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Eckardt NA, Ainsworth EA, Bahuguna RN, Broadley MR, Busch W, Carpita NC, Castrillo G, Chory J, DeHaan LR, Duarte CM, Henry A, Jagadish SVK, Langdale JA, Leakey ADB, Liao JC, Lu KJ, McCann MC, McKay JK, Odeny DA, Jorge de Oliveira E, Platten JD, Rabbi I, Rim EY, Ronald PC, Salt DE, Shigenaga AM, Wang E, Wolfe M, Zhang X. Climate change challenges, plant science solutions. Plant Cell 2023; 35:24-66. [PMID: 36222573 PMCID: PMC9806663 DOI: 10.1093/plcell/koac303] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
Climate change is a defining challenge of the 21st century, and this decade is a critical time for action to mitigate the worst effects on human populations and ecosystems. Plant science can play an important role in developing crops with enhanced resilience to harsh conditions (e.g. heat, drought, salt stress, flooding, disease outbreaks) and engineering efficient carbon-capturing and carbon-sequestering plants. Here, we present examples of research being conducted in these areas and discuss challenges and open questions as a call to action for the plant science community.
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Affiliation(s)
| | - Elizabeth A Ainsworth
- USDA ARS Global Change and Photosynthesis Research Unit, Urbana, Illinois 61801, USA
| | - Rajeev N Bahuguna
- Centre for Advanced Studies on Climate Change, Dr Rajendra Prasad Central Agricultural University, Samastipur 848125, Bihar, India
| | - Martin R Broadley
- School of Biosciences, University of Nottingham, Nottingham, NG7 2RD, UK
- Rothamsted Research, West Common, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - Wolfgang Busch
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Nicholas C Carpita
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, USA
| | - Gabriel Castrillo
- School of Biosciences, University of Nottingham, Nottingham, NG7 2RD, UK
- Future Food Beacon of Excellence, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Joanne Chory
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | | | - Carlos M Duarte
- Red Sea Research Center (RSRC) and Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Amelia Henry
- International Rice Research Institute, Rice Breeding Innovations Platform, Los Baños, Laguna 4031, Philippines
| | - S V Krishna Jagadish
- Department of Plant and Soil Science, Texas Tech University, Lubbock, Texas 79410, USA
| | - Jane A Langdale
- Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - Andrew D B Leakey
- Department of Plant Biology, Department of Crop Sciences, and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Illinois 61801, USA
| | - James C Liao
- Institute of Biological Chemistry, Academia Sinica, Taipei 11528, Taiwan
| | - Kuan-Jen Lu
- Institute of Biological Chemistry, Academia Sinica, Taipei 11528, Taiwan
| | - Maureen C McCann
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, USA
| | - John K McKay
- Department of Agricultural Biology, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Damaris A Odeny
- The International Crops Research Institute for the Semi-Arid Tropics–Eastern and Southern Africa, Gigiri 39063-00623, Nairobi, Kenya
| | | | - J Damien Platten
- International Rice Research Institute, Rice Breeding Innovations Platform, Los Baños, Laguna 4031, Philippines
| | - Ismail Rabbi
- International Institute of Tropical Agriculture (IITA), PMB 5320 Ibadan, Oyo, Nigeria
| | - Ellen Youngsoo Rim
- Department of Plant Pathology and the Genome Center, University of California, Davis, California 95616, USA
| | - Pamela C Ronald
- Department of Plant Pathology and the Genome Center, University of California, Davis, California 95616, USA
- Innovative Genomics Institute, Berkeley, California 94704, USA
| | - David E Salt
- School of Biosciences, University of Nottingham, Nottingham, NG7 2RD, UK
- Future Food Beacon of Excellence, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Alexandra M Shigenaga
- Department of Plant Pathology and the Genome Center, University of California, Davis, California 95616, USA
| | - Ertao Wang
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Marnin Wolfe
- Auburn University, Dept. of Crop Soil and Environmental Sciences, College of Agriculture, Auburn, Alabama 36849, USA
| | - Xiaowei Zhang
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
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Olek AT, Rushton PS, Kihara D, Ciesielski P, Aryal UK, Zhang Z, Stauffacher CV, McCann MC, Carpita NC. Essential amino acids in the Plant-Conserved and Class-Specific Regions of cellulose synthases. Plant Physiol 2023; 191:142-160. [PMID: 36250895 PMCID: PMC9806608 DOI: 10.1093/plphys/kiac479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 09/24/2022] [Indexed: 05/05/2023]
Abstract
The Plant-Conserved Region (P-CR) and the Class-Specific Region (CSR) are two plant-unique sequences in the catalytic core of cellulose synthases (CESAs) for which specific functions have not been established. Here, we used site-directed mutagenesis to replace amino acids and motifs within these sequences predicted to be essential for assembly and function of CESAs. We developed an in vivo method to determine the ability of mutated CesA1 transgenes to complement an Arabidopsis (Arabidopsis thaliana) temperature-sensitive root-swelling1 (rsw1) mutant. Replacement of a Cys residue in the CSR, which blocks dimerization in vitro, rendered the AtCesA1 transgene unable to complement the rsw1 mutation. Examination of the CSR sequences from 33 diverse angiosperm species showed domains of high-sequence conservation in a class-specific manner but with variation in the degrees of disorder, indicating a nonredundant role of the CSR structures in different CESA isoform classes. The Cys residue essential for dimerization was not always located in domains of intrinsic disorder. Expression of AtCesA1 transgene constructs, in which Pro417 and Arg453 were substituted for Ala or Lys in the coiled-coil of the P-CR, were also unable to complement the rsw1 mutation. Despite an expected role for Arg457 in trimerization of CESA proteins, AtCesA1 transgenes with Arg457Ala mutations were able to fully restore the wild-type phenotype in rsw1. Our data support that Cys662 within the CSR and Pro417 and Arg453 within the P-CR of Arabidopsis CESA1 are essential residues for functional synthase complex formation, but our data do not support a specific role for Arg457 in trimerization in native CESA complexes.
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Affiliation(s)
- Anna T Olek
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907, USA
| | - Phillip S Rushton
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA
| | - Daisuke Kihara
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA
- Department of Computer Science, Purdue University, West Lafayette, Indiana 47907, USA
| | - Peter Ciesielski
- Renewable Resources & Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, USA
| | - Uma K Aryal
- Bindley Biosciences Center, Purdue University, West Lafayette, Indiana 47907, USA
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, Indiana 47907, USA
| | - Zicong Zhang
- Department of Computer Science, Purdue University, West Lafayette, Indiana 47907, USA
| | - Cynthia V Stauffacher
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA
| | - Maureen C McCann
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, USA
| | - Nicholas C Carpita
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907, USA
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, USA
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Hill MJ, Penning BW, McCann MC, Carpita NC. COMPILE: a GWAS computational pipeline for gene discovery in complex genomes. BMC Plant Biol 2022; 22:315. [PMID: 35778686 PMCID: PMC9250234 DOI: 10.1186/s12870-022-03668-9] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Genome-Wide Association Studies (GWAS) are used to identify genes and alleles that contribute to quantitative traits in large and genetically diverse populations. However, traits with complex genetic architectures create an enormous computational load for discovery of candidate genes with acceptable statistical certainty. We developed a streamlined computational pipeline for GWAS (COMPILE) to accelerate identification and annotation of candidate maize genes associated with a quantitative trait, and then matches maize genes to their closest rice and Arabidopsis homologs by sequence similarity. RESULTS COMPILE executed GWAS using a Mixed Linear Model that incorporated, without compression, recent advancements in population structure control, then linked significant Quantitative Trait Loci (QTL) to candidate genes and RNA regulatory elements contained in any genome. COMPILE was validated using published data to identify QTL associated with the traits of α-tocopherol biosynthesis and flowering time, and identified published candidate genes as well as additional genes and non-coding RNAs. We then applied COMPILE to 274 genotypes of the maize Goodman Association Panel to identify candidate loci contributing to resistance of maize stems to penetration by larvae of the European Corn Borer (Ostrinia nubilalis). Candidate genes included those that encode a gene of unknown function, WRKY and MYB-like transcriptional factors, receptor-kinase signaling, riboflavin synthesis, nucleotide-sugar interconversion, and prolyl hydroxylation. Expression of the gene of unknown function has been associated with pathogen stress in maize and in rice homologs closest in sequence identity. CONCLUSIONS The relative speed of data analysis using COMPILE allowed comparison of population size and compression. Limitations in population size and diversity are major constraints for a trait and are not overcome by increasing marker density. COMPILE is customizable and is readily adaptable for application to species with robust genomic and proteome databases.
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Affiliation(s)
- Matthew J Hill
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, 47907, USA
- Present address: Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA, 02142, USA
- Present address: Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Bryan W Penning
- USDA-ARS Corn, Soybean and Wheat Quality Research Unit, Wooster, OH, 44691, USA
| | - Maureen C McCann
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, 47907, USA
- Present address: Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
| | - Nicholas C Carpita
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, 47907, USA.
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, 47907, USA.
- Present address: Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA.
