype Gig-311 with drought stress when grown in nutrient-poor compost. Sugar release by enzymatic hydrolysis, used as a biomass quality measure, was significantly affected by the different environmental conditions in a stress-, genotype- and organ-dependent manner. A combination of abundant water and low nutrients resulted in the highest sugar release from leaves, while for stems this was generally associated with the combination of drought and nutrient-rich conditions. Cell-wall composition analyses suggest that changes in fine structure of cell-wall polysaccharides, including heteroxylans and pectins, possibly in association with lignin, contribute to the observed differences in cell-wall biomass sugar release. CONCLUSIONS The results highlight the importance of the assessment of miscanthus biomass quality measures in addition to biomass yield determinations and the requirement for selecting suitable miscanthus genotypes for different environmental conditions.
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Affiliation(s)
- Ricardo M F da Costa
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Plas Gogerddan, Aberystwyth, UK
| | - Rachael Simister
- CNAP, Department of Biology, University of York, Heslington, York, UK
| | - Luned A Roberts
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Plas Gogerddan, Aberystwyth, UK
| | - Emma Timms-Taravella
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Plas Gogerddan, Aberystwyth, UK
| | - Arthur B Cambler
- Department of Botany, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Fiona M K Corke
- The National Plant Phenomics Centre, Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Jiwan Han
- The National Plant Phenomics Centre, Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Richard J Ward
- Department of Chemistry, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, University of São Paulo, Ribeirão Preto-SP, Brazil
| | - Marcos S Buckeridge
- Department of Botany, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Leonardo D Gomez
- CNAP, Department of Biology, University of York, Heslington, York, UK
| | - Maurice Bosch
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Plas Gogerddan, Aberystwyth, UK
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21
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Vastano M, Pellis A, Botelho Machado C, Simister R, McQueen‐Mason SJ, Farmer TJ, Gomez LD. Sustainable Galactarate‐Based Polymers: Multi‐Enzymatic Production of Pectin‐Derived Polyesters. Macromol Rapid Commun 2019; 40:e1900361. [DOI: 10.1002/marc.201900361] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 08/30/2019] [Indexed: 11/05/2022]
Affiliation(s)
- Marco Vastano
- Green Chemistry Centre of ExcellenceDepartment of ChemistryUniversity of York Heslington York YO10 5DD UK
| | - Alessandro Pellis
- Green Chemistry Centre of ExcellenceDepartment of ChemistryUniversity of York Heslington York YO10 5DD UK
| | - Carla Botelho Machado
- Centre for Novel Agricultural ProductsDepartment of BiologyUniversity of York Heslington York YO10 5DD UK
| | - Rachael Simister
- Centre for Novel Agricultural ProductsDepartment of BiologyUniversity of York Heslington York YO10 5DD UK
| | - Simon J. McQueen‐Mason
- Centre for Novel Agricultural ProductsDepartment of BiologyUniversity of York Heslington York YO10 5DD UK
| | - Thomas J. Farmer
- Green Chemistry Centre of ExcellenceDepartment of ChemistryUniversity of York Heslington York YO10 5DD UK
| | - Leonardo D. Gomez
- Centre for Novel Agricultural ProductsDepartment of BiologyUniversity of York Heslington York YO10 5DD UK
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22
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Besser K, Malyon GP, Eborall WS, Paro da Cunha G, Filgueiras JG, Dowle A, Cruz Garcia L, Page SJ, Dupree R, Kern M, Gomez LD, Li Y, Elias L, Sabbadin F, Mohamad SE, Pesante G, Steele-King C, Ribeiro de Azevedo E, Polikarpov I, Dupree P, Cragg SM, Bruce NC, McQueen-Mason SJ. Hemocyanin facilitates lignocellulose digestion by wood-boring marine crustaceans. Nat Commun 2018; 9:5125. [PMID: 30510200 PMCID: PMC6277391 DOI: 10.1038/s41467-018-07575-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 11/07/2018] [Indexed: 12/22/2022] Open
Abstract
Woody (lignocellulosic) plant biomass is an abundant renewable feedstock, rich in polysaccharides that are bound into an insoluble fiber composite with lignin. Marine crustacean woodborers of the genus Limnoria are among the few animals that can survive on a diet of this recalcitrant material without relying on gut resident microbiota. Analysis of fecal pellets revealed that Limnoria targets hexose-containing polysaccharides (mainly cellulose, and also glucomannans), corresponding with the abundance of cellulases in their digestive system, but xylans and lignin are largely unconsumed. We show that the limnoriid respiratory protein, hemocyanin, is abundant in the hindgut where wood is digested, that incubation of wood with hemocyanin markedly enhances its digestibility by cellulases, and that it modifies lignin. We propose that this activity of hemocyanins is instrumental to the ability of Limnoria to feed on wood in the absence of gut symbionts. These findings may hold potential for innovations in lignocellulose biorefining.
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Affiliation(s)
- Katrin Besser
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, United Kingdom
| | - Graham P Malyon
- School of Biological Sciences, University of Portsmouth, Portsmouth, PO1 2DY, United Kingdom
| | - William S Eborall
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, United Kingdom
| | - Giovanni Paro da Cunha
- Institute of Physics of São Carlos, University of São Paulo, 13566-590 São Carlos, Brazil
| | - Jefferson G Filgueiras
- Institute of Physics of São Carlos, University of São Paulo, 13566-590 São Carlos, Brazil
| | - Adam Dowle
- Bioscience Technology Facility, Department of Biology, University of York, York, YO10 5DD, United Kingdom
| | - Lourdes Cruz Garcia
- School of Biological Sciences, University of Portsmouth, Portsmouth, PO1 2DY, United Kingdom
| | - Samuel J Page
- Department of Physics, University of Warwick, Coventry, CV4 7AL, United Kingdom
| | - Ray Dupree
- Department of Physics, University of Warwick, Coventry, CV4 7AL, United Kingdom
| | - Marcelo Kern
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, United Kingdom
| | - Leonardo D Gomez
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, United Kingdom
| | - Yi Li
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, United Kingdom
| | - Luisa Elias
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, United Kingdom
| | - Federico Sabbadin
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, United Kingdom
| | - Shaza E Mohamad
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, United Kingdom.,Malaysia Japan International Institute of Technology, University of Technology, Malaysia, 54100, Kuala Lumpur, Malaysia
| | - Giovanna Pesante
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, United Kingdom
| | - Clare Steele-King
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, United Kingdom
| | | | - Igor Polikarpov
- Institute of Physics of São Carlos, University of São Paulo, 13566-590 São Carlos, Brazil
| | - Paul Dupree
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, United Kingdom
| | - Simon M Cragg
- School of Biological Sciences, University of Portsmouth, Portsmouth, PO1 2DY, United Kingdom
| | - Neil C Bruce
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, United Kingdom.
| | - Simon J McQueen-Mason
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, United Kingdom.
