Gene stacking of multiple traits for high yield of fermentable sugars in plant biomass

Aznar, Aude; Chalvin, Camille; Shih, Patrick M.; Maimann, Michael; Ebert, Berit; Birdseye, Devon S.; Loqué, Dominique; Scheller, Henrik V.

doi:10.1186/s13068-017-1007-6

Title: Gene stacking of multiple traits for high yield of fermentable sugars in plant biomass

Journal Article · Tue Jan 09 00:00:00 EST 2018 · Biotechnology for Biofuels

DOI:https://doi.org/10.1186/s13068-017-1007-6· OSTI ID:1425435

Aznar, Aude ^[1]; Chalvin, Camille ^[2]; Shih, Patrick M. ^[1]; Maimann, Michael ^[3]; Ebert, Berit ^[4]; Birdseye, Devon S. ^[1]; Loqué, Dominique ^[5];

^[6]

Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Joint BioEnergy Inst., Feedstocks Division
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Joint BioEnergy Inst., Feedstocks Division; Ecole Normale Superieure de Cachan, Cachan (France)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Joint BioEnergy Inst., Feedstocks Division; Technical Univ. of Denmark, Lyngby (Denmark)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Joint BioEnergy Inst., Feedstocks Division; Univ. of Copenhagen (Denmark). Dept. of Plant and Environmental Sciences; Univ. of Melbourne (Australia). School of BioSciences
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Joint BioEnergy Inst., Feedstocks Division; Univ. Claude Bernard Lyon 1, Villeurbanne (France); Univ. of California, Berkeley, CA (United States). Dept. of Plant and Microbial Biology
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Joint BioEnergy Inst., Feedstocks Division; Univ. of California, Berkeley, CA (United States). Dept. of Plant and Microbial Biology

Second-generation biofuels produced from biomass can help to decrease dependency on fossil fuels, bringing about many economic and environmental benefits. To make biomass more suitable for biorefinery use, we need a better understanding of plant cell wall biosynthesis. Increasing the ratio of C6 to C5 sugars in the cell wall and decreasing the lignin content are two important targets in engineering of plants that are more suitable for downstream processing for second-generation biofuel production. Here, we have studied the basic mechanisms of cell wall biosynthesis and identified genes involved in biosynthesis of pectic galactan, including the GALS1 galactan synthase and the UDP-galactose/UDP-rhamnose transporter URGT1. We have engineered plants with a more suitable biomass composition by applying these findings, in conjunction with synthetic biology and gene stacking tools. Plants were engineered to have up to fourfold more pectic galactan in stems by overexpressing GALS1, URGT1, and UGE2, a UDP-glucose epimerase. Furthermore, the increased galactan trait was engineered into plants that were already engineered to have low xylan content by restricting xylan biosynthesis to vessels where this polysaccharide is essential. Finally, the high galactan and low xylan traits were stacked with the low lignin trait obtained by expressing the QsuB gene encoding dehydroshikimate dehydratase in lignifying cells. In conclusion, the results show that approaches to increasing C6 sugar content, decreasing xylan, and reducing lignin content can be combined in an additive manner. Thus, the engineered lines obtained by this trait-stacking approach have substantially improved properties from the perspective of biofuel production, and they do not show any obvious negative growth effects. The approach used in this study can be readily transferred to bioenergy crop plants.

View Accepted Manuscript (DOE)

Cite

Export

Save

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1425435

Journal Information:: Biotechnology for Biofuels, Vol. 11, Issue 1; ISSN 1754-6834

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

Citation Metrics:

Cited by: 25 works

Citation information provided by
Web of Science

References (44)