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Sowinski EE, Westman BM, Redmond CR, Kong Y, Olek AT, Olek J, McCann MC, Carpita NC. Lack of xyloglucan in the cell walls of the Arabidopsis xxt1/xxt2 mutant results in specific increases in homogalacturonan and glucomannan. Plant J 2022; 110:212-227. [PMID: 35041247 DOI: 10.1111/tpj.15666] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 12/29/2021] [Accepted: 01/03/2022] [Indexed: 06/14/2023]
Affiliation(s)
- Evan E Sowinski
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, 47907, USA
| | - Bryce M Westman
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, 47907, USA
| | - Celeste R Redmond
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, 47907, USA
| | - Yingzhen Kong
- College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, China
| | - Anna T Olek
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, 47907, USA
| | - Jan Olek
- Lyles School of Civil Engineering, Purdue University, West Lafayette, Indiana, 47907, USA
| | - Maureen C McCann
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, 47907, USA
| | - Nicholas C Carpita
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, 47907, USA
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, 47907, USA
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Julius BT, McCubbin TJ, Mertz RA, Baert N, Knoblauch J, Grant DG, Conner K, Bihmidine S, Chomet P, Wagner R, Woessner J, Grote K, Peevers J, Slewinski TL, McCann MC, Carpita NC, Knoblauch M, Braun DM. Maize Brittle Stalk2-Like3, encoding a COBRA protein, functions in cell wall formation and carbohydrate partitioning. Plant Cell 2021; 33:3348-3366. [PMID: 34323976 PMCID: PMC8505866 DOI: 10.1093/plcell/koab193] [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] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 07/16/2021] [Indexed: 05/14/2023]
Abstract
Carbohydrate partitioning from leaves to sink tissues is essential for plant growth and development. The maize (Zea mays) recessive carbohydrate partitioning defective28 (cpd28) and cpd47 mutants exhibit leaf chlorosis and accumulation of starch and soluble sugars. Transport studies with 14C-sucrose (Suc) found drastically decreased export from mature leaves in cpd28 and cpd47 mutants relative to wild-type siblings. Consistent with decreased Suc export, cpd28 mutants exhibited decreased phloem pressure in mature leaves, and altered phloem cell wall ultrastructure in immature and mature leaves. We identified the causative mutations in the Brittle Stalk2-Like3 (Bk2L3) gene, a member of the COBRA family, which is involved in cell wall development across angiosperms. None of the previously characterized COBRA genes are reported to affect carbohydrate export. Consistent with other characterized COBRA members, the BK2L3 protein localized to the plasma membrane, and the mutants condition a dwarf phenotype in dark-grown shoots and primary roots, as well as the loss of anisotropic cell elongation in the root elongation zone. Likewise, both mutants exhibit a significant cellulose deficiency in mature leaves. Therefore, Bk2L3 functions in tissue growth and cell wall development, and this work elucidates a unique connection between cellulose deposition in the phloem and whole-plant carbohydrate partitioning.
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Affiliation(s)
- Benjamin T Julius
- Divisions of Plant Science and Technology, Biological Sciences, Interdisciplinary Plant Group, and the Missouri Maize Center, University of Missouri, Columbia, Missouri 65211, USA
- Bayer Crop Science, Chesterfield, Missouri 63017, USA
| | - Tyler J McCubbin
- Divisions of Plant Science and Technology, Biological Sciences, Interdisciplinary Plant Group, and the Missouri Maize Center, University of Missouri, Columbia, Missouri 65211, USA
| | - Rachel A Mertz
- Divisions of Plant Science and Technology, Biological Sciences, Interdisciplinary Plant Group, and the Missouri Maize Center, University of Missouri, Columbia, Missouri 65211, USA
- Present address: Inari Agriculture, West Lafayette, Indiana 47906, USA
| | - Nick Baert
- Divisions of Plant Science and Technology, Biological Sciences, Interdisciplinary Plant Group, and the Missouri Maize Center, University of Missouri, Columbia, Missouri 65211, USA
| | - Jan Knoblauch
- School of Biological Sciences, Washington State University, Pullman, Washington 99164, USA
| | - DeAna G Grant
- Electron Microscopy Core Facility, University of Missouri, Columbia, Missouri 65211, USA
| | - Kyle Conner
- Divisions of Plant Science and Technology, Biological Sciences, Interdisciplinary Plant Group, and the Missouri Maize Center, University of Missouri, Columbia, Missouri 65211, USA
| | - Saadia Bihmidine
- Divisions of Plant Science and Technology, Biological Sciences, Interdisciplinary Plant Group, and the Missouri Maize Center, University of Missouri, Columbia, Missouri 65211, USA
| | - Paul Chomet
- NRGene Inc., 8910 University Center Lane, San Diego, California 92122, USA
| | - Ruth Wagner
- Bayer Crop Science, Chesterfield, Missouri 63017, USA
| | - Jeff Woessner
- Bayer Crop Science, Chesterfield, Missouri 63017, USA
| | - Karen Grote
- Bayer Crop Science, Chesterfield, Missouri 63017, USA
| | | | | | - Maureen C McCann
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907, USA
| | - Nicholas C Carpita
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907, USA
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907, USA
| | - Michael Knoblauch
- School of Biological Sciences, Washington State University, Pullman, Washington 99164, USA
| | - David M Braun
- Divisions of Plant Science and Technology, Biological Sciences, Interdisciplinary Plant Group, and the Missouri Maize Center, University of Missouri, Columbia, Missouri 65211, USA
- Author for correspondence:
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Lin CY, Donohoe BS, Bomble YJ, Yang H, Yunes M, Sarai NS, Shollenberger T, Decker SR, Chen X, McCann MC, Tucker MP, Wei H, Himmel ME. Iron incorporation both intra- and extra-cellularly improves the yield and saccharification of switchgrass (Panicum virgatum L.) biomass. Biotechnol Biofuels 2021; 14:55. [PMID: 33663584 PMCID: PMC7931346 DOI: 10.1186/s13068-021-01891-4] [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: 06/20/2020] [Accepted: 01/27/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Pretreatments are commonly used to facilitate the deconstruction of lignocellulosic biomass to its component sugars and aromatics. Previously, we showed that iron ions can be used as co-catalysts to reduce the severity of dilute acid pretreatment of biomass. Transgenic iron-accumulating Arabidopsis and rice plants exhibited higher iron content in grains, increased biomass yield, and importantly, enhanced sugar release from the biomass. RESULTS In this study, we used intracellular ferritin (FerIN) alone and in combination with an improved version of cell wall-bound carbohydrate-binding module fused iron-binding peptide (IBPex) specifically targeting switchgrass, a bioenergy crop species. The FerIN switchgrass improved by 15% in height and 65% in yield, whereas the FerIN/IBPex transgenics showed enhancement up to 30% in height and 115% in yield. The FerIN and FerIN/IBPex switchgrass had 27% and 51% higher in planta iron accumulation than the empty vector (EV) control, respectively, under normal growth conditions. Improved pretreatability was observed in FerIN switchgrass (~ 14% more glucose release than the EV), and the FerIN/IBPex plants showed further enhancement in glucose release up to 24%. CONCLUSIONS We conclude that this iron-accumulating strategy can be transferred from model plants and applied to bioenergy crops, such as switchgrass. The intra- and extra-cellular iron incorporation approach improves biomass pretreatability and digestibility, providing upgraded feedstocks for the production of biofuels and bioproducts.
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Affiliation(s)
- Chien-Yuan Lin
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
- Present Address: Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608 USA
- Present Address: Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Bryon S. Donohoe
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Yannick J. Bomble
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Haibing Yang
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907 USA
- Present Address: South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 China
| | - Manal Yunes
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
- Present Address: Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO 80309 USA
| | - Nicholas S. Sarai
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
- Present Address: Division of Chemistry and Chemical Engineering 210-41, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125 USA
| | - Todd Shollenberger
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Stephen R. Decker
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Xiaowen Chen
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Maureen C. McCann
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907 USA
| | - Melvin P. Tucker
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Hui Wei
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Michael E. Himmel
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
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Abstract
Lignocellulosic biomass-the lignin, cellulose, and hemicellulose that comprise major components of the plant cell well-is a sustainable resource that could be utilized in the United States to displace oil consumption from heavy vehicles, planes, and marine-going vessels and commodity chemicals. Biomass-derived sugars can also be supplied for microbial fermentative processing to fuels and chemicals or chemically deoxygenated to hydrocarbons. However, the economic value of biomass might be amplified by diversifying the range of target products that are synthesized in living plants. Genetic engineering of lignocellulosic biomass has previously focused on changing lignin content or composition to overcome recalcitrance, the intrinsic resistance of cell walls to deconstruction. New capabilities to remove lignin catalytically without denaturing the carbohydrate moiety have enabled the concept of the "lignin-first" biorefinery that includes high-value aromatic products. The structural complexity of plant cell-wall components also provides substrates for polymeric and functionalized target products, such as thermosets, thermoplastics, composites, cellulose nanocrystals, and nanofibers. With recent advances in the design of synthetic pathways, lignocellulosic biomass can be regarded as a substrate at various length scales for liquid hydrocarbon fuels, chemicals, and materials. In this review, we describe the architectures of plant cell walls and recent progress in overcoming recalcitrance and illustrate the potential for natural or engineered biomass to be used in the emerging bioeconomy.
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Affiliation(s)
- Nicholas C Carpita
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, USA; Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Maureen C McCann
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA; Center for Plant Biology, Purdue University, West Lafayette, Indiana, USA.
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8
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Affiliation(s)
- Maureen C. McCann
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
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9
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Yang H, Benatti MR, Karve RA, Fox A, Meilan R, Carpita NC, McCann MC. Rhamnogalacturonan-I is a determinant of cell-cell adhesion in poplar wood. Plant Biotechnol J 2020; 18:1027-1040. [PMID: 31584248 PMCID: PMC7061878 DOI: 10.1111/pbi.13271] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [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: 08/07/2019] [Revised: 09/16/2019] [Accepted: 09/29/2019] [Indexed: 05/19/2023]
Abstract
The molecular basis of cell-cell adhesion in woody tissues is not known. Xylem cells in wood particles of hybrid poplar (Populus tremula × P. alba cv. INRA 717-1B4) were separated by oxidation of lignin with acidic sodium chlorite when combined with extraction of xylan and rhamnogalacturonan-I (RG-I) using either dilute alkali or a combination of xylanase and RG-lyase. Acidic chlorite followed by dilute alkali treatment enables cell-cell separation by removing material from the compound middle lamellae between the primary walls. Although lignin is known to contribute to adhesion between wood cells, we found that removing lignin is a necessary but not sufficient condition to effect complete cell-cell separation in poplar lines with various ratios of syringyl:guaiacyl lignin. Transgenic poplar lines expressing an Arabidopsis thaliana gene encoding an RG-lyase (AtRGIL6) showed enhanced cell-cell separation, increased accessibility of cellulose and xylan to hydrolytic enzyme activities, and increased fragmentation of intact wood particles into small cell clusters and single cells under mechanical stress. Our results indicate a novel function for RG-I, and also for xylan, as determinants of cell-cell adhesion in poplar wood cell walls. Genetic control of RG-I content provides a new strategy to increase catalyst accessibility and saccharification yields from woody biomass for biofuels and industrial chemicals.