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23
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Rezende CA, Atta BW, Breitkreitz MC, Simister R, Gomez LD, McQueen-Mason SJ. Optimization of biomass pretreatments using fractional factorial experimental design. Biotechnol Biofuels 2018; 11:206. [PMID: 30061928 PMCID: PMC6058377 DOI: 10.1186/s13068-018-1200-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 07/07/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Pretreatments are one of the main bottlenecks for the lignocellulose conversion process and the search for cheaper and effective pretreatment methodologies for each biomass is a complex but fundamental task. Here, we used a 2ν5-1 fractional factorial design (FFD) to optimize five pretreatment variables: milling time, temperature, double treatment, chemical concentration, and pretreatment time in acid-alkali (EA) and acid-organosolv (EO) pretreatments, applied to elephant grass leaves. RESULTS FFD allowed optimization of the pretreatment conditions using a reduced number of experiments and allowed the identification of secondary interactions between the factors. FFD showed that the temperature can be kept at its lower level and that the first acid step can be eliminated in both pretreatments, without significant losses to enzymatic hydrolysis. EA resulted in the highest release of reducing sugars (maximum of 205 mg/g substrate in comparison to 152 mg/g in EO and 40 mg/g in the untreated sample), using the following conditions in the alkali step: [NaOH] = 4.5% w/v; 85 °C and 100 min after ball milling the sample. The factors statistically significant (P < 0.05) in EA pretreatment were NaOH concentration, which contributes to improved hydrolysis by lignin and silica removal, and the milling time, which has a mechanical effect. For EO samples, the statistically significant factors to improved hydrolysis were ethanol and catalyst concentrations, which are both correlated to higher cellulose amounts in the pretreated substrates. The catalyst is also correlated to lignin removal. The detailed characterization of the main hemicellulosic sugars in the solids after pretreatments revealed their distinct recalcitrance: glucose was typically more recalcitrant than xylose and arabinose, which could be almost completely removed under specific pretreatments. In EA samples, the removal of hemicellulose derivatives was very dependent on the acid step, especially arabinose removal. CONCLUSION The results presented herewith contribute to the development of more efficient and viable pretreatments to produce cellulosic ethanol from grass biomasses, saving time, costs and energy. They also facilitate the design of enzymatic cocktails and a more appropriate use of the sugars contained in the pretreatment liquors, by establishing the key recalcitrant polymers in the solids resulting from each processing step.
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Affiliation(s)
- Camila A. Rezende
- Institute of Chemistry, University of Campinas-UNICAMP, P.O. Box 6154, Campinas, SP 13083-970 Brazil
| | - Beatriz W. Atta
- Institute of Chemistry, University of Campinas-UNICAMP, P.O. Box 6154, Campinas, SP 13083-970 Brazil
| | - Marcia C. Breitkreitz
- Institute of Chemistry, University of Campinas-UNICAMP, P.O. Box 6154, Campinas, SP 13083-970 Brazil
| | - Rachael Simister
- Centre for Novel Agricultural Products-CNAP, University of York, Heslington, York, YO10 5YW UK
| | - Leonardo D. Gomez
- Centre for Novel Agricultural Products-CNAP, University of York, Heslington, York, YO10 5YW UK
| | - Simon J. McQueen-Mason
- Centre for Novel Agricultural Products-CNAP, University of York, Heslington, York, YO10 5YW UK
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24
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Whitehead C, Ostos Garrido FJ, Reymond M, Simister R, Distelfeld A, Atienza SG, Piston F, Gomez LD, McQueen‐Mason SJ. A glycosyl transferase family 43 protein involved in xylan biosynthesis is associated with straw digestibility in Brachypodium distachyon. New Phytol 2018; 218:974-985. [PMID: 29574807 PMCID: PMC5947151 DOI: 10.1111/nph.15089] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 02/05/2018] [Indexed: 05/27/2023]
Abstract
The recalcitrance of secondary plant cell walls to digestion constrains biomass use for the production of sustainable bioproducts and for animal feed. We screened a population of Brachypodium recombinant inbred lines (RILs) for cell wall digestibility using commercial cellulases and detected a quantitative trait locus (QTL) associated with this trait. Examination of the chromosomal region associated with this QTL revealed a candidate gene that encodes a putative glycosyl transferase family (GT) 43 protein, orthologue of IRX14 in Arabidopsis, and hence predicted to be involved in the biosynthesis of xylan. Arabinoxylans form the major matrix polysaccharides in cell walls of grasses, such as Brachypodium. The parental lines of the RIL population carry alternative nonsynonymous polymorphisms in the BdGT43A gene, which were inherited in the RIL progeny in a manner compatible with a causative role in the variation in straw digestibility. In order to validate the implied role of our candidate gene in affecting straw digestibility, we used RNA interference to lower the expression levels of the BdGT43A gene in Brachypodium. The biomass of the silenced lines showed higher digestibility supporting a causative role of the BdGT43A gene, suggesting that it might form a good target for improving straw digestibility in crops.
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Affiliation(s)
- Caragh Whitehead
- Centre for Novel Agricultural ProductsDepartment of BiologyUniversity of YorkPO Box 373Wentworth WayYorkYO10 5DDUK
| | - Francisco J. Ostos Garrido
- Departamento de Mejora Genética VegetalInstituto de Agricultura Sostenible – Consejo Superior de Investigaciones CientíficasCórdobaSpain
| | - Matthieu Reymond
- Institut Jean‐Pierre BourginUMR 1318 INRA‐AgroParisTechINRA Centre de Versailles‐GrignonRoute de Saint‐Cyr78026VersaillesFrance
| | - Rachael Simister
- Centre for Novel Agricultural ProductsDepartment of BiologyUniversity of YorkPO Box 373Wentworth WayYorkYO10 5DDUK
| | - Assaf Distelfeld
- Deparment of Molecular Biology and Ecology of PlantsTel Aviv UniversityTel AvivIsrael
| | - Sergio G. Atienza
- Departamento de Mejora Genética VegetalInstituto de Agricultura Sostenible – Consejo Superior de Investigaciones CientíficasCórdobaSpain
| | - Fernando Piston
- Departamento de Mejora Genética VegetalInstituto de Agricultura Sostenible – Consejo Superior de Investigaciones CientíficasCórdobaSpain
| | - Leonardo D. Gomez
- Centre for Novel Agricultural ProductsDepartment of BiologyUniversity of YorkPO Box 373Wentworth WayYorkYO10 5DDUK
| | - Simon J. McQueen‐Mason
- Centre for Novel Agricultural ProductsDepartment of BiologyUniversity of YorkPO Box 373Wentworth WayYorkYO10 5DDUK
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25
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Bhatia R, Gallagher JA, Gomez LD, Bosch M. Genetic engineering of grass cell wall polysaccharides for biorefining. Plant Biotechnol J 2017; 15:1071-1092. [PMID: 28557198 PMCID: PMC5552484 DOI: 10.1111/pbi.12764] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 05/17/2017] [Accepted: 05/24/2017] [Indexed: 05/10/2023]
Abstract
Grasses represent an abundant and widespread source of lignocellulosic biomass, which has yet to fulfil its potential as a feedstock for biorefining into renewable and sustainable biofuels and commodity chemicals. The inherent recalcitrance of lignocellulosic materials to deconstruction is the most crucial limitation for the commercial viability and economic feasibility of biomass biorefining. Over the last decade, the targeted genetic engineering of grasses has become more proficient, enabling rational approaches to modify lignocellulose with the aim of making it more amenable to bioconversion. In this review, we provide an overview of transgenic strategies and targets to tailor grass cell wall polysaccharides for biorefining applications. The bioengineering efforts and opportunities summarized here rely primarily on (A) reprogramming gene regulatory networks responsible for the biosynthesis of lignocellulose, (B) remodelling the chemical structure and substitution patterns of cell wall polysaccharides and (C) expressing lignocellulose degrading and/or modifying enzymes in planta. It is anticipated that outputs from the rational engineering of grass cell wall polysaccharides by such strategies could help in realizing an economically sustainable, grass-derived lignocellulose processing industry.