Optimizing pentose utilization in yeast: the need for novel tools and approaches Young, Eric; Lee, Sun-Mi; Alper, Hal Biotechnology for Biofuels, Vol. 3, Issue 1 https://doi.org/10.1186/1754-6834-3-24	journal	January 2010
Expression of a bacterial 3-dehydroshikimate dehydratase reduces lignin content and improves biomass saccharification efficiency Eudes, Aymerick; Sathitsuksanoh, Noppadon; Baidoo, Edward E. K. Plant Biotechnology Journal, Vol. 13, Issue 9 https://doi.org/10.1111/pbi.12310	journal	January 2015
Leaf biomechanical properties in Arabidopsis thaliana polysaccharide mutants affect drought survival Balsamo, Ronald; Boak, Merewyn; Nagle, Kayla Journal of Biomechanics, Vol. 48, Issue 15 https://doi.org/10.1016/j.jbiomech.2015.10.016	journal	November 2015
The Cooperative Activities of CSLD2, CSLD3, and CSLD5 Are Required for Normal Arabidopsis Development Yin, Lan; Verhertbruggen, Yves; Oikawa, Ai Molecular Plant, Vol. 4, Issue 6 https://doi.org/10.1093/mp/ssr026	journal	November 2011
Pectin Biosynthesis: GALS1 in Arabidopsis thaliana Is a β-1,4-Galactan β-1,4-Galactosyltransferase Liwanag, April Jennifer Madrid; Ebert, Berit; Verhertbruggen, Yves The Plant Cell, Vol. 24, Issue 12 https://doi.org/10.1105/tpc.112.106625	journal	December 2012
Rhamnogalacturonan I in Solanum tuberosum tubers contains complex arabinogalactan structures Øbro, Jens; Harholt, Jesper; Scheller, Henrik Vibe Phytochemistry, Vol. 65, Issue 10 https://doi.org/10.1016/j.phytochem.2004.05.002	journal	May 2004
Hemicelluloses Scheller, Henrik Vibe; Ulvskov, Peter Annual Review of Plant Biology, Vol. 61, Issue 1 https://doi.org/10.1146/annurev-arplant-042809-112315	journal	June 2010
Fasciclin-like arabinogalactan proteins: specialization for stem biomechanics and cell wall architecture in Arabidopsis and Eucalyptus: FLAs specialized for stem biomechanics and cell walls MacMillan, Colleen P.; Mansfield, Shawn D.; Stachurski, Zbigniew H. The Plant Journal, Vol. 62, Issue 4 https://doi.org/10.1111/j.1365-313X.2010.04181.x	journal	February 2010
The Arabidopsis REF8 gene encodes the 3-hydroxylase of phenylpropanoid metabolism Franke, Rochus; Humphreys, John M.; Hemm, Matthew R. The Plant Journal, Vol. 30, Issue 1, p. 33-45 https://doi.org/10.1046/j.1365-313X.2002.01266.x	journal	April 2002
Genome-Wide Identification and Testing of Superior Reference Genes for Transcript Normalization in Arabidopsis Czechowski, Tomasz; Stitt, Mark; Altmann, Thomas Plant Physiology, Vol. 139, Issue 1 https://doi.org/10.1104/pp.105.063743	journal	September 2005
Analyzing real-time PCR data by the comparative CT method Schmittgen, Thomas D.; Livak, Kenneth J. Nature Protocols, Vol. 3, Issue 6 https://doi.org/10.1038/nprot.2008.73	journal	June 2008
Antisense Down-Regulation of 4CL Expression Alters Lignification, Tree Growth, and Saccharification Potential of Field-Grown Poplar Voelker, Steven L.; Lachenbruch, Barbara; Meinzer, Frederick C. Plant Physiology, Vol. 154, Issue 2 https://doi.org/10.1104/pp.110.159269	journal	August 2010
Use of Dinitrosalicylic Acid Reagent for Determination of Reducing Sugar Miller, G. L. Analytical Chemistry, Vol. 31, Issue 3 https://doi.org/10.1021/ac60147a030	journal	March 1959
Unlocking the potential of lignocellulosic biomass through plant science Marriott, Poppy E.; Gómez, Leonardo D.; McQueen-Mason, Simon J. New Phytologist, Vol. 209, Issue 4 https://doi.org/10.1111/nph.13684	journal	October 2015
Interactions among three distinct CesA proteins essential for cellulose synthesis Taylor, N. G.; Howells, R. M.; Huttly, A. K. Proceedings of the National Academy of Sciences, Vol. 100, Issue 3 https://doi.org/10.1073/pnas.0337628100	journal	January 2003
Xylem development - from the cradle to the grave Růžička, Kamil; Ursache, Robertas; Hejátko, Jan New Phytologist, Vol. 207, Issue 3 https://doi.org/10.1111/nph.13383	journal	March 2015
Exploiting the Substrate Promiscuity of Hydroxycinnamoyl-CoA:Shikimate Hydroxycinnamoyl Transferase to Reduce Lignin Eudes, Aymerick; Pereira, Jose H.; Yogiswara, Sasha Plant and Cell Physiology, Vol. 57, Issue 3 https://doi.org/10.1093/pcp/pcw016	journal	February 2016
Down-regulation of hydroxycinnamoyl CoA: Shikimate hydroxycinnamoyl transferase in transgenic alfalfa affects lignification, development and forage quality Shadle, Gail; Chen, Fang; Srinivasa Reddy, M. S. Phytochemistry, Vol. 68, Issue 11 https://doi.org/10.1016/j.phytochem.2007.03.022	journal	June 2007
Engineering secondary cell wall deposition in plants Yang, Fan; Mitra, Prajakta; Zhang, Ling Plant Biotechnology Journal, Vol. 11, Issue 3 https://doi.org/10.1111/pbi.12016	journal	November 2012
Engineering of plants with improved properties as biofuels feedstocks by vessel-specific complementation of xylan biosynthesis mutants Petersen, Pia Damm; Lau, Jane; Ebert, Berit Biotechnology for Biofuels, Vol. 5, Issue 1, Article No. 84 https://doi.org/10.1186/1754-6834-5-84	journal	January 2012
Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes Vandesompele, Jo; De Preter, Katleen; Pattyn, Filip Genome Biology, Vol. 3, Issue 7 https://doi.org/10.1186/gb-2002-3-7-research0034	journal	June 2002
Engineering of plant cell walls for enhanced biofuel production Loqué, Dominique; Scheller, Henrik V.; Pauly, Markus Current Opinion in Plant Biology, Vol. 25 https://doi.org/10.1016/j.pbi.2015.05.018	journal	June 2015
Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana Clough, Steven J.; Bent, Andrew F. The Plant Journal, Vol. 16, Issue 6, p. 735-743 https://doi.org/10.1046/j.1365-313x.1998.00343.x	journal	December 1998
UDP-Glucose 4-Epimerase Isoforms UGE2 and UGE4 Cooperate in Providing UDP-Galactose for Cell Wall Biosynthesis and Growth of Arabidopsis thaliana Rösti, Johannes; Barton, Christopher J.; Albrecht, Sandra The Plant Cell, Vol. 19, Issue 5 https://doi.org/10.1105/tpc.106.049619	journal	May 2007
Regulation of Expression of Genes Involved in Quinate and Shikimate Utilization in Corynebacterium glutamicum Teramoto, H.; Inui, M.; Yukawa, H. Applied and Environmental Microbiology, Vol. 75, Issue 11 https://doi.org/10.1128/AEM.00163-09	journal	April 2009
The NAC Transcription Factors NST1 and NST2 of Arabidopsis Regulate Secondary Wall Thickenings and Are Required for Anther Dehiscence Mitsuda, Nobutaka; Seki, Motoaki; Shinozaki, Kazuo The Plant Cell, Vol. 17, Issue 11 https://doi.org/10.1105/tpc.105.036004	journal	October 2005
Localization of Pectic Galactan in Tomato Cell Walls Using a Monoclonal Antibody Specific to (1[->]4)-[beta]-D-Galactan Jones, L.; Seymour, G. B.; Knox, J. P. Plant Physiology, Vol. 113, Issue 4 https://doi.org/10.1104/pp.113.4.1405	journal	April 1997
Genetic evidence for three unique components in primary cell-wall cellulose synthase complexes in Arabidopsis Persson, S.; Paredez, A.; Carroll, A. Proceedings of the National Academy of Sciences, Vol. 104, Issue 39 https://doi.org/10.1073/pnas.0706592104	journal	September 2007
Design, implementation and practice of JBEI-ICE: an open source biological part registry platform and tools Ham, T. S.; Dmytriv, Z.; Plahar, H. Nucleic Acids Research, Vol. 40, Issue 18 https://doi.org/10.1093/nar/gks531	journal	June 2012
ARABINAN DEFICIENT 1 Is a Putative Arabinosyltransferase Involved in Biosynthesis of Pectic Arabinan in Arabidopsis Harholt, Jesper; Jensen, Jacob Krüger; Sørensen, Susanne Oxenbøll Plant Physiology, Vol. 140, Issue 1 https://doi.org/10.1104/pp.105.072744	journal	December 2005
Self-processing 2A-polyproteins - a system for co-ordinate expression of multiple proteins in transgenic plants Halpin, Claire; Cooke, Susan E.; Barakate, Abdellah The Plant Journal, Vol. 17, Issue 4 https://doi.org/10.1046/j.1365-313X.1999.00394.x	journal	February 1999
The Golgi localized bifunctional UDP-rhamnose/UDP-galactose transporter family of Arabidopsis Rautengarten, C.; Ebert, B.; Moreno, I. Proceedings of the National Academy of Sciences, Vol. 111, Issue 31 https://doi.org/10.1073/pnas.1406073111	journal	July 2014
Distinct and conserved transcriptomic changes during nematode-induced giant cell development in tomato compared with Arabidopsis: a functional role for gene repression Portillo, Mary; Cabrera, Javier; Lindsey, Keith New Phytologist, Vol. 197, Issue 4 https://doi.org/10.1111/nph.12121	journal	February 2013
A robust gene-stacking method utilizing yeast assembly for plant synthetic biology Shih, Patrick M.; Vuu, Khanh; Mansoori, Nasim Nature Communications, Vol. 7, Issue 1 https://doi.org/10.1038/ncomms13215	journal	October 2016
Efficient transformation of Agrobacterium spp. by high voltage electroporation Wen-jun, Shen; Forde, Brian G. Nucleic Acids Research, Vol. 17, Issue 20 https://doi.org/10.1093/nar/17.20.8385	journal	January 1989
Characterization of the LM5 pectic galactan epitope with synthetic analogues of β-1,4-d-galactotetraose Andersen, Mathias C. F.; Boos, Irene; Marcus, Susan E. Carbohydrate Research, Vol. 436 https://doi.org/10.1016/j.carres.2016.10.012	journal	December 2016
Biosynthesis of Pectin Harholt, J.; Suttangkakul, A.; Vibe Scheller, H. Plant Physiology, Vol. 153, Issue 2, p. 384-395 https://doi.org/10.1104/pp.110.156588	journal	April 2010
Comparison of five xylan synthesis mutants reveals new insight into the mechanisms of xylan synthesis Brown, David M.; Goubet, Florence; Wong, Vicky W. The Plant Journal, Vol. 52, Issue 6 https://doi.org/10.1111/j.1365-313X.2007.03307.x	journal	December 2007
NIH Image to ImageJ: 25 years of image analysis Schneider, Caroline A.; Rasband, Wayne S.; Eliceiri, Kevin W. Nature Methods, Vol. 9, Issue 7 https://doi.org/10.1038/nmeth.2089	journal	June 2012
Yeast metabolic engineering for hemicellulosic ethanol production Van Vleet, J. H.; Jeffries, T. W. Current Opinion in Biotechnology, Vol. 20, Issue 3, p. 300-306 https://doi.org/10.1016/j.copbio.2009.06.001	journal	June 2009
A gene stacking approach leads to engineered plants with highly increased galactan levels in Arabidopsis Gondolf, Vibe M.; Stoppel, Rhea; Ebert, Berit BMC Plant Biology, Vol. 14, Issue 1 https://doi.org/10.1186/s12870-014-0344-x	journal	December 2014
Drilling accurate nanopores for biosensors by energetic multi-wall carbon nanotubes: a molecular dynamics investigation Li, Changsheng; Wang, Zilin; Ma, Lei Journal of Molecular Modeling, Vol. 28, Issue 10 https://doi.org/10.1007/s00894-022-05276-8	journal	September 2022
Influence of cluster thinning and girdling on aroma composition in ‘Jumeigui’ table grape Xi, Xiaojun; Zha, Qian; He, Yani Scientific Reports, Vol. 10, Issue 1 https://doi.org/10.1038/s41598-020-63826-7	journal	April 2020
Inhibition of acetyl-CoA carboxylase by spirotetramat causes growth arrest and lipid depletion in nematodes Gutbrod, Philipp; Gutbrod, Katharina; Nauen, Ralf Scientific Reports, Vol. 10, Issue 1 https://doi.org/10.1038/s41598-020-69624-5	journal	July 2020