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Affiliation(s)
- Haibing Yang
- Department of Biological SciencesPurdue UniversityWest LafayetteINUSA
| | | | - Rucha A. Karve
- Department of Forestry and Natural ResourcesPurdue UniversityWest LafayetteINUSA
| | - Arizona Fox
- Department of Biological SciencesPurdue UniversityWest LafayetteINUSA
- Present address:
Arcadis U.S., Inc150 West Market St., Suite 728IndianapolisIN46204USA
| | - Richard Meilan
- Department of Forestry and Natural ResourcesPurdue UniversityWest LafayetteINUSA
- Purdue Center for Plant BiologyWest LafayetteINUSA
| | - Nicholas C. Carpita
- Department of Biological SciencesPurdue UniversityWest LafayetteINUSA
- Purdue Center for Plant BiologyWest LafayetteINUSA
- Department of Botany and Plant PathologyPurdue UniversityWest LafayetteINUSA
| | - Maureen C. McCann
- Department of Biological SciencesPurdue UniversityWest LafayetteINUSA
- Purdue Center for Plant BiologyWest LafayetteINUSA
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10
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Penning BW, Shiga TM, Klimek JF, SanMiguel PJ, Shreve J, Thimmapuram J, Sykes RW, Davis MF, McCann MC, Carpita NC. Expression profiles of cell-wall related genes vary broadly between two common maize inbreds during stem development. BMC Genomics 2019; 20:785. [PMID: 31664907 PMCID: PMC6819468 DOI: 10.1186/s12864-019-6117-z] [Citation(s) in RCA: 5] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 09/20/2019] [Indexed: 11/23/2022] Open
Abstract
Background The cellular machinery for cell wall synthesis and metabolism is encoded by members of large multi-gene families. Maize is both a genetic model for grass species and a potential source of lignocellulosic biomass from crop residues. Genetic improvement of maize for its utility as a bioenergy feedstock depends on identification of the specific gene family members expressed during secondary wall development in stems. Results High-throughput sequencing of transcripts expressed in developing rind tissues of stem internodes provided a comprehensive inventory of cell wall-related genes in maize (Zea mays, cultivar B73). Of 1239 of these genes, 854 were expressed among the internodes at ≥95 reads per 20 M, and 693 of them at ≥500 reads per 20 M. Grasses have cell wall compositions distinct from non-commelinid species; only one-quarter of maize cell wall-related genes expressed in stems were putatively orthologous with those of the eudicot Arabidopsis. Using a slope-metric algorithm, five distinct patterns for sub-sets of co-expressed genes were defined across a time course of stem development. For the subset of genes associated with secondary wall formation, fifteen sequence motifs were found in promoter regions. The same members of gene families were often expressed in two maize inbreds, B73 and Mo17, but levels of gene expression between them varied, with 30% of all genes exhibiting at least a 5-fold difference at any stage. Although presence-absence and copy-number variation might account for much of these differences, fold-changes of expression of a CADa and a FLA11 gene were attributed to polymorphisms in promoter response elements. Conclusions Large genetic variation in maize as a species precludes the extrapolation of cell wall-related gene expression networks even from one common inbred line to another. Elucidation of genotype-specific expression patterns and their regulatory controls will be needed for association panels of inbreds and landraces to fully exploit genetic variation in maize and other bioenergy grass species.
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Affiliation(s)
- Bryan W Penning
- Department of Botany & Plant Pathology, Purdue University, 915 West State Street, West Lafayette, IN, 47907, USA.,Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN, 47907, USA.,, Present Address: USDA-ARS, Wheat Quality Research Unit, 1680 Madison Avenue, Wooster, OH, 44691, USA
| | - Tânia M Shiga
- Department of Botany & Plant Pathology, Purdue University, 915 West State Street, West Lafayette, IN, 47907, USA.,Present Address: Departamento de Alimentos e Nutrição Experimental, FCF-USP F, 3091-3647 / 3091-3007, Av. Prof. Lineu Prestes, 580 - BL-14 CEP 05508-000, Butantã, Sâo Paulo, SP, Brazil
| | - John F Klimek
- Department of Botany & Plant Pathology, Purdue University, 915 West State Street, West Lafayette, IN, 47907, USA
| | - Philip J SanMiguel
- Genomics Core Facility, Purdue University, 170 South University Street, Purdue University, West Lafayette, IN, 47907, USA
| | - Jacob Shreve
- Bioinformatics Core Facility, Purdue University, 155 South Grant Street, West Lafayette, IN, 47907, USA.,, Present Address: Department of Internal Medicine, Cleveland Clinic, 9500 Euclid Ave, Cleveland, OH, 44195, USA
| | - Jyothi Thimmapuram
- Present Address: Departamento de Alimentos e Nutrição Experimental, FCF-USP F, 3091-3647 / 3091-3007, Av. Prof. Lineu Prestes, 580 - BL-14 CEP 05508-000, Butantã, Sâo Paulo, SP, Brazil.,Bioinformatics Core Facility, Purdue University, 155 South Grant Street, West Lafayette, IN, 47907, USA
| | - Robert W Sykes
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA.,, Present Address: Los Alamos National Laboratory, P.O. Box 1663, Los Alamos, NM, Los Alamos, NM, 87545, USA
| | - Mark F Davis
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Maureen C McCann
- Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN, 47907, USA.,Purdue Center for Plant Biology, West Lafayette, USA
| | - Nicholas C Carpita
- Department of Botany & Plant Pathology, Purdue University, 915 West State Street, West Lafayette, IN, 47907, USA. .,Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN, 47907, USA. .,Purdue Center for Plant Biology, West Lafayette, USA.
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11
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Okekeogbu IO, Aryal UK, Fernández-Niño SMG, Penning BW, Heazlewood JL, McCann MC, Carpita NC. Differential distributions of trafficking and signaling proteins of the maize ER-Golgi apparatus. Plant Signal Behav 2019; 14:1672513. [PMID: 31564200 PMCID: PMC6866702 DOI: 10.1080/15592324.2019.1672513] [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: 08/25/2019] [Revised: 09/17/2019] [Accepted: 09/20/2019] [Indexed: 06/10/2023]
Abstract
The Endoplasmic Reticulum (ER)-Golgi apparatus of plants is the site of synthesis of non-cellulosic polysaccharides that then traffic to the cell wall. A two-step protocol of flotation centrifugation followed by free-flow electrophoresis (FFE) resolved ER and Golgi proteins into three profiles: an ER-rich fraction, two Golgi-rich fractions, and an intermediate fraction enriched in cellulose synthases. Nearly three dozen Rab-like proteins of eight different subgroups were distributed differentially in ER- vs. Golgi-rich fractions, whereas seven 14-3-3 proteins co-fractionated with cellulose synthases in the intermediate fraction. FFE offers a powerful means to classify resident and transient proteins in cell-free assays of cellular location.
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Affiliation(s)
- Ikenna O. Okekeogbu
- Department of Botany & Plant Pathology, Purdue University, West Lafayette, IN, USA
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Uma K. Aryal
- Purdue Proteomics Facility, Bindley Biosciences Center, Purdue University, West Lafayette, IN, USA
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, IN, USA
| | | | - Bryan W. Penning
- USDA-ARS, Corn, Soybean and Wheat Quality Research, Wooster, OH, USA
| | - Joshua L. Heazlewood
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Maureen C. McCann
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, USA
| | - Nicholas C. Carpita
- Department of Botany & Plant Pathology, Purdue University, West Lafayette, IN, USA
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, USA
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12
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Okekeogbu IO, Pattathil S, González Fernández-Niño SM, Aryal UK, Penning BW, Lao J, Heazlewood JL, Hahn MG, McCann MC, Carpita NC. Glycome and Proteome Components of Golgi Membranes Are Common between Two Angiosperms with Distinct Cell-Wall Structures. Plant Cell 2019; 31:1094-1112. [PMID: 30914498 PMCID: PMC6533026 DOI: 10.1105/tpc.18.00755] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 02/28/2019] [Accepted: 03/24/2019] [Indexed: 05/20/2023]
Abstract
The plant endoplasmic reticulum-Golgi apparatus is the site of synthesis, assembly, and trafficking of all noncellulosic polysaccharides, proteoglycans, and proteins destined for the cell wall. As grass species make cell walls distinct from those of dicots and noncommelinid monocots, it has been assumed that the differences in cell-wall composition stem from differences in biosynthetic capacities of their respective Golgi. However, immunosorbence-based screens and carbohydrate linkage analysis of polysaccharides in Golgi membranes, enriched by flotation centrifugation from etiolated coleoptiles of maize (Zea mays) and leaves of Arabidopsis (Arabidopsis thaliana), showed that arabinogalactan-proteins and arabinans represent substantial portions of the Golgi-resident polysaccharides not typically found in high abundance in cell walls of either species. Further, hemicelluloses accumulated in Golgi at levels that contrasted with those found in their respective cell walls, with xyloglucans enriched in maize Golgi, and xylans enriched in Arabidopsis. Consistent with this finding, maize Golgi membranes isolated by flotation centrifugation and enriched further by free-flow electrophoresis, yielded >200 proteins known to function in the biosynthesis and metabolism of cell-wall polysaccharides common to all angiosperms, and not just those specific to cell-wall type. We propose that the distinctive compositions of grass primary cell walls compared with other angiosperms result from differential gating or metabolism of secreted polysaccharides post-Golgi by an as-yet unknown mechanism, and not necessarily by differential expression of genes encoding specific synthase complexes.