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Affiliation(s)
- Rakesh Bhatia
- Institute of Biological, Environmental and Rural Sciences (IBERS)Aberystwyth UniversityAberystwythUK
| | - Joe A. Gallagher
- Institute of Biological, Environmental and Rural Sciences (IBERS)Aberystwyth UniversityAberystwythUK
| | | | - Maurice Bosch
- Institute of Biological, Environmental and Rural Sciences (IBERS)Aberystwyth UniversityAberystwythUK
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26
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van der Weijde T, Kamei CLA, Severing EI, Torres AF, Gomez LD, Dolstra O, Maliepaard CA, McQueen-Mason SJ, Visser RGF, Trindade LM. Genetic complexity of miscanthus cell wall composition and biomass quality for biofuels. BMC Genomics 2017; 18:406. [PMID: 28545405 PMCID: PMC5445440 DOI: 10.1186/s12864-017-3802-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [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: 02/01/2017] [Accepted: 05/17/2017] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Miscanthus sinensis is a high yielding perennial grass species with great potential as a bioenergy feedstock. One of the challenges that currently impedes commercial cellulosic biofuel production is the technical difficulty to efficiently convert lignocellulosic biomass into biofuel. The development of feedstocks with better biomass quality will improve conversion efficiency and the sustainability of the value-chain. Progress in the genetic improvement of biomass quality may be substantially expedited by the development of genetic markers associated to quality traits, which can be used in a marker-assisted selection program. RESULTS To this end, a mapping population was developed by crossing two parents of contrasting cell wall composition. The performance of 182 F1 offspring individuals along with the parents was evaluated in a field trial with a randomized block design with three replicates. Plants were phenotyped for cell wall composition and conversion efficiency characters in the second and third growth season after establishment. A new SNP-based genetic map for M. sinensis was built using a genotyping-by-sequencing (GBS) approach, which resulted in 464 short-sequence uniparental markers that formed 16 linkage groups in the male map and 17 linkage groups in the female map. A total of 86 QTLs for a variety of biomass quality characteristics were identified, 20 of which were detected in both growth seasons. Twenty QTLs were directly associated to different conversion efficiency characters. Marker sequences were aligned to the sorghum reference genome to facilitate cross-species comparisons. Analyses revealed that for some traits previously identified QTLs in sorghum occurred in homologous regions on the same chromosome. CONCLUSION In this work we report for the first time the genetic mapping of cell wall composition and bioconversion traits in the bioenergy crop miscanthus. These results are a first step towards the development of marker-assisted selection programs in miscanthus to improve biomass quality and facilitate its use as feedstock for biofuel production.
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Affiliation(s)
- Tim van der Weijde
- Wageningen UR Plant Breeding, Wageningen University and Research, PO Box 386, 6700 AJ, Wageningen, Netherlands.,Graduate School Experimental Plant Sciences, Wageningen University, 6708 PB, Wageningen, Netherlands.,Present address: Research, Barenbrug Holland B.V, Duitsekampweg 60, 6748 ZB, Wolfheze, Netherlands
| | - Claire L Alvim Kamei
- Wageningen UR Plant Breeding, Wageningen University and Research, PO Box 386, 6700 AJ, Wageningen, Netherlands.,Present address: Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Edouard I Severing
- Wageningen UR Plant Breeding, Wageningen University and Research, PO Box 386, 6700 AJ, Wageningen, Netherlands.,Present address: Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Andres F Torres
- Wageningen UR Plant Breeding, Wageningen University and Research, PO Box 386, 6700 AJ, Wageningen, Netherlands
| | - Leonardo D Gomez
- Center for Novel Agricultural Products, University of York, YO10 5 DD, York, UK
| | - Oene Dolstra
- Wageningen UR Plant Breeding, Wageningen University and Research, PO Box 386, 6700 AJ, Wageningen, Netherlands
| | - Chris A Maliepaard
- Wageningen UR Plant Breeding, Wageningen University and Research, PO Box 386, 6700 AJ, Wageningen, Netherlands
| | | | - Richard G F Visser
- Wageningen UR Plant Breeding, Wageningen University and Research, PO Box 386, 6700 AJ, Wageningen, Netherlands
| | - Luisa M Trindade
- Wageningen UR Plant Breeding, Wageningen University and Research, PO Box 386, 6700 AJ, Wageningen, Netherlands.
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Caruso G, Gomez LD, Ferriello F, Andolfi A, Borgonuovo C, Evidente A, Simister R, McQueen-Mason SJ, Carputo D, Frusciante L, Ercolano MR. Exploring tomato Solanum pennellii introgression lines for residual biomass and enzymatic digestibility traits. BMC Genet 2016; 17:56. [PMID: 27044251 PMCID: PMC4820949 DOI: 10.1186/s12863-016-0362-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [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: 10/09/2015] [Accepted: 03/17/2016] [Indexed: 01/09/2023] Open
Abstract
Background Residual biomass production for fuel conversion represents a unique opportunity to avoid concerns about compromising food supply by using dedicated feedstock crops. Developing tomato varieties suitable for both food consumption and fuel conversion requires the establishment of new selection methods. Results A tomato Solanum pennellii introgression population was assessed for fruit yield, biomass phenotypic diversity, and for saccharification potential. Introgression lines 2–5, 2–6, 6–3, 7–2, 10–2 and 12–4 showed the best combination of fruit and residual biomass production. Lignin, cellulose, hemicellulose content and saccharification rate showed a wide variation in the tested lines. Within hemicellulose, xylose value was high in IL 6–3, IL 7–2 and IL 6–2, whereas arabinose showed a low content in IL 10–2, IL 6–3 and IL 2–6. The latter line showed also the highest ethanol potential production. Alkali pre-treatment resulted in the highest values of saccharification in most of lines tested, suggesting that chemical pretreatment is an important factor for improving biomass processability. Interestingly, extreme genotypes for more than one single trait were found, allowing the identification of better genotypes. Cell wall related genes mapping in genomic regions involved into tomato biomass production and digestibility variation highlighted potential candidate genes. Molecular expression profile of few of them provided useful information about challenged pathways. Conclusions The screening of S. pennellii introgression population resulted very useful for delving into complex traits such as biomass production and digestibility. The extreme genotypes identified could be fruitfully employed for both genetic studies and breeding. Electronic supplementary material The online version of this article (doi:10.1186/s12863-016-0362-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- G Caruso
- Department of Agricultural Sciences, University of Naples 'Federico II', via Università 133, 80055, Portici, Italy
| | - L D Gomez
- Department of Biology, Center for Novel Agricultural Products, University of York, Heslington, York, YO10 5DD, UK.
| | - F Ferriello
- Department of Agricultural Sciences, University of Naples 'Federico II', via Università 133, 80055, Portici, Italy
| | - A Andolfi
- Department of Chemical Sciences, University of Naples Federico II, via Cinthia 4, 80126, Naples, Italy
| | - C Borgonuovo
- Department of Agricultural Sciences, University of Naples 'Federico II', via Università 133, 80055, Portici, Italy
| | - A Evidente
- Department of Chemical Sciences, University of Naples Federico II, via Cinthia 4, 80126, Naples, Italy
| | - R Simister
- Department of Biology, Center for Novel Agricultural Products, University of York, Heslington, York, YO10 5DD, UK
| | - S J McQueen-Mason
- Department of Biology, Center for Novel Agricultural Products, University of York, Heslington, York, YO10 5DD, UK
| | - D Carputo
- Department of Agricultural Sciences, University of Naples 'Federico II', via Università 133, 80055, Portici, Italy
| | - L Frusciante
- Department of Agricultural Sciences, University of Naples 'Federico II', via Università 133, 80055, Portici, Italy
| | - M R Ercolano
- Department of Agricultural Sciences, University of Naples 'Federico II', via Università 133, 80055, Portici, Italy.