Cited By (6)

Transcriptome analysis highlights key differentially expressed genes involved in cellulose and lignin biosynthesis of sugarcane genotypes varying in fiber content Kasirajan, Lakshmi; Hoang, Nam V.; Furtado, Agnelo Scientific Reports, Vol. 8, Issue 1 https://doi.org/10.1038/s41598-018-30033-4	journal	August 2018
The Three Members of the Arabidopsis Glycosyltransferase Family 92 are Functional β-1,4-Galactan Synthases Ebert, Berit; Birdseye, Devon; Liwanag, April J. M. Plant and Cell Physiology, Vol. 59, Issue 12 https://doi.org/10.1093/pcp/pcy180	journal	September 2018
Plant synthetic biology could drive a revolution in biofuels and medicine Mortimer, Jenny C. Experimental Biology and Medicine, Vol. 244, Issue 4 https://doi.org/10.1177/1535370218793890	journal	September 2018
Increased drought tolerance in plants engineered for low lignin and low xylan content Yan, Jingwei; Aznar, Aude; Chalvin, Camille Biotechnology for Biofuels, Vol. 11, Issue 1 https://doi.org/10.1186/s13068-018-1196-7	journal	July 2018
A screening method to identify efficient sgRNAs in Arabidopsis, used in conjunction with cell-specific lignin reduction Liang, Yan; Eudes, Aymerick; Yogiswara, Sasha Biotechnology for Biofuels, Vol. 12, Issue 1 https://doi.org/10.1186/s13068-019-1467-y	journal	May 2019
Engineering of Bioenergy Crops: Dominant Genetic Approaches to Improve Polysaccharide Properties and Composition in Biomass Brandon, Andrew G.; Scheller, Henrik V. Frontiers in Plant Science, Vol. 11 https://doi.org/10.3389/fpls.2020.00282	journal	March 2020