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Affiliation(s)
- Ikenna O Okekeogbu
- Department of Botany & Plant Pathology, Purdue University, West Lafayette, Indiana 47907
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907
| | - Sivakumar Pattathil
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602
| | | | | | - Bryan W Penning
- U.S. Department of Agriculture, Agricultural Research Service, Corn, Soybean and Wheat Quality Research, Wooster, Ohio 44691
| | - Jeemeng Lao
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Joshua L Heazlewood
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Michael G Hahn
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602
| | - Maureen C McCann
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907
- Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907
| | - Nicholas C Carpita
- Department of Botany & Plant Pathology, Purdue University, West Lafayette, Indiana 47907
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907
- Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907
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13
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Yang H, Zhang X, Luo H, Liu B, Shiga TM, Li X, Kim JI, Rubinelli P, Overton JC, Subramanyam V, Cooper BR, Mo H, Abu-Omar MM, Chapple C, Donohoe BS, Makowski L, Mosier NS, McCann MC, Carpita NC, Meilan R. Overcoming cellulose recalcitrance in woody biomass for the lignin-first biorefinery. Biotechnol Biofuels 2019; 12:171. [PMID: 31297159 PMCID: PMC6599248 DOI: 10.1186/s13068-019-1503-y] [Citation(s) in RCA: 6] [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] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 06/15/2019] [Indexed: 05/03/2023]
Abstract
BACKGROUND Low-temperature swelling of cotton linter cellulose and subsequent gelatinization in trifluoroacetic acid (TFA) greatly enhance rates of enzymatic digestion or maleic acid-AlCl3 catalyzed conversion to hydroxymethylfurfural (HMF) and levulinic acid (LA). However, lignin inhibits low-temperature swelling of TFA-treated intact wood particles from hybrid poplar (Populus tremula × P. alba) and results in greatly reduced yields of glucose or catalytic conversion compared to lignin-free cellulose. Previous studies have established that wood particles from transgenic lines of hybrid poplar with high syringyl (S) lignin content give greater glucose yields following enzymatic digestion. RESULTS Low-temperature (- 20 °C) treatment of S-lignin-rich poplar wood particles in TFA slightly increased yields of glucose from enzymatic digestions and HMF and LA from maleic acid-AlCl3 catalysis. Subsequent gelatinization at 55 °C resulted in over 80% digestion of cellulose in only 3 to 6 h with high-S-lignin wood, compared to 20-60% digestion in the wild-type poplar hybrid and transgenic lines high in guaiacyl lignin or 5-hydroxy-G lignin. Disassembly of lignin in woody particles by Ni/C catalytic systems improved yields of glucose by enzymatic digestion or catalytic conversion to HMF and LA. Although lignin was completely removed by Ni/C-catalyzed delignification (CDL) treatment, recalcitrance to enzymatic digestion of cellulose from the high-S lines was reduced compared to other lignin variants. However, cellulose still exhibited considerable recalcitrance to complete enzymatic digestion or catalytic conversion after complete delignification. Low-temperature swelling of the CDL-treated wood particles in TFA resulted in nearly complete enzymatic hydrolysis, regardless of original lignin composition. CONCLUSIONS Genetic modification of lignin composition can enhance the portfolio of aromatic products obtained from lignocellulosic biomass while promoting disassembly into biofuel and bioproduct substrates. CDL enhances rates of enzymatic digestion and chemical conversion, but cellulose remains intrinsically recalcitrant. Cold TFA is sufficient to overcome this recalcitrance after CDL treatment. Our results inform a 'no carbon left behind' strategy to convert total woody biomass into lignin, cellulose, and hemicellulose value streams for the future biorefinery.
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Affiliation(s)
- Haibing Yang
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907 USA
| | - Ximing Zhang
- Laboratory of Renewable Resource Engineering (LORRE), Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907 USA
- Present Address: College of Biosystems Engineering and Food Science, Zhejiang University, 38 Zheda Rd, Xihu Qu, Hangzhou Shi, 310027 Zhejiang Sheng China
| | - Hao Luo
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, CA 93106 USA
| | - Baoyuan Liu
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, CA 93106 USA
| | - Tânia M. Shiga
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907 USA
- Department of Food Science and Experimental Nutrition, University of São Paulo, Av. Prof. Lineu Prestes, 580, Bloco 14, São Paulo, SP 05508-000 Brazil
| | - Xu Li
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907 USA
- Plants for Human Health Institute, North Carolina State University, 600 Laureate Way, Room 3227, Kannapolis, NC 28081 USA
| | - Jeong Im Kim
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907 USA
- Department of Horticulture, University of Florida, 1253 Fifield Hall, P.O. Box 110690, Gainesville, FL 32611 USA
| | - Peter Rubinelli
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN 47907 USA
- Department of Food Science, University of Arkansas, Fayetteville, AR 72701 USA
| | - Jonathan C. Overton
- Laboratory of Renewable Resource Engineering (LORRE), Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907 USA
| | - Varun Subramanyam
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907 USA
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Bruce R. Cooper
- Bindley Bioscience Center, Purdue University, West Lafayette, IN 47907 USA
| | - Huaping Mo
- Department of Chemistry, Purdue University, West Lafayette, IN 47907 USA
| | - Mahdi M. Abu-Omar
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, CA 93106 USA
| | - Clint Chapple
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907 USA
- Purdue Center for Plant Biology, West Lafayette, USA
| | - Bryon S. Donohoe
- National Renewable Energy Laboratory, Biosciences Center, Golden, CO 80401 USA
| | - Lee Makowski
- Department of Bioengineering, Northeastern University, Boston, MA 02115 USA
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115 USA
| | - Nathan S. Mosier
- Laboratory of Renewable Resource Engineering (LORRE), Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907 USA
| | - Maureen C. McCann
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907 USA
- Purdue Center for Plant Biology, West Lafayette, USA
| | - Nicholas C. Carpita
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907 USA
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907 USA
- Purdue Center for Plant Biology, West Lafayette, USA
| | - Richard Meilan
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN 47907 USA
- Purdue Center for Plant Biology, West Lafayette, USA
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14
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Penning BW, McCann MC, Carpita NC. Evolution of the Cell Wall Gene Families of Grasses. Front Plant Sci 2019; 10:1205. [PMID: 31681352 PMCID: PMC6805987 DOI: 10.3389/fpls.2019.01205] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 09/02/2019] [Indexed: 05/06/2023]
Abstract
Grasses and related commelinid monocot species synthesize cell walls distinct in composition from other angiosperm species. With few exceptions, the genomes of all angiosperms contain the genes that encode the enzymes for synthesis of all cell-wall polysaccharide, phenylpropanoid, and protein constituents known in vascular plants. RNA-seq analysis of transcripts expressed during development of the upper and lower internodes of maize (Zea mays) stem captured the expression of cell-wall-related genes associated with primary or secondary wall formation. High levels of transcript abundances were not confined to genes associated with the distinct walls of grasses but also of those associated with xyloglucan and pectin synthesis. Combined with proteomics data to confirm that expressed genes are translated, we propose that the distinctive cell-wall composition of grasses results from sorting downstream from their sites of synthesis in the Golgi apparatus and hydrolysis of the uncharacteristic polysaccharides and not from differential expression of synthases of grass-specific polysaccharides.
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Affiliation(s)
- Bryan W. Penning
- Corn, Soybean and Wheat Quality Research, USDA-ARS, Wooster, OH, United States
| | - Maureen C. McCann
- Department of Biological Sciences, Purdue University, West Lafayette, IN, United States
- Purdue Center for Plant Biology, West Lafayette, IN, United States
| | - Nicholas C. Carpita
- Department of Biological Sciences, Purdue University, West Lafayette, IN, United States
- Purdue Center for Plant Biology, West Lafayette, IN, United States
- Department of Botany & Plant Pathology, Purdue University, West Lafayette, IN, United States
- *Correspondence: Nicholas C. Carpita,
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15
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Griffin BD, Micklem LR, McCann MC, James K, Pepper DS. The Production and Characterisation of a Panel of Ten Murine Monoclonal Antibodies to Human Procoagulant Factor VIII. Thromb Haemost 2018. [DOI: 10.1055/s-0038-1661443] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
SummaryA panel of 10 murine monoclonal antibodies to procoagulant FVIII has been developed from the fusion of a single spleen. Balb/c mice were injected with a purified preparation of FVIII: Ag, and antibody production in sera and hybrid culture supernatants was monitored using a specific radiometric screening assay. The antibodies all inhibit FVIII clotting activity in normal plasma, and when immobilised on agarose retain their ability to recognise and bind the FVIII procoagulant protein. Studies on protein A-purified immunoglobulins demonstrate a range of properties within the panel of antibodies with regard to species crossreactivity, clotting inhibition and immunoadsorption. The panel of antibodies has been used to screen heat-treated FVIII concentrates for the occurrence of heat-induced neoantigens.
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Affiliation(s)
- B D Griffin
- The Scottish National Blood Transfusion Service Headquarters Unit Laboratory, Edinburgh, Scotland, UK
| | - L R Micklem
- The Department of Surgery, University of Edinburgh Medical School, Edinburgh, Scotland, UK
| | - M C McCann
- The Department of Surgery, University of Edinburgh Medical School, Edinburgh, Scotland, UK
| | - K James
- The Department of Surgery, University of Edinburgh Medical School, Edinburgh, Scotland, UK
| | - D S Pepper
- The Scottish National Blood Transfusion Service Headquarters Unit Laboratory, Edinburgh, Scotland, UK
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Hornsey V, Micklem LR, McCann MC, James K, Dawes J, McClelland DBL, Prowse CV. Enhancement of Factor VIII-von Willebrand Factor Ristocetin Cofactor Activity by Monoclonal Antibodies. Thromb Haemost 2018. [DOI: 10.1055/s-0038-1657885] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
SummaryFive monoclonal antibodies to human von Willebrand factor were selected for characterization from 18 produced in murine hybridomas. All showed a high and specific affinity for human von Willebrand factor (vWf) but exhibited little if any crossreaction with sera from other species. The antibodies defined four epitopes on vWf, none of which were involved in platelet binding. Binding of two distinct antibodies at one of these epitopes was associated with enhancement of the rate of vWf-dependent platelet agglutination in the presence of ristocetin. This effect was more noticeable when cryosupernatant plasma was used in place of normal plasma as the source of vWf, and was not explicable simply in terms of antibody-induced cross-linking of vWf.