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Zhu Z, Macquarrie DJ, Simister R, Gomez LD, McQueen-Mason SJ. Microwave assisted chemical pretreatment of Miscanthus under different temperature regimes. ACTA ACUST UNITED AC 2015. [DOI: 10.1186/s40508-015-0041-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Attard TM, Theeuwes E, Gomez LD, Johansson E, Dimitriou I, Wright PC, Clark JH, McQueen-Mason SJ, Hunt AJ. Supercritical extraction as an effective first-step in a maize stover biorefinery. RSC Adv 2015. [DOI: 10.1039/c5ra07485a] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Supercritical carbon dioxide (scCO2) extraction has been investigated for the generation of valuable waxy compounds and as an added-value technology in a holistic maize stover biorefinery.
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Affiliation(s)
| | | | | | - Emma Johansson
- SP Processum AB
- SP Technical Research Institute of Sweden Box 70
- Örnsköldsvik
- Sweden
| | - Ioanna Dimitriou
- Department of Chemical and Biological Engineering
- The University of Sheffield
- Sheffield
- UK
| | - Phillip C. Wright
- Department of Chemical and Biological Engineering
- The University of Sheffield
- Sheffield
- UK
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Zhu Z, Simister R, Bird S, J. McQueen-Mason S, D. Gomez L, J. Macquarrie D. Microwave assisted acid and alkali pretreatment of Miscanthus biomas s for biorefineries. AIMS Bioengineering 2015. [DOI: 10.3934/bioeng.2015.4.449] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Lima MA, Gomez LD, Steele-King CG, Simister R, Bernardinelli OD, Carvalho MA, Rezende CA, Labate CA, deAzevedo ER, McQueen-Mason SJ, Polikarpov I. Evaluating the composition and processing potential of novel sources of Brazilian biomass for sustainable biorenewables production. Biotechnol Biofuels 2014; 7:10. [PMID: 24438499 PMCID: PMC4028816 DOI: 10.1186/1754-6834-7-10] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Accepted: 12/06/2013] [Indexed: 05/04/2023]
Abstract
BACKGROUND The search for promising and renewable sources of carbohydrates for the production of biofuels and other biorenewables has been stimulated by an increase in global energy demand in the face of growing concern over greenhouse gas emissions and fuel security. In particular, interest has focused on non-food lignocellulosic biomass as a potential source of abundant and sustainable feedstock for biorefineries. Here we investigate the potential of three Brazilian grasses (Panicum maximum, Pennisetum purpureum and Brachiaria brizantha), as well as bark residues from the harvesting of two commercial Eucalyptus clones (E. grandis and E. grandis x urophylla) for biofuel production, and compare these to sugarcane bagasse. The effects of hot water, acid, alkaline and sulfite pretreatments (at increasing temperatures) on the chemical composition, morphology and saccharification yields of these different biomass types were evaluated. RESULTS The average yield (per hectare), availability and general composition of all five biomasses were compared. Compositional analyses indicate a high level of hemicellulose and lignin removal in all grass varieties (including sugarcane bagasse) after acid and alkaline pretreatment with increasing temperatures, whilst the biomasses pretreated with hot water or sulfite showed little variation from the control. For all biomasses, higher cellulose enrichment resulted from treatment with sodium hydroxide at 130°C. At 180°C, a decrease in cellulose content was observed, which is associated with high amorphous cellulose removal and 5-hydroxymethyl-furaldehyde production. Morphological analysis showed the effects of different pretreatments on the biomass surface, revealing a high production of microfibrillated cellulose on grass surfaces, after treatment with 1% sodium hydroxide at 130°C for 30 minutes. This may explain the higher hydrolysis yields resulting from these pretreatments, since these cellulosic nanoparticles can be easily accessed and cleaved by cellulases. CONCLUSION Our results show the potential of three Brazilian grasses with high productivity yields as valuable sources of carbohydrates for ethanol production and other biomaterials. Sodium hydroxide at 130°C was found to be the most effective pretreatment for enhanced saccharification yields. It was also efficient in the production of microfibrillated cellulose on grass surfaces, thereby revealing their potential as a source of natural fillers used for bionanocomposites production.
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Affiliation(s)
- Marisa A Lima
- Instituto de Física de São Carlos, Universidade de São Paulo, Caixa Postal 369, São Carlos SP 13560-970, Brazil
| | - Leonardo D Gomez
- CNAP, Department of Biology, University of York, York, Heslington YO10 5DD, UK
| | - Clare G Steele-King
- CNAP, Department of Biology, University of York, York, Heslington YO10 5DD, UK
| | - Rachael Simister
- CNAP, Department of Biology, University of York, York, Heslington YO10 5DD, UK
| | - Oigres D Bernardinelli
- Instituto de Física de São Carlos, Universidade de São Paulo, Caixa Postal 369, São Carlos SP 13560-970, Brazil
| | - Marcelo A Carvalho
- Embrapa Cerrados, Genética e Melhoramento de Forrageiras, Br 020, Km 18 – Cx. P. 08223, Planaltina DF 73301-970, Brazil
| | - Camila A Rezende
- Instituto de Química, Universidade de Campinas, Caixa Postal 6154, Campinas SP 13083-970, Brazil
| | - Carlos A Labate
- Laboratório Max Feffer de Genética de Plantas, Departamento de Genética -ESALQ, Universidade de São Paulo, Caixa Postal 83, Piracicaba SP 13418-900, Brazil
- Centro Nacional de Pesquisa em Energia e Materiais, Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Campinas, SP, Brazil
| | - Eduardo R deAzevedo
- Instituto de Física de São Carlos, Universidade de São Paulo, Caixa Postal 369, São Carlos SP 13560-970, Brazil
| | | | - Igor Polikarpov
- Instituto de Física de São Carlos, Universidade de São Paulo, Caixa Postal 369, São Carlos SP 13560-970, Brazil
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Oakey H, Shafiei R, Comadran J, Uzrek N, Cullis B, Gomez LD, Whitehead C, McQueen-Mason SJ, Waugh R, Halpin C. Identification of crop cultivars with consistently high lignocellulosic sugar release requires the use of appropriate statistical design and modelling. Biotechnol Biofuels 2013; 6:185. [PMID: 24359577 PMCID: PMC3878416 DOI: 10.1186/1754-6834-6-185] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 12/06/2013] [Indexed: 05/09/2023]
Abstract
BACKGROUND In this study, a multi-parent population of barley cultivars was grown in the field for two consecutive years and then straw saccharification (sugar release by enzymes) was subsequently analysed in the laboratory to identify the cultivars with the highest consistent sugar yield. This experiment was used to assess the benefit of accounting for both the multi-phase and multi-environment aspects of large-scale phenotyping experiments with field-grown germplasm through sound statistical design and analysis. RESULTS Complementary designs at both the field and laboratory phases of the experiment ensured that non-genetic sources of variation could be separated from the genetic variation of cultivars, which was the main target of the study. The field phase included biological replication and plot randomisation. The laboratory phase employed re-randomisation and technical replication of samples within a batch, with a subset of cultivars chosen as duplicates that were randomly allocated across batches. The resulting data was analysed using a linear mixed model that incorporated field and laboratory variation and a cultivar by trial interaction, and ensured that the cultivar means were more accurately represented than if the non-genetic variation was ignored. The heritability detected was more than doubled in each year of the trial by accounting for the non-genetic variation in the analysis, clearly showing the benefit of this design and approach. CONCLUSIONS The importance of accounting for both field and laboratory variation, as well as the cultivar by trial interaction, by fitting a single statistical model (multi-environment trial, MET, model), was evidenced by the changes in list of the top 40 cultivars showing the highest sugar yields. Failure to account for this interaction resulted in only eight cultivars that were consistently in the top 40 in different years. The correspondence between the rankings of cultivars was much higher at 25 in the MET model. This approach is suited to any multi-phase and multi-environment population-based genetic experiment.