Linked Research (10)

Similar Records

A gene stacking approach leads to engineered plants with highly increased galactan levels in Arabidopsis

Journal Article · Wed Dec 10 00:00:00 EST 2014 · BMC Plant Biology · OSTI ID:1425435

Gondolf, Vibe M.; Stoppel, Rhea; Ebert, Berit; +4 more

Increased drought tolerance in plants engineered for low lignin and low xylan content

Journal Article · Wed Jul 18 00:00:00 EDT 2018 · Biotechnology for Biofuels · OSTI ID:1425435

Yan, Jingwei; Aznar, Aude; Chalvin, Camille; +7 more

Downregulation of GAUT12 in Populus deltoides by RNA silencing results in reduced recalcitrance, increased growth and reduced xylan and pectin in a woody biofuel feedstock. Biotechnology For Biofuels

Journal Article · Thu Mar 12 00:00:00 EDT 2015 · Biotechnology for Biofuels · OSTI ID:1425435

Biswal, Ajaya K.; Hao, Zhangying; Pattathil, Sivakumar; +17 more

Related Subjects

09 BIOMASS FUELS
59 BASIC BIOLOGICAL SCIENCES
Plant cell wall
Galactan
Arabidopsis
Pectin
jStack
Xylan
Lignin
Plant engineering

MOESM1 of Gene stacking of multiple traits for high yield of fermentable sugars in plant biomass Aznar, Aude; Chalvin, Camille; Shih, Patrick https://doi.org/10.6084/m9.figshare.5768493.v1 The current record is supplemented by this dataset	dataset	January 2018
MOESM2 of Gene stacking of multiple traits for high yield of fermentable sugars in plant biomass Aznar, Aude; Chalvin, Camille; Shih, Patrick https://doi.org/10.6084/m9.figshare.5768502 The current record is supplemented by this text	text	January 2018
MOESM2 of Gene stacking of multiple traits for high yield of fermentable sugars in plant biomass Aznar, Aude; Chalvin, Camille; Shih, Patrick https://doi.org/10.6084/m9.figshare.5768502.v1 The current record is supplemented by this dataset	dataset	January 2018
MOESM3 of Gene stacking of multiple traits for high yield of fermentable sugars in plant biomass Aznar, Aude; Chalvin, Camille; Shih, Patrick https://doi.org/10.6084/M9.FIGSHARE.5768526 The current record is supplemented by this dataset	dataset	January 2018
MOESM3 of Gene stacking of multiple traits for high yield of fermentable sugars in plant biomass Aznar, Aude; Chalvin, Camille; Shih, Patrick https://doi.org/10.6084/m9.figshare.5768526.v1 The current record is supplemented by this dataset	dataset	January 2018
MOESM4 of Gene stacking of multiple traits for high yield of fermentable sugars in plant biomass Aznar, Aude; Chalvin, Camille; Shih, Patrick https://doi.org/10.6084/m9.figshare.5768550 The current record is supplemented by this text	text	January 2018
MOESM4 of Gene stacking of multiple traits for high yield of fermentable sugars in plant biomass Aznar, Aude; Chalvin, Camille; Shih, Patrick https://doi.org/10.6084/m9.figshare.5768550.v1 The current record is supplemented by this dataset	dataset	September 2018
Gene stacking of multiple traits for high yield of fermentable sugars in plant biomass [Supplemental Data] Aznar, Aude; Chalvin, Camille; Shih, Patrick https://doi.org/10.6084/m9.figshare.c.3971556 The current record is supplemented by this collection	collection	January 2018
Gene stacking of multiple traits for high yield of fermentable sugars in plant biomass Aznar, Aude; Chalvin, Camille; Shih, Patrick https://doi.org/10.6084/m9.figshare.c.3971556.v1 The current record is supplemented by this dataset	dataset	January 2018
MOESM1 of Gene stacking of multiple traits for high yield of fermentable sugars in plant biomass Aznar, Aude; Chalvin, Camille; Shih, Patrick https://doi.org/10.6084/m9.figshare.5768493 The current record is supplemented by this text	text	January 2018