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Affiliation(s)
- V Hornsey
- The Edinburgh and South-East Scotland Blood Transfusion Service, Royal Infirmary, Edinburgh, UK
| | - L R Micklem
- The Department of Surgery, Edinburgh University, Edinburgh, UK
| | - M C McCann
- The Department of Surgery, Edinburgh University, Edinburgh, UK
| | - K James
- The Department of Surgery, Edinburgh University, Edinburgh, UK
| | - J Dawes
- The MRC/SNBTS Blood Components Assay Group, Edinburgh, UK
| | - D B L McClelland
- The Edinburgh and South-East Scotland Blood Transfusion Service, Royal Infirmary, Edinburgh, UK
| | - C V Prowse
- The Edinburgh and South-East Scotland Blood Transfusion Service, Royal Infirmary, Edinburgh, UK
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17
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Shiga TM, Xiao W, Yang H, Zhang X, Olek AT, Donohoe BS, Liu J, Makowski L, Hou T, McCann MC, Carpita NC, Mosier NS. Enhanced rates of enzymatic saccharification and catalytic synthesis of biofuel substrates in gelatinized cellulose generated by trifluoroacetic acid. Biotechnol Biofuels 2017; 10:310. [PMID: 29299060 PMCID: PMC5744396 DOI: 10.1186/s13068-017-0999-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 12/14/2017] [Indexed: 05/19/2023]
Abstract
BACKGROUND The crystallinity of cellulose is a principal factor limiting the efficient hydrolysis of biomass to fermentable sugars or direct catalytic conversion to biofuel components. We evaluated the impact of TFA-induced gelatinization of crystalline cellulose on enhancement of enzymatic digestion and catalytic conversion to biofuel substrates. RESULTS Low-temperature swelling of cotton linter cellulose in TFA at subzero temperatures followed by gentle heating to 55 °C dissolves the microfibril structure and forms composites of crystalline and amorphous gels upon addition of ethanol. The extent of gelatinization of crystalline cellulose was determined by reduction of birefringence in darkfield microscopy, loss of X-ray diffractability, and loss of resistance to acid hydrolysis. Upon freeze-drying, an additional degree of crystallinity returned as mostly cellulose II. Both enzymatic digestion with a commercial cellulase cocktail and maleic acid/AlCl3-catalyzed conversion to 5-hydroxymethylfurfural and levulinic acid were markedly enhanced with the low-temperature swollen cellulose. Only small improvements in rates and extent of hydrolysis and catalytic conversion were achieved upon heating to fully dissolve cellulose. CONCLUSIONS Low-temperature swelling of cellulose in TFA substantially reduces recalcitrance of crystalline cellulose to both enzymatic digestion and catalytic conversion. In a closed system to prevent loss of fluorohydrocarbons, the relative ease of recovery and regeneration of TFA by distillation makes it a potentially useful agent in large-scale deconstruction of biomass, not only for enzymatic depolymerization but also for enhancing rates of catalytic conversion to biofuel components and useful bio-products.
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Affiliation(s)
- Tânia M. Shiga
- Department of Botany & Plant Pathology, Purdue University, West Lafayette, IN 47907 USA
- Present Address: Department of Food Science and Experimental Nutrition, University of São Paulo, Av. Prof. Lineu Prestes, 580, Bloco 14, São Paul, SP 05508-000 Brazil
| | - Weihua Xiao
- College of Engineering, China Agricultural University, Beijing, 100083 People’s Republic of China
- Laboratory of Renewable Resources Engineering, Purdue University, West Lafayette, IN 47907 USA
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907 USA
| | - Haibing Yang
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907 USA
| | - Ximing Zhang
- Laboratory of Renewable Resources Engineering, Purdue University, West Lafayette, IN 47907 USA
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907 USA
| | - Anna T. Olek
- Department of Botany & Plant Pathology, Purdue University, West Lafayette, IN 47907 USA
| | - Bryon S. Donohoe
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Jiliang Liu
- Department of Bioengineering, Northeastern University, Boston, MA 02115 USA
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115 USA
- Present Address: Center for Functional Nanomaterials, Brookhaven National Laboratory, Shirley, New York, USA
| | - Lee Makowski
- Department of Bioengineering, Northeastern University, Boston, MA 02115 USA
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115 USA
| | - Tao Hou
- College of Engineering, China Agricultural University, Beijing, 100083 People’s Republic of China
| | - Maureen C. McCann
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907 USA
- Bindley Bioscience Center, Purdue University, West Lafayette, IN 47907 USA
| | - Nicholas C. Carpita
- Department of Botany & Plant Pathology, Purdue University, West Lafayette, IN 47907 USA
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907 USA
- Bindley Bioscience Center, Purdue University, West Lafayette, IN 47907 USA
| | - Nathan S. Mosier
- Laboratory of Renewable Resources Engineering, Purdue University, West Lafayette, IN 47907 USA
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907 USA
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18
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Lin CY, Jakes JE, Donohoe BS, Ciesielski PN, Yang H, Gleber SC, Vogt S, Ding SY, Peer WA, Murphy AS, McCann MC, Himmel ME, Tucker MP, Wei H. Directed plant cell-wall accumulation of iron: embedding co-catalyst for efficient biomass conversion. Biotechnol Biofuels 2016; 9:225. [PMID: 27777626 PMCID: PMC5073452 DOI: 10.1186/s13068-016-0639-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 10/08/2016] [Indexed: 05/14/2023]
Abstract
BACKGROUND Plant lignocellulosic biomass is an abundant, renewable feedstock for the production of biobased fuels and chemicals. Previously, we showed that iron can act as a co-catalyst to improve the deconstruction of lignocellulosic biomass. However, directly adding iron catalysts into biomass prior to pretreatment is diffusion limited, and increases the cost of biorefinery operations. Recently, we developed a new strategy for expressing iron-storage protein ferritin intracellularly to accumulate iron as a catalyst for the downstream deconstruction of lignocellulosic biomass. In this study, we extend this approach by fusing the heterologous ferritin gene with a signal peptide for secretion into Arabidopsis cell walls (referred to here as FerEX). RESULTS The transgenic Arabidopsis plants. FerEX. accumulated iron under both normal and iron-fertilized growth conditions; under the latter (iron-fertilized) condition, FerEX transgenic plants showed an increase in plant height and dry weight by 12 and 18 %, respectively, compared with the empty vector control plants. The SDS- and native-PAGE separation of cell-wall protein extracts followed by Western blot analyses confirmed the extracellular expression of ferritin in FerEX plants. Meanwhile, Perls' Prussian blue staining and X-ray fluorescence microscopy (XFM) maps revealed iron depositions in both the secondary and compound middle lamellae cell-wall layers, as well as in some of the corner compound middle lamella in FerEX. Remarkably, their harvested biomasses showed enhanced pretreatability and digestibility, releasing, respectively, 21 % more glucose and 34 % more xylose than the empty vector control plants. These values are significantly higher than those of our recently obtained ferritin intracellularly expressed plants. CONCLUSIONS This study demonstrated that extracellular expression of ferritin in Arabidopsis can produce plants with increased growth and iron accumulation, and reduced thermal and enzymatic recalcitrance. The results are attributed to the intimate colocation of the iron co-catalyst and the cellulose and hemicellulose within the plant cell-wall region, supporting the genetic modification strategy for incorporating conversion catalysts into energy crops prior to harvesting or processing at the biorefinery.
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Affiliation(s)
- Chien-Yuan Lin
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Joseph E. Jakes
- Forest Biopolymer Science and Engineering, USDA Forest Service, Forest Products Laboratory, Madison, WI 53726 USA
| | - Bryon S. Donohoe
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Peter N. Ciesielski
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Haibing Yang
- Department of Biological Science, Purdue University, West Lafayette, IN 47907 USA
| | - Sophie-Charlotte Gleber
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439 USA
| | - Stefan Vogt
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439 USA
| | - Shi-You Ding
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824 USA
| | - Wendy A. Peer
- Department of Environmental Science and Technology, University of Maryland, College Park, MD 20742 USA
| | - Angus S. Murphy
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742 USA
| | - Maureen C. McCann
- Department of Biological Science, Purdue University, West Lafayette, IN 47907 USA
| | - Michael E. Himmel
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Melvin P. Tucker
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Hui Wei
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
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Yang H, Wei H, Ma G, Antunes MS, Vogt S, Cox J, Zhang X, Liu X, Bu L, Gleber SC, Carpita NC, Makowski L, Himmel ME, Tucker MP, McCann MC, Murphy AS, Peer WA. Cell wall targeted in planta iron accumulation enhances biomass conversion and seed iron concentration in Arabidopsis and rice. Plant Biotechnol J 2016; 14:1998-2009. [PMID: 26929151 PMCID: PMC5043494 DOI: 10.1111/pbi.12557] [Citation(s) in RCA: 6] [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: 06/13/2014] [Revised: 02/12/2016] [Accepted: 02/23/2016] [Indexed: 05/27/2023]
Abstract
Conversion of nongrain biomass into liquid fuel is a sustainable approach to energy demands as global population increases. Previously, we showed that iron can act as a catalyst to enhance the degradation of lignocellulosic biomass for biofuel production. However, direct addition of iron catalysts to biomass pretreatment is diffusion-limited, would increase the cost and complexity of biorefinery unit operations and may have deleterious environmental impacts. Here, we show a new strategy for in planta accumulation of iron throughout the volume of the cell wall where iron acts as a catalyst in the deconstruction of lignocellulosic biomass. We engineered CBM-IBP fusion polypeptides composed of a carbohydrate-binding module family 11 (CBM11) and an iron-binding peptide (IBP) for secretion into Arabidopsis and rice cell walls. CBM-IBP transformed Arabidopsis and rice plants show significant increases in iron accumulation and biomass conversion compared to respective controls. Further, CBM-IBP rice shows a 35% increase in seed iron concentration and a 40% increase in seed yield in greenhouse experiments. CBM-IBP rice potentially could be used to address iron deficiency, the most common and widespread nutritional disorder according to the World Health Organization.