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Affiliation(s)
- Helena Oakey
- Division of Plant Sciences, College of Life Sciences, University of Dundee at The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Reza Shafiei
- Division of Plant Sciences, College of Life Sciences, University of Dundee at The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Jordi Comadran
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA Scotland, UK
| | - Nicola Uzrek
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA Scotland, UK
| | - Brian Cullis
- National Institute for Applied Statistics Research Australia, University of Wollongong, Wollongong, NSW 2522, Australia
- Computational Informatics, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Canberra, ACT 2600, Australia
| | - Leonardo D Gomez
- Biology Department, Centre for Novel Agricultural Products (CNAP), University of York, Wentworth Way, York YO10 5DD, UK
| | - Caragh Whitehead
- Biology Department, Centre for Novel Agricultural Products (CNAP), University of York, Wentworth Way, York YO10 5DD, UK
| | - Simon J McQueen-Mason
- Biology Department, Centre for Novel Agricultural Products (CNAP), University of York, Wentworth Way, York YO10 5DD, UK
| | - Robbie Waugh
- Division of Plant Sciences, College of Life Sciences, University of Dundee at The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA Scotland, UK
| | - Claire Halpin
- Division of Plant Sciences, College of Life Sciences, University of Dundee at The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
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Lima MA, Lavorente GB, da Silva HKP, Bragatto J, Rezende CA, Bernardinelli OD, deAzevedo ER, Gomez LD, McQueen-Mason SJ, Labate CA, Polikarpov I. Effects of pretreatment on morphology, chemical composition and enzymatic digestibility of eucalyptus bark: a potentially valuable source of fermentable sugars for biofuel production - part 1. Biotechnol Biofuels 2013; 6:75. [PMID: 23657132 PMCID: PMC3667114 DOI: 10.1186/1754-6834-6-75] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Accepted: 04/26/2013] [Indexed: 05/04/2023]
Abstract
BACKGROUND In recent years, the growing demand for biofuels has encouraged the search for different sources of underutilized lignocellulosic feedstocks that are available in sufficient abundance to be used for sustainable biofuel production. Much attention has been focused on biomass from grass. However, large amounts of timber residues such as eucalyptus bark are available and represent a potential source for conversion to bioethanol. In the present paper, we investigate the effects of a delignification process with increasing sodium hydroxide concentrations, preceded or not by diluted acid, on the bark of two eucalyptus clones: Eucalyptus grandis (EG) and the hybrid, E. grandis x urophylla (HGU). The enzymatic digestibility and total cellulose conversion were measured, along with the effect on the composition of the solid and the liquor fractions. Barks were also assessed using Fourier-transform infrared spectroscopy (FTIR), solid-state nuclear magnetic resonance (NMR), X-Ray diffraction, and scanning electron microscopy (SEM). RESULTS Compositional analysis revealed an increase in the cellulose content, reaching around 81% and 76% of glucose for HGU and EG, respectively, using a two-step treatment with HCl 1%, followed by 4% NaOH. Lignin removal was 84% (HGU) and 79% (EG), while the hemicellulose removal was 95% and 97% for HGU and EG, respectively. However, when we applied a one-step treatment, with 4% NaOH, higher hydrolysis efficiencies were found after 48 h for both clones, reaching almost 100% for HGU and 80% for EG, in spite of the lower lignin and hemicellulose removal. Total cellulose conversion increased from 5% and 7% to around 65% for HGU and 59% for EG. NMR and FTIR provided important insight into the lignin and hemicellulose removal and SEM studies shed light on the cell-wall unstructuring after pretreatment and lignin migration and precipitation on the fibers surface, which explain the different hydrolysis rates found for the clones. CONCLUSION Our results show that the single step alkaline pretreatment improves the enzymatic digestibility of Eucalyptus bark. Furthermore, the chemical and physical methods combined in this study provide a better comprehension of the pretreatment effects on cell-wall and the factors that influence enzymatic digestibility of this forest residue.
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Affiliation(s)
- Marisa A Lima
- Instituto de Física de São Carlos, Universidade de São Paulo, Caixa Postal 369, 13560-970, São Carlos, SP, Brazil
| | - Gabriela B Lavorente
- Laboratório Max Feffer de Genética de Plantas, Departamento de Genética - ESALQ, Universidade de São Paulo, Caixa Postal 83, 13418-900, Piracicaba, SP, Brazil
| | - Hana KP da Silva
- Laboratório Max Feffer de Genética de Plantas, Departamento de Genética - ESALQ, Universidade de São Paulo, Caixa Postal 83, 13418-900, Piracicaba, SP, Brazil
| | - Juliano Bragatto
- Laboratório Max Feffer de Genética de Plantas, Departamento de Genética - ESALQ, Universidade de São Paulo, Caixa Postal 83, 13418-900, Piracicaba, SP, Brazil
| | - Camila A Rezende
- Instituto de Física de São Carlos, Universidade de São Paulo, Caixa Postal 369, 13560-970, São Carlos, SP, Brazil
| | - Oigres D Bernardinelli
- Instituto de Física de São Carlos, Universidade de São Paulo, Caixa Postal 369, 13560-970, São Carlos, SP, Brazil
| | - Eduardo R deAzevedo
- Instituto de Física de São Carlos, Universidade de São Paulo, Caixa Postal 369, 13560-970, São Carlos, SP, Brazil
| | - Leonardo D Gomez
- CNAP, Department of Biology, University of York, Heslington, York YO10 5YW, UK
| | | | - Carlos A Labate
- Laboratório Max Feffer de Genética de Plantas, Departamento de Genética - ESALQ, Universidade de São Paulo, Caixa Postal 83, 13418-900, Piracicaba, SP, Brazil
| | - Igor Polikarpov
- Instituto de Física de São Carlos, Universidade de São Paulo, Caixa Postal 369, 13560-970, São Carlos, SP, Brazil
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Comont D, Winters A, Gomez LD, McQueen-Mason SJ, Gwynn-Jones D. Latitudinal variation in ambient UV-B radiation is an important determinant of Lolium perenne forage production, quality, and digestibility. J Exp Bot 2013; 64:2193-2204. [PMID: 23580749 PMCID: PMC3654412 DOI: 10.1093/jxb/ert077] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Few studies to date have considered the responses of agriculturally important forage grasses to UV-B radiation. Yet grasses such as Lolium perenne have a wide current distribution, representing exposure to a significant variation in ambient UV-B. The current study investigated the responses of L. perenne (cv. AberDart) to a simulated latitudinal gradient of UV-B exposure, representing biologically effective UV-B doses at simulated 70, 60, 50, 40, and 30° N latitudes. Aspects of growth, soluble compounds, and digestibility were assessed, and results are discussed in relation to UV-B effects on forage properties and the implications for livestock and bio-ethanol production. Aboveground biomass production was reduced by approximately 12.67% with every 1 kJ m(-2) day(-1) increase in biologically weighted UV-B. As a result, plants grown in the highest UV-B treatment had a total biomass of just 13.7% of controls. Total flavonoids were increased by approximately 76% by all UV-B treatments, while hydroxycinnamic acids increased in proportion to the UV-B dose. Conversely, the digestibility of the aboveground biomass and concentrations of soluble fructans were reduced by UV-B exposure, although soluble sucrose, glucose, and fructose concentrations were unaffected. These results highlight the capacity for UV-B to directly affect forage productivity and chemistry, with negative consequences for digestibility and bioethanol production. Results emphasize the need for future development and distribution of L. perenne varieties to take UV-B irradiance into consideration.