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Affiliation(s)
- Haibing Yang
- Center for Direct Catalytic Conversion Of Biomass to Biofuels (C3Bio), Purdue University, West Lafayette, IN, USA
- Department of Horticulture, Purdue University, West Lafayette, IN, USA
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Hui Wei
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, USA
| | - Guojie Ma
- Center for Direct Catalytic Conversion Of Biomass to Biofuels (C3Bio), Purdue University, West Lafayette, IN, USA
- Department of Horticulture, Purdue University, West Lafayette, IN, USA
| | - Mauricio S Antunes
- Center for Direct Catalytic Conversion Of Biomass to Biofuels (C3Bio), Purdue University, West Lafayette, IN, USA
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Stefan Vogt
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, IL, USA
| | - Joseph Cox
- Center for Direct Catalytic Conversion Of Biomass to Biofuels (C3Bio), Purdue University, West Lafayette, IN, USA
- Department of Horticulture, Purdue University, West Lafayette, IN, USA
| | - Xiao Zhang
- Department of Horticulture, Purdue University, West Lafayette, IN, USA
| | - Xiping Liu
- Center for Direct Catalytic Conversion Of Biomass to Biofuels (C3Bio), Purdue University, West Lafayette, IN, USA
- Department of Horticulture, Purdue University, West Lafayette, IN, USA
| | - Lintao Bu
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, USA
| | - S Charlotte Gleber
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, IL, USA
| | - Nicholas C Carpita
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, USA
| | - Lee Makowski
- Department of Bioengineering, Northeastern University, Boston, MA, USA
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - Michael E Himmel
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, USA
| | - Melvin P Tucker
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, IL, USA
| | - Maureen C McCann
- Center for Direct Catalytic Conversion Of Biomass to Biofuels (C3Bio), Purdue University, West Lafayette, IN, USA
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Angus S Murphy
- Center for Direct Catalytic Conversion Of Biomass to Biofuels (C3Bio), Purdue University, West Lafayette, IN, USA.
- Department of Horticulture, Purdue University, West Lafayette, IN, USA.
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA.
| | - Wendy A Peer
- Center for Direct Catalytic Conversion Of Biomass to Biofuels (C3Bio), Purdue University, West Lafayette, IN, USA
- Department of Horticulture, Purdue University, West Lafayette, IN, USA
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
- Department of Environmental Science and Technology, University of Maryland, College Park, MD, USA
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20
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Dugard CK, Mertz RA, Rayon C, Mercadante D, Hart C, Benatti MR, Olek AT, SanMiguel PJ, Cooper BR, Reiter WD, McCann MC, Carpita NC. The Cell Wall Arabinose-Deficient Arabidopsis thaliana Mutant murus5 Encodes a Defective Allele of REVERSIBLY GLYCOSYLATED POLYPEPTIDE2. Plant Physiol 2016; 171:1905-20. [PMID: 27217494 PMCID: PMC4936543 DOI: 10.1104/pp.15.01922] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 05/19/2016] [Indexed: 05/23/2023]
Abstract
Traditional marker-based mapping and next-generation sequencing was used to determine that the Arabidopsis (Arabidopsis thaliana) low cell wall arabinose mutant murus5 (mur5) encodes a defective allele of REVERSIBLY GLYCOSYLATED POLYPEPTIDE2 (RGP2). Marker analysis of 13 F2 confirmed mutant progeny from a recombinant mapping population gave a rough map position on the upper arm of chromosome 5, and deep sequencing of DNA from these 13 lines gave five candidate genes with G→A (C→T) transitions predicted to result in amino acid changes. Of these five, only insertional mutant alleles of RGP2, a gene that encodes a UDP-arabinose mutase that interconverts UDP-arabinopyranose and UDP-arabinofuranose, exhibited the low cell wall arabinose phenotype. The identities of mur5 and two SALK insertional alleles were confirmed by allelism tests and overexpression of wild-type RGP2 complementary DNA placed under the control of the 35S promoter in the three alleles. The mur5 mutation results in the conversion of cysteine-257 to tyrosine-257 within a conserved hydrophobic cluster predicted to be distal to the active site and essential for protein stability and possible heterodimerization with other isoforms of RGP.
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Affiliation(s)
- Christopher K Dugard
- Department of Botany and Plant Pathology (C.K.D., R.A.M., A.T.O., N.C.C.), Department of Biological Sciences (M.R.B., M.C.M., N.C.C.), Bindley Bioscience Center (B.R.C., M.C.M., N.C.C.), and Department of Horticulture and Landscape Architecture (P.J.S.), Purdue University, West Lafayette, Indiana 47907-2054;Université de Picardie Jules Verne, EA 3900-BIOPI, 80039 Amiens, France (C.R.);Heidelberg Institut für Theoretische Studien, Molecular Biomechanics, 69118 Heidelberg, Germany (D.M.); andDepartment of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269 (C.H., W.-D.R.)
| | - Rachel A Mertz
- Department of Botany and Plant Pathology (C.K.D., R.A.M., A.T.O., N.C.C.), Department of Biological Sciences (M.R.B., M.C.M., N.C.C.), Bindley Bioscience Center (B.R.C., M.C.M., N.C.C.), and Department of Horticulture and Landscape Architecture (P.J.S.), Purdue University, West Lafayette, Indiana 47907-2054;Université de Picardie Jules Verne, EA 3900-BIOPI, 80039 Amiens, France (C.R.);Heidelberg Institut für Theoretische Studien, Molecular Biomechanics, 69118 Heidelberg, Germany (D.M.); andDepartment of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269 (C.H., W.-D.R.)
| | - Catherine Rayon
- Department of Botany and Plant Pathology (C.K.D., R.A.M., A.T.O., N.C.C.), Department of Biological Sciences (M.R.B., M.C.M., N.C.C.), Bindley Bioscience Center (B.R.C., M.C.M., N.C.C.), and Department of Horticulture and Landscape Architecture (P.J.S.), Purdue University, West Lafayette, Indiana 47907-2054;Université de Picardie Jules Verne, EA 3900-BIOPI, 80039 Amiens, France (C.R.);Heidelberg Institut für Theoretische Studien, Molecular Biomechanics, 69118 Heidelberg, Germany (D.M.); andDepartment of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269 (C.H., W.-D.R.)
| | - Davide Mercadante
- Department of Botany and Plant Pathology (C.K.D., R.A.M., A.T.O., N.C.C.), Department of Biological Sciences (M.R.B., M.C.M., N.C.C.), Bindley Bioscience Center (B.R.C., M.C.M., N.C.C.), and Department of Horticulture and Landscape Architecture (P.J.S.), Purdue University, West Lafayette, Indiana 47907-2054;Université de Picardie Jules Verne, EA 3900-BIOPI, 80039 Amiens, France (C.R.);Heidelberg Institut für Theoretische Studien, Molecular Biomechanics, 69118 Heidelberg, Germany (D.M.); andDepartment of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269 (C.H., W.-D.R.)
| | - Christopher Hart
- Department of Botany and Plant Pathology (C.K.D., R.A.M., A.T.O., N.C.C.), Department of Biological Sciences (M.R.B., M.C.M., N.C.C.), Bindley Bioscience Center (B.R.C., M.C.M., N.C.C.), and Department of Horticulture and Landscape Architecture (P.J.S.), Purdue University, West Lafayette, Indiana 47907-2054;Université de Picardie Jules Verne, EA 3900-BIOPI, 80039 Amiens, France (C.R.);Heidelberg Institut für Theoretische Studien, Molecular Biomechanics, 69118 Heidelberg, Germany (D.M.); andDepartment of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269 (C.H., W.-D.R.)
| | - Matheus R Benatti
- Department of Botany and Plant Pathology (C.K.D., R.A.M., A.T.O., N.C.C.), Department of Biological Sciences (M.R.B., M.C.M., N.C.C.), Bindley Bioscience Center (B.R.C., M.C.M., N.C.C.), and Department of Horticulture and Landscape Architecture (P.J.S.), Purdue University, West Lafayette, Indiana 47907-2054;Université de Picardie Jules Verne, EA 3900-BIOPI, 80039 Amiens, France (C.R.);Heidelberg Institut für Theoretische Studien, Molecular Biomechanics, 69118 Heidelberg, Germany (D.M.); andDepartment of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269 (C.H., W.-D.R.)
| | - Anna T Olek
- Department of Botany and Plant Pathology (C.K.D., R.A.M., A.T.O., N.C.C.), Department of Biological Sciences (M.R.B., M.C.M., N.C.C.), Bindley Bioscience Center (B.R.C., M.C.M., N.C.C.), and Department of Horticulture and Landscape Architecture (P.J.S.), Purdue University, West Lafayette, Indiana 47907-2054;Université de Picardie Jules Verne, EA 3900-BIOPI, 80039 Amiens, France (C.R.);Heidelberg Institut für Theoretische Studien, Molecular Biomechanics, 69118 Heidelberg, Germany (D.M.); andDepartment of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269 (C.H., W.-D.R.)
| | - Phillip J SanMiguel
- Department of Botany and Plant Pathology (C.K.D., R.A.M., A.T.O., N.C.C.), Department of Biological Sciences (M.R.B., M.C.M., N.C.C.), Bindley Bioscience Center (B.R.C., M.C.M., N.C.C.), and Department of Horticulture and Landscape Architecture (P.J.S.), Purdue University, West Lafayette, Indiana 47907-2054;Université de Picardie Jules Verne, EA 3900-BIOPI, 80039 Amiens, France (C.R.);Heidelberg Institut für Theoretische Studien, Molecular Biomechanics, 69118 Heidelberg, Germany (D.M.); andDepartment of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269 (C.H., W.-D.R.)
| | - Bruce R Cooper
- Department of Botany and Plant Pathology (C.K.D., R.A.M., A.T.O., N.C.C.), Department of Biological Sciences (M.R.B., M.C.M., N.C.C.), Bindley Bioscience Center (B.R.C., M.C.M., N.C.C.), and Department of Horticulture and Landscape Architecture (P.J.S.), Purdue University, West Lafayette, Indiana 47907-2054;Université de Picardie Jules Verne, EA 3900-BIOPI, 80039 Amiens, France (C.R.);Heidelberg Institut für Theoretische Studien, Molecular Biomechanics, 69118 Heidelberg, Germany (D.M.); andDepartment of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269 (C.H., W.-D.R.)
| | - Wolf-Dieter Reiter
- Department of Botany and Plant Pathology (C.K.D., R.A.M., A.T.O., N.C.C.), Department of Biological Sciences (M.R.B., M.C.M., N.C.C.), Bindley Bioscience Center (B.R.C., M.C.M., N.C.C.), and Department of Horticulture and Landscape Architecture (P.J.S.), Purdue University, West Lafayette, Indiana 47907-2054;Université de Picardie Jules Verne, EA 3900-BIOPI, 80039 Amiens, France (C.R.);Heidelberg Institut für Theoretische Studien, Molecular Biomechanics, 69118 Heidelberg, Germany (D.M.); andDepartment of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269 (C.H., W.-D.R.)
| | - Maureen C McCann
- Department of Botany and Plant Pathology (C.K.D., R.A.M., A.T.O., N.C.C.), Department of Biological Sciences (M.R.B., M.C.M., N.C.C.), Bindley Bioscience Center (B.R.C., M.C.M., N.C.C.), and Department of Horticulture and Landscape Architecture (P.J.S.), Purdue University, West Lafayette, Indiana 47907-2054;Université de Picardie Jules Verne, EA 3900-BIOPI, 80039 Amiens, France (C.R.);Heidelberg Institut für Theoretische Studien, Molecular Biomechanics, 69118 Heidelberg, Germany (D.M.); andDepartment of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269 (C.H., W.-D.R.)
| | - Nicholas C Carpita
- Department of Botany and Plant Pathology (C.K.D., R.A.M., A.T.O., N.C.C.), Department of Biological Sciences (M.R.B., M.C.M., N.C.C.), Bindley Bioscience Center (B.R.C., M.C.M., N.C.C.), and Department of Horticulture and Landscape Architecture (P.J.S.), Purdue University, West Lafayette, Indiana 47907-2054;Université de Picardie Jules Verne, EA 3900-BIOPI, 80039 Amiens, France (C.R.);Heidelberg Institut für Theoretische Studien, Molecular Biomechanics, 69118 Heidelberg, Germany (D.M.); andDepartment of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269 (C.H., W.-D.R.)
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21
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Abstract
About 10% of a plant's genome is devoted to generating the protein machinery to synthesize, remodel, and deconstruct the cell wall. High-throughput genome sequencing technologies have enabled a reasonably complete inventory of wall-related genes that can be assembled into families of common evolutionary origin. Assigning function to each gene family member has been aided immensely by identification of mutants with visible phenotypes or by chemical and spectroscopic analysis of mutants with 'invisible' phenotypes of modified cell wall composition and architecture that do not otherwise affect plant growth or development. This review connects the inference of gene function on the basis of deviation from the wild type in genetic functional analyses to insights provided by modern analytical techniques that have brought us ever closer to elucidating the sequence structures of the major polysaccharide components of the plant cell wall.
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Affiliation(s)
- Nicholas C Carpita
- Department of Botany & Plant Pathology, 915 West State Street, Purdue University, West Lafayette, IN 47907, USA Department of Biological Sciences, 915 West State Street, Purdue University, West Lafayette, IN 47907, USA Bindley Bioscience Center, 1203 West State Street, Purdue University, West Lafayette, IN 47907, USA
| | - Maureen C McCann
- Department of Biological Sciences, 915 West State Street, Purdue University, West Lafayette, IN 47907, USA Bindley Bioscience Center, 1203 West State Street, Purdue University, West Lafayette, IN 47907, USA
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22
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Abstract
Recalcitrance of plant biomass to enzymatic hydrolysis for biofuel production is thought to be a property conferred by lignin or lignin-carbohydrate complexes. However, chemical catalytic and thermochemical conversion pathways, either alone or in combination with biochemical and fermentative pathways, now provide avenues to utilize lignin and to expand the product range beyond ethanol or butanol. To capture all of the carbon in renewable biomass, both lignin-derived aromatics and polysaccharide-derived sugars need to be transformed by catalysts to liquid hydrocarbons and high-value co-products. We offer a new definition of recalcitrance as those features of biomass which disproportionately increase energy requirements in conversion processes, increase the cost and complexity of operations in the biorefinery, and/or reduce the recovery of biomass carbon into desired products. The application of novel processing technologies applied to biomass reveal new determinants of recalcitrance that comprise a broad range of molecular, nanoscale, and macroscale factors. Sampling natural genetic diversity within a species, transgenic approaches, and synthetic biology approaches are all strategies that can be used to select biomass for reduced recalcitrance in various pretreatments and conversion pathways.
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Affiliation(s)
- Maureen C McCann
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907-1392, USA
| | - Nicholas C Carpita
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907-1392, USA Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907-1392, USA
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23
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Penning BW, Sykes RW, Babcock NC, Dugard CK, Held MA, Klimek JF, Shreve JT, Fowler M, Ziebell A, Davis MF, Decker SR, Turner GB, Mosier NS, Springer NM, Thimmapuram J, Weil CF, McCann MC, Carpita NC. Genetic Determinants for Enzymatic Digestion of Lignocellulosic Biomass Are Independent of Those for Lignin Abundance in a Maize Recombinant Inbred Population. Plant Physiol 2014; 165:1475-1487. [PMID: 24972714 PMCID: PMC4119032 DOI: 10.1104/pp.114.242446] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Biotechnological approaches to reduce or modify lignin in biomass crops are predicated on the assumption that it is the principal determinant of the recalcitrance of biomass to enzymatic digestion for biofuels production. We defined quantitative trait loci (QTL) in the Intermated B73 × Mo17 recombinant inbred maize (Zea mays) population using pyrolysis molecular-beam mass spectrometry to establish stem lignin content and an enzymatic hydrolysis assay to measure glucose and xylose yield. Among five multiyear QTL for lignin abundance, two for 4-vinylphenol abundance, and four for glucose and/or xylose yield, not a single QTL for aromatic abundance and sugar yield was shared. A genome-wide association study for lignin abundance and sugar yield of the 282-member maize association panel provided candidate genes in the 11 QTL of the B73 and Mo17 parents but showed that many other alleles impacting these traits exist among this broader pool of maize genetic diversity. B73 and Mo17 genotypes exhibited large differences in gene expression in developing stem tissues independent of allelic variation. Combining these complementary genetic approaches provides a narrowed list of candidate genes. A cluster of SCARECROW-LIKE9 and SCARECROW-LIKE14 transcription factor genes provides exceptionally strong candidate genes emerging from the genome-wide association study. In addition to these and genes associated with cell wall metabolism, candidates include several other transcription factors associated with vascularization and fiber formation and components of cellular signaling pathways. These results provide new insights and strategies beyond the modification of lignin to enhance yields of biofuels from genetically modified biomass.
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Affiliation(s)
- Bryan W Penning
- Departments of Biological Sciences (B.W.P., M.C.M., N.C.C.), Botany and Plant Pathology (C.K.D., M.A.H., J.F.K., N.C.C.), and Agronomy (N.C.B., C.F.W.), Laboratory of Renewable Resources Engineering and Agricultural and Biological Engineering (N.S.M.), and Bioinformatics Core (J.T.S., J.T.), Purdue University, West Lafayette, Indiana 47907;National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401 (R.W.S., M.F., A.Z., M.F.D., S.R.D., G.B.T.); andDepartment of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108 (N.M.S.)
| | - Robert W Sykes
- Departments of Biological Sciences (B.W.P., M.C.M., N.C.C.), Botany and Plant Pathology (C.K.D., M.A.H., J.F.K., N.C.C.), and Agronomy (N.C.B., C.F.W.), Laboratory of Renewable Resources Engineering and Agricultural and Biological Engineering (N.S.M.), and Bioinformatics Core (J.T.S., J.T.), Purdue University, West Lafayette, Indiana 47907;National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401 (R.W.S., M.F., A.Z., M.F.D., S.R.D., G.B.T.); andDepartment of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108 (N.M.S.)
| | - Nicholas C Babcock
- Departments of Biological Sciences (B.W.P., M.C.M., N.C.C.), Botany and Plant Pathology (C.K.D., M.A.H., J.F.K., N.C.C.), and Agronomy (N.C.B., C.F.W.), Laboratory of Renewable Resources Engineering and Agricultural and Biological Engineering (N.S.M.), and Bioinformatics Core (J.T.S., J.T.), Purdue University, West Lafayette, Indiana 47907;National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401 (R.W.S., M.F., A.Z., M.F.D., S.R.D., G.B.T.); andDepartment of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108 (N.M.S.)
| | - Christopher K Dugard
- Departments of Biological Sciences (B.W.P., M.C.M., N.C.C.), Botany and Plant Pathology (C.K.D., M.A.H., J.F.K., N.C.C.), and Agronomy (N.C.B., C.F.W.), Laboratory of Renewable Resources Engineering and Agricultural and Biological Engineering (N.S.M.), and Bioinformatics Core (J.T.S., J.T.), Purdue University, West Lafayette, Indiana 47907;National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401 (R.W.S., M.F., A.Z., M.F.D., S.R.D., G.B.T.); andDepartment of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108 (N.M.S.)
| | - Michael A Held
- Departments of Biological Sciences (B.W.P., M.C.M., N.C.C.), Botany and Plant Pathology (C.K.D., M.A.H., J.F.K., N.C.C.), and Agronomy (N.C.B., C.F.W.), Laboratory of Renewable Resources Engineering and Agricultural and Biological Engineering (N.S.M.), and Bioinformatics Core (J.T.S., J.T.), Purdue University, West Lafayette, Indiana 47907;National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401 (R.W.S., M.F., A.Z., M.F.D., S.R.D., G.B.T.); andDepartment of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108 (N.M.S.)