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Affiliation(s)
- David Comont
- Institute of Biological Environmental and Rural Sciences, Aberystwyth University, Ceredigion, SY23 3DA, Wales, UK
| | - Ana Winters
- Institute of Biological Environmental and Rural Sciences, Aberystwyth University, Ceredigion, SY23 3DA, Wales, UK
| | - Leonardo D Gomez
- CNAP, Biology Department, University of York, Heslington, York, YO10 5DD, UK
| | | | - Dylan Gwynn-Jones
- Institute of Biological Environmental and Rural Sciences, Aberystwyth University, Ceredigion, SY23 3DA, Wales, UK
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Bouvier d'Yvoire M, Bouchabke-Coussa O, Voorend W, Antelme S, Cézard L, Legée F, Lebris P, Legay S, Whitehead C, McQueen-Mason SJ, Gomez LD, Jouanin L, Lapierre C, Sibout R. Disrupting the cinnamyl alcohol dehydrogenase 1 gene (BdCAD1) leads to altered lignification and improved saccharification in Brachypodium distachyon. Plant J 2013; 73:496-508. [PMID: 23078216 DOI: 10.1111/tpj.12053] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Revised: 10/09/2012] [Accepted: 10/12/2012] [Indexed: 05/17/2023]
Abstract
Brachypodium distachyon (Brachypodium) has been proposed as a model for grasses, but there is limited knowledge regarding its lignins and no data on lignin-related mutants. The cinnamyl alcohol dehydrogenase (CAD) genes involved in lignification are promising targets to improve the cellulose-to-ethanol conversion process. Down-regulation of CAD often induces a reddish coloration of lignified tissues. Based on this observation, we screened a chemically induced population of Brachypodium mutants (Bd21-3 background) for red culm coloration. We identified two mutants (Bd4179 and Bd7591), with mutations in the BdCAD1 gene. The mature stems of these mutants displayed reduced CAD activity and lower lignin content. Their lignins were enriched in 8-O-4- and 4-O-5-coupled sinapaldehyde units, as well as resistant inter-unit bonds and free phenolic groups. By contrast, there was no increase in coniferaldehyde end groups. Moreover, the amount of sinapic acid ester-linked to cell walls was measured for the first time in a lignin-related CAD grass mutant. Functional complementation of the Bd4179 mutant with the wild-type BdCAD1 allele restored the wild-type phenotype and lignification. Saccharification assays revealed that Bd4179 and Bd7591 lines were more susceptible to enzymatic hydrolysis than wild-type plants. Here, we have demonstrated that BdCAD1 is involved in lignification of Brachypodium. We have shown that a single nucleotide change in BdCAD1 reduces the lignin level and increases the degree of branching of lignins through incorporation of sinapaldehyde. These changes make saccharification of cells walls pre-treated with alkaline easier without compromising plant growth.
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Affiliation(s)
- Madeleine Bouvier d'Yvoire
- Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318 INRA-AgroParisTech, Institut National de la Recherche Agronomique Centre de Versailles-Grignon, Route de St Cyr (RD10), 78026, Versailles, France
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Vuttipongchaikij S, Brocklehurst D, Steele-King C, Ashford DA, Gomez LD, McQueen-Mason SJ. Arabidopsis GT34 family contains five xyloglucan α-1,6-xylosyltransferases. New Phytol 2012; 195:585-595. [PMID: 22670626 DOI: 10.1111/j.1469-8137.2012.04196.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The Arabidopsis genome includes seven family 34 glycosyltransferase (GT34) encoding genes. XXT1 and XXT2 have previously been shown to encode XyG α-1,6-xylosyltransferases, while knockout mutants of a third, XXT5, exhibit decreased XyG content, suggesting a similar activity. Here, we extend the study to the rest of the Arabidopsis GT34 genes in terms of biochemical activity and their roles in XyG biosynthesis. The enzyme activity of XXTs was investigated using recombinant protein expressed in E. coli. XyG analysis of single and double T-DNA insertion knockouts, together with overexpression of GT34s in selected mutant lines, provided detailed function of each gene. We reveal the activity of the third member of the GT34 gene family (XXT4) that exhibits xylosyltransferase activity. Double mutants for either xxt2 or xxt5 had a large impact on XyG content, structure and size distribution. Overexpression of the remaining member, XXT3, was able to restore XyG epitopes in xxt2, xxt5 and xxt2 xxt5 double knockouts, suggesting that it also encodes a protein with XXT activity. Our work demonstrates that five of the seven Arabidopsis GT34 genes encode XXT enzymes.
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Affiliation(s)
- Supachai Vuttipongchaikij
- Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Road, Chatuchak, Bangkok 10900, Thailand
- Center for Advanced Studies in Tropical Natural Resources, Kasetsart University, Ngam Wong Wan, Chatuchak, Bangkok 10900, Thailand
| | - David Brocklehurst
- CNAP, Biology Department, University of York, Heslington, York YO10 5DD, UK
| | - Clare Steele-King
- CNAP, Biology Department, University of York, Heslington, York YO10 5DD, UK
| | - David A Ashford
- CNAP, Biology Department, University of York, Heslington, York YO10 5DD, UK
| | - Leonardo D Gomez
- CNAP, Biology Department, University of York, Heslington, York YO10 5DD, UK
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Abstract
Polysaccharides that make up plant lignocellulosic biomass can be broken down to produce a range of sugars that subsequently can be used in establishing a biorefinery. These raw materials would constitute a new industrial platform, which is both sustainable and carbon neutral, to replace the current dependency on fossil fuel. The recalcitrance to deconstruction observed in lignocellulosic materials is produced by several intrinsic properties of plant cell walls. Crystalline cellulose is embedded in matrix polysaccharides such as xylans and arabinoxylans, and the whole structure is encased by the phenolic polymer lignin, that is also difficult to digest 1. In order to improve the digestibility of plant materials we need to discover the main bottlenecks for the saccharification of cell walls and also screen mutant and breeding populations to evaluate the variability in saccharification 2. These tasks require a high throughput approach and here we present an analytical platform that can perform saccharification analysis in a 96-well plate format. This platform has been developed to allow the screening of lignocellulose digestibility of large populations from varied plant species. We have scaled down the reaction volumes for gentle pretreatment, partial enzymatic hydrolysis and sugar determination, to allow large numbers to be assessed rapidly in an automated system. This automated platform works with milligram amounts of biomass, performing ball milling under controlled conditions to reduce the plant materials to a standardised particle size in a reproducible manner. Once the samples are ground, the automated formatting robot dispenses specified and recorded amounts of material into the corresponding wells of 96 deep well plate (Figure 1). Normally, we dispense the same material into 4 wells to have 4 replicates for analysis. Once the plates are filled with the plant material in the desired layout, they are manually moved to a liquid handling station (Figure 2). In this station the samples are subjected to a mild pretreatment with either dilute acid or alkaline and incubated at temperatures of up to 90°C. The pretreatment solution is subsequently removed and the samples are rinsed with buffer to return them to a suitable pH for hydrolysis. The samples are then incubated with an enzyme mixture for a variable length of time at 50°C. An aliquot is taken from the hydrolyzate and the reducing sugars are automatically determined by the MBTH colorimetric method.
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Brown D, Wightman R, Zhang Z, Gomez LD, Atanassov I, Bukowski JP, Tryfona T, McQueen-Mason SJ, Dupree P, Turner S. Arabidopsis genes IRREGULAR XYLEM (IRX15) and IRX15L encode DUF579-containing proteins that are essential for normal xylan deposition in the secondary cell wall. Plant J 2011; 66:401-13. [PMID: 21251108 DOI: 10.1111/j.1365-313x.2011.04501.x] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
There are 10 genes in the Arabidopsis genome that contain a domain described in the Pfam database as domain of unknown function 579 (DUF579). Although DUF579 is widely distributed in eukaryotic species, there is no direct experimental evidence to assign a function to it. Five of the 10 Arabidopsis DUF579 family members are co-expressed with marker genes for secondary cell wall formation. Plants in which two closely related members of the DUF579 family have been disrupted by T-DNA insertions contain less xylose in the secondary cell wall as a result of decreased xylan content, and exhibit mildly distorted xylem vessels. Consequently we have named these genes IRREGULAR XYLEM 15 (IRX15) and IRX15L. These mutant plants exhibit many features of previously described xylan synthesis mutants, such as the replacement of glucuronic acid side chains with methylglucuronic acid side chains. By contrast, immunostaining of xylan and transmission electron microscopy (TEM) reveals that the walls of these irx15 irx15l double mutants are disorganized, compared with the wild type or other previously described xylan mutants, and exhibit dramatic increases in the quantity of sugar released in cell wall digestibility assays. Furthermore, localization studies using fluorescent fusion proteins label both the Golgi and also an unknown intracellular compartment. These data are consistent with irx15 and irx15l defining a new class of genes involved in xylan biosynthesis. How these genes function during xylan biosynthesis and deposition is discussed.
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Affiliation(s)
- David Brown
- Faculty of Life Science, University of Manchester, Oxford Road, Manchester M139PT, UK
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Gomez LD, Whitehead C, Barakate A, Halpin C, McQueen-Mason SJ. Automated saccharification assay for determination of digestibility in plant materials. Biotechnol Biofuels 2010; 3:23. [PMID: 20979637 PMCID: PMC2974669 DOI: 10.1186/1754-6834-3-23] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2010] [Accepted: 10/27/2010] [Indexed: 05/02/2023]
Abstract
BACKGROUND Cell wall resistance represents the main barrier for the production of second generation biofuels. The deconstruction of lignocellulose can provide sugars for the production of fuels or other industrial products through fermentation. Understanding the biochemical basis of the recalcitrance of cell walls to digestion will allow development of more effective and cost efficient ways to produce sugars from biomass. One approach is to identify plant genes that play a role in biomass recalcitrance, using association genetics. Such an approach requires a robust and reliable high throughput (HT) assay for biomass digestibility, which can be used to screen the large numbers of samples involved in such studies. RESULTS We developed a HT saccharification assay based on a robotic platform that can carry out in a 96-well plate format the enzymatic digestion and quantification of the released sugars. The handling of the biomass powder for weighing and formatting into 96 wells is performed by a robotic station, where the plant material is ground, delivered to the desired well in the plates and weighed with a precision of 0.1 mg. Once the plates are loaded, an automated liquid handling platform delivers an optional mild pretreatment (< 100°C) followed by enzymatic hydrolysis of the biomass. Aliquots from the hydrolysis are then analyzed for the release of reducing sugar equivalents. The same platform can be used for the comparative evaluation of different enzymes and enzyme cocktails. The sensitivity and reliability of the platform was evaluated by measuring the saccharification of stems from lignin modified tobacco plants, and the results of automated and manual analyses compared. CONCLUSIONS The automated assay systems are sensitive, robust and reliable. The system can reliably detect differences in the saccharification of plant tissues, and is able to process large number of samples with a minimum amount of human intervention. The automated system uncovered significant increases in the digestibility of certain lignin modified lines in a manner compatible with known effects of lignin modification on cell wall properties. We conclude that this automated assay platform is of sufficient sensitivity and reliability to undertake the screening of the large populations of plants necessary for mutant identification and genetic association studies.
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Affiliation(s)
- Leonardo D Gomez
- CNAP, Department of Biology, University of York, Heslington, York YO10 5YW, UK
| | - Caragh Whitehead
- CNAP, Department of Biology, University of York, Heslington, York YO10 5YW, UK
| | - Abdellah Barakate
- Division of Plant Sciences, College of Life Sciences, University of Dundee at SCRI, Dundee, DD2 5DA, UK
| | - Claire Halpin
- Division of Plant Sciences, College of Life Sciences, University of Dundee at SCRI, Dundee, DD2 5DA, UK
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Lizana XC, Riegel R, Gomez LD, Herrera J, Isla A, McQueen-Mason SJ, Calderini DF. Expansins expression is associated with grain size dynamics in wheat (Triticum aestivum L.). J Exp Bot 2010; 61:1147-57. [PMID: 20080826 PMCID: PMC2826655 DOI: 10.1093/jxb/erp380] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2009] [Revised: 12/01/2009] [Accepted: 12/08/2009] [Indexed: 05/18/2023]
Abstract
Grain weight is one of the most important components of cereal yield and quality. A clearer understanding of the physiological and molecular determinants of this complex trait would provide an insight into the potential benefits for plant breeding. In the present study, the dynamics of dry matter accumulation, water uptake, and grain size in parallel with the expression of expansins during grain growth in wheat were analysed. The stabilized water content of grains showed a strong association with final grain weight (r(2)=0.88, P <0.01). Grain length was found to be the trait that best correlated with final grain weight (r(2)=0.98, P <0.01) and volume (r(2)=0.94, P <0.01). The main events that defined final grain weight occurred during the first third of grain-filling when maternal tissues (the pericarp of grains) undergo considerable expansion. Eight expansin coding sequences were isolated from pericarp RNA and the temporal profiles of accumulation of these transcripts were monitored. Sequences showing high homology with TaExpA6 were notably abundant during early grain expansion and declined as maturity was reached. RNA in situ hybridization studies revealed that the transcript for TaExpA6 was principally found in the pericarp during early growth in grain development and, subsequently, in both the endosperm and pericarp. The signal in these images is likely to be the sum of the transcript levels of all three sequences with high similarity to the TaExpA6 gene. The early part of the expression profile of this putative expansin gene correlates well with the critical periods of early grain expansion, suggesting it as a possible factor in the final determination of grain size.
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Affiliation(s)
- X Carolina Lizana
- Graduate School, Faculty of Agricultural Sciences, Universidad Austral de Chile, Campus Isla Teja, Valdivia, Chile.
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Gomez LD, Steele-King CG, Jones L, Foster JM, Vuttipongchaikij S, McQueen-Mason SJ. Arabinan metabolism during seed development and germination in Arabidopsis. Mol Plant 2009; 2:966-976. [PMID: 19825672 DOI: 10.1093/mp/ssp050] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Arabinans are found in the pectic network of many cell walls, where, along with galactan, they are present as side chains of Rhamnogalacturonan l. Whilst arabinans have been reported to be abundant polymers in the cell walls of seeds from a range of plant species, their proposed role as a storage reserve has not been thoroughly investigated. In the cell walls of Arabidopsis seeds, arabinose accounts for approximately 40% of the monosaccharide composition of non-cellulosic polysaccharides of embryos. Arabinose levels decline to approximately 15% during seedling establishment, indicating that cell wall arabinans may be mobilized during germination. Immunolocalization of arabinan in embryos, seeds, and seedlings reveals that arabinans accumulate in developing and mature embryos, but disappear during germination and seedling establishment. Experiments using 14C-arabinose show that it is readily incorporated and metabolized in growing seedlings, indicating an active catabolic pathway for this sugar. We found that depleting arabinans in seeds using a fungal arabinanase causes delayed seedling growth, lending support to the hypothesis that these polymers may help fuel early seedling growth.
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Affiliation(s)
- Leonardo D Gomez
- CNAP, Department of Biology, University of York, Heslington, York YO10 5YW, United Kingdom
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Gomez LD, Bristow JK, Statham ER, McQueen-Mason SJ. Analysis of saccharification in Brachypodium distachyon stems under mild conditions of hydrolysis. Biotechnol Biofuels 2008; 1:15. [PMID: 18945335 PMCID: PMC2577630 DOI: 10.1186/1754-6834-1-15] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2008] [Accepted: 10/22/2008] [Indexed: 05/18/2023]
Abstract
BACKGROUND Brachypodium distachyon constitutes an excellent model species for grasses. It is a small, easily propagated, temperate grass with a rapid life cycle and a small genome. It is a self-fertile plant that can be transformed with high efficiency using Agrobacteria and callus derived from immature embryos. In addition, considerable genetic and genomic resources are becoming available for this species in the form of mapping populations, large expressed sequence tag collections, T-DNA insertion lines and, in the near future, the complete genome sequence. The development of Brachypodium as a model species is of particular value in the areas of cell wall and biomass research, where differences between dicots and grasses are greatest. Here we explore the effect of mild conditions of pretreatment and hydrolysis in Brachypodium stem segments as a contribution for the establishment of sensitive screening of the saccharification properties in different genetic materials. RESULTS The non-cellulosic monosaccharide composition of Brachypodium is closely related to grasses of agricultural importance and significantly different from the dicot model Arabidopsis thaliana. Diluted acid pretreatment of stem segments produced significant release of sugars and negatively affected the amount of sugars obtained by enzymatic hydrolysis. Monosaccharide and oligosaccharide analysis showed that the hemicellulose fraction is the main target of the enzymatic activity under the modest hydrolytic conditions used in our assays. Scanning electron microscopy analysis of the treated materials showed progressive exposure of fibrils in the stem segments. CONCLUSION Results presented here indicate that under mild conditions cellulose and hemicellulose are hydrolysed to differing extents, with hemicellulose hydrolysis predominating. We anticipate that the sub-optimal conditions for hydrolysis identified here will provide a sensitive assay to detect variations in saccharification among Brachypodium plants, providing a useful analytical tool for identifying plants with alterations in this trait.
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Affiliation(s)
- Leonardo D Gomez
- CNAP, Department of Biology, University of York, Heslington, York YO10 5YW, UK
| | - Jennifer K Bristow
- CNAP, Department of Biology, University of York, Heslington, York YO10 5YW, UK
| | - Emily R Statham
- CNAP, Department of Biology, University of York, Heslington, York YO10 5YW, UK
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Abstract
Domination of the global biosphere by human beings is unprecedented in the history of the planet, and our impact is such that substantive changes in ecosystems, and the global environment as a whole, are now becoming apparent. Our activity drives the steady increase in global temperature observed in recent decades. The realization of the adverse effects of greenhouse gas emissions on the environment, together with declining petroleum reserves, has ensured that the quest for sustainable and environmentally benign sources of energy for our industrial economies and consumer societies has become urgent in recent years. Consequently, there is renewed interest in the production and use of fuels from plants. The 'first-generation' biofuels made from starch and sugar appear unsustainable because of the potential stress that their production places on food commodities. Second-generation biofuels, produced from cheap and abundant plant biomass, are seen as the most attractive solution to this problem, but a number of technical hurdles must be overcome before their potential is realized. This review will focus on the underpinning research necessary to enable the cost-effective production of liquid fuels from plant biomass, with a particular focus on aspects related to plant cell walls and their bioconversion.
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Affiliation(s)
- Leonardo D Gomez
- CNAP, Department of Biology, University of York, Heslington, York YO10 5YW, UK
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Abstract
The glutathione redox couple is an information-rich redox buffer that interacts with numerous cellular components. To explore the role of glutathione in redox signalling, leaf contents were increased either chemically, by feeding reduced glutathione (GSH), or genetically, by over-expressing the first enzyme of the GSH biosynthetic pathway, gamma-glutamylcysteine synthetase (gamma-ECS). Leaf discs were also fed glutathione disulphide (GSSG), leading to increases in both GSH and GSSG. The effects of increases in GSH were compared with non-specific changes in leaf thiol status induced by feeding dithiothreitol (DTT) or the monothiol beta-mercaptoethanol (beta-ME). Photosynthesis measurements showed that none of the feeding treatments greatly disrupted leaf physiology. Transgenic plants expressing aequorin were used to analyse calcium signatures during the feeding treatments. Calcium release occurred soon after the onset of GSH or GSSG feeding, but was unaffected by DTT or beta-ME. Pathogenesis-related protein 1 (PR-1) was induced both in the gamma-ECS overexpressors and by feeding GSH, but not GSSG. Feeding DTT also induced PR-1. Key transcripts encoding antioxidative enzymes were much less affected, although glutathione synthetase was suppressed by feeding thiols or GSSG. It is concluded that modulation of glutathione contents transmits information through diverse signalling mechanisms, including (i) the establishment of an appropriate redox potential for thiol/disulphide exchange and (ii) the release of calcium to the cytosol.
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Affiliation(s)
- L D Gomez
- Crop Performance and Improvement Division, Rothamsted Research, Harpenden, Herts AL5 2JQ, UK
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Abstract
The hourly variation of SCC in milk throughout the period between milkings was studied in 60 half udders of 30 Manchega ewes (10 each in first, second, and third parities) for 2 consecutive d. The interval between milkings was 12 h. The effects half udder, sampling time and day, interaction hour by day, and parity were statistically significant and explained 58.9, 11.9, 1.3, .6, and .3%, respectively, of total variance. The hourly repeatabilities of SCC and log SCC within each day (.83 and .86, respectively) were high. The SCC increased 70% in the 1st h postmilking and then gradually decreased until the next milking. The variations in SCC from 6 h postmilking were statistically significant but of less quantitative importance than those from the previous hours. The mean SCC of a.m. and p.m. milkings were very similar on both days (112 and 114 x 10(3) cells/ml). The mean SCC difference of milk between a.m. and p.m. milkings was 14%. This variation could be considered to be normal in the ewe for an interval of 12 h between milkings. These results suggest the standardization of time of sampling to avoid erroneous classifications of sheep based on SCC of milk.
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Affiliation(s)
- C Gonzalo
- Departamento de Producción Animal, Universidad de León, Spain
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