| | - John F Klimek
- Departments of Biological Sciences (B.W.P., M.C.M., N.C.C.), Botany and Plant Pathology (C.K.D., M.A.H., J.F.K., N.C.C.), and Agronomy (N.C.B., C.F.W.), Laboratory of Renewable Resources Engineering and Agricultural and Biological Engineering (N.S.M.), and Bioinformatics Core (J.T.S., J.T.), Purdue University, West Lafayette, Indiana 47907;National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401 (R.W.S., M.F., A.Z., M.F.D., S.R.D., G.B.T.); andDepartment of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108 (N.M.S.)
| | - Jacob T Shreve
- Departments of Biological Sciences (B.W.P., M.C.M., N.C.C.), Botany and Plant Pathology (C.K.D., M.A.H., J.F.K., N.C.C.), and Agronomy (N.C.B., C.F.W.), Laboratory of Renewable Resources Engineering and Agricultural and Biological Engineering (N.S.M.), and Bioinformatics Core (J.T.S., J.T.), Purdue University, West Lafayette, Indiana 47907;National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401 (R.W.S., M.F., A.Z., M.F.D., S.R.D., G.B.T.); andDepartment of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108 (N.M.S.)
| | - Matthew Fowler
- Departments of Biological Sciences (B.W.P., M.C.M., N.C.C.), Botany and Plant Pathology (C.K.D., M.A.H., J.F.K., N.C.C.), and Agronomy (N.C.B., C.F.W.), Laboratory of Renewable Resources Engineering and Agricultural and Biological Engineering (N.S.M.), and Bioinformatics Core (J.T.S., J.T.), Purdue University, West Lafayette, Indiana 47907;National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401 (R.W.S., M.F., A.Z., M.F.D., S.R.D., G.B.T.); andDepartment of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108 (N.M.S.)
| | - Angela Ziebell
- Departments of Biological Sciences (B.W.P., M.C.M., N.C.C.), Botany and Plant Pathology (C.K.D., M.A.H., J.F.K., N.C.C.), and Agronomy (N.C.B., C.F.W.), Laboratory of Renewable Resources Engineering and Agricultural and Biological Engineering (N.S.M.), and Bioinformatics Core (J.T.S., J.T.), Purdue University, West Lafayette, Indiana 47907;National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401 (R.W.S., M.F., A.Z., M.F.D., S.R.D., G.B.T.); andDepartment of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108 (N.M.S.)
| | - Mark F Davis
- Departments of Biological Sciences (B.W.P., M.C.M., N.C.C.), Botany and Plant Pathology (C.K.D., M.A.H., J.F.K., N.C.C.), and Agronomy (N.C.B., C.F.W.), Laboratory of Renewable Resources Engineering and Agricultural and Biological Engineering (N.S.M.), and Bioinformatics Core (J.T.S., J.T.), Purdue University, West Lafayette, Indiana 47907;National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401 (R.W.S., M.F., A.Z., M.F.D., S.R.D., G.B.T.); andDepartment of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108 (N.M.S.)
| | - Stephen R Decker
- Departments of Biological Sciences (B.W.P., M.C.M., N.C.C.), Botany and Plant Pathology (C.K.D., M.A.H., J.F.K., N.C.C.), and Agronomy (N.C.B., C.F.W.), Laboratory of Renewable Resources Engineering and Agricultural and Biological Engineering (N.S.M.), and Bioinformatics Core (J.T.S., J.T.), Purdue University, West Lafayette, Indiana 47907;National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401 (R.W.S., M.F., A.Z., M.F.D., S.R.D., G.B.T.); andDepartment of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108 (N.M.S.)
| | - Geoffrey B Turner
- Departments of Biological Sciences (B.W.P., M.C.M., N.C.C.), Botany and Plant Pathology (C.K.D., M.A.H., J.F.K., N.C.C.), and Agronomy (N.C.B., C.F.W.), Laboratory of Renewable Resources Engineering and Agricultural and Biological Engineering (N.S.M.), and Bioinformatics Core (J.T.S., J.T.), Purdue University, West Lafayette, Indiana 47907;National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401 (R.W.S., M.F., A.Z., M.F.D., S.R.D., G.B.T.); andDepartment of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108 (N.M.S.)
| | - Nathan S Mosier
- Departments of Biological Sciences (B.W.P., M.C.M., N.C.C.), Botany and Plant Pathology (C.K.D., M.A.H., J.F.K., N.C.C.), and Agronomy (N.C.B., C.F.W.), Laboratory of Renewable Resources Engineering and Agricultural and Biological Engineering (N.S.M.), and Bioinformatics Core (J.T.S., J.T.), Purdue University, West Lafayette, Indiana 47907;National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401 (R.W.S., M.F., A.Z., M.F.D., S.R.D., G.B.T.); andDepartment of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108 (N.M.S.)
| | - Nathan M Springer
- Departments of Biological Sciences (B.W.P., M.C.M., N.C.C.), Botany and Plant Pathology (C.K.D., M.A.H., J.F.K., N.C.C.), and Agronomy (N.C.B., C.F.W.), Laboratory of Renewable Resources Engineering and Agricultural and Biological Engineering (N.S.M.), and Bioinformatics Core (J.T.S., J.T.), Purdue University, West Lafayette, Indiana 47907;National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401 (R.W.S., M.F., A.Z., M.F.D., S.R.D., G.B.T.); andDepartment of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108 (N.M.S.)
| | - Jyothi Thimmapuram
- Departments of Biological Sciences (B.W.P., M.C.M., N.C.C.), Botany and Plant Pathology (C.K.D., M.A.H., J.F.K., N.C.C.), and Agronomy (N.C.B., C.F.W.), Laboratory of Renewable Resources Engineering and Agricultural and Biological Engineering (N.S.M.), and Bioinformatics Core (J.T.S., J.T.), Purdue University, West Lafayette, Indiana 47907;National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401 (R.W.S., M.F., A.Z., M.F.D., S.R.D., G.B.T.); andDepartment of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108 (N.M.S.)
| | - Clifford F Weil
- Departments of Biological Sciences (B.W.P., M.C.M., N.C.C.), Botany and Plant Pathology (C.K.D., M.A.H., J.F.K., N.C.C.), and Agronomy (N.C.B., C.F.W.), Laboratory of Renewable Resources Engineering and Agricultural and Biological Engineering (N.S.M.), and Bioinformatics Core (J.T.S., J.T.), Purdue University, West Lafayette, Indiana 47907;National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401 (R.W.S., M.F., A.Z., M.F.D., S.R.D., G.B.T.); andDepartment of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108 (N.M.S.)
| | - Maureen C McCann
- Departments of Biological Sciences (B.W.P., M.C.M., N.C.C.), Botany and Plant Pathology (C.K.D., M.A.H., J.F.K., N.C.C.), and Agronomy (N.C.B., C.F.W.), Laboratory of Renewable Resources Engineering and Agricultural and Biological Engineering (N.S.M.), and Bioinformatics Core (J.T.S., J.T.), Purdue University, West Lafayette, Indiana 47907;National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401 (R.W.S., M.F., A.Z., M.F.D., S.R.D., G.B.T.); andDepartment of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108 (N.M.S.)
| | - Nicholas C Carpita
- Departments of Biological Sciences (B.W.P., M.C.M., N.C.C.), Botany and Plant Pathology (C.K.D., M.A.H., J.F.K., N.C.C.), and Agronomy (N.C.B., C.F.W.), Laboratory of Renewable Resources Engineering and Agricultural and Biological Engineering (N.S.M.), and Bioinformatics Core (J.T.S., J.T.), Purdue University, West Lafayette, Indiana 47907;National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401 (R.W.S., M.F., A.Z., M.F.D., S.R.D., G.B.T.); andDepartment of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108 (N.M.S.)
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Fraysse LC, Wells B, McCann MC, Kjellbom P. Specific plasma membrane aquaporins of the PIP1 subfamily are expressed in sieve elements and guard cells. Biol Cell 2012; 97:519-34. [PMID: 15898953 DOI: 10.1042/bc20040122] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
BACKGROUND INFORMATION Transmembrane water flow is aided by water-specific channel proteins, aquaporins. Plant genomes code for approx. 35 expressed and functional aquaporin isoforms. Plant aquaporins fall into four different subfamilies of which the PIPs (plasma membrane intrinsic proteins) constitute the largest and evolutionarily most conserved subfamily with 13 members in Arabidopsis and maize. Furthermore, the PIPs can be divided into two phylogenetic groups, PIP1 and PIP2, of which the PIP1 isoforms are most tightly conserved, sharing >90% amino acid sequence identity. As the nomenclature implies, the majority of PIPs have been shown to be localized at the plasma membrane. Recently, two highly abundant plasma membrane aquaporins, SoPIP2;1 and SoPIP1;2, have been purified and structurally characterized. RESULTS We report the cloning of a cDNA encoding SoPIP1;2 and show that there are at least five additional sequences homologous with SoPIP2;1 and SoPIP1;2 in the spinach genome. To understand their role in planta, we have investigated the cellular localization of the aquaporin homologues SoPIP1;2 and SoPIP1;1. By Western- and Northern-blot analyses and by immunocytochemical detection at the light and electron microscopic levels, we show that SoPIP1;2 is highly expressed in phloem sieve elements of leaves, roots and petioles and that SoPIP1;1 is present in stomatal guard cells. CONCLUSIONS Localization of the two abundant aquaporin isoforms suggests roles for specific PIPs of the PIP1 subgroup in phloem loading, transport and unloading, and in stomatal movements.
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Affiliation(s)
- Laure C Fraysse
- Department of Plant Biochemistry, Lund University, P.O. Box 124, S-22100 Lund, Sweden
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Benatti MR, Penning BW, Carpita NC, McCann MC. We are good to grow: dynamic integration of cell wall architecture with the machinery of growth. Front Plant Sci 2012; 3:187. [PMID: 22936938 PMCID: PMC3424494 DOI: 10.3389/fpls.2012.00187] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Accepted: 08/01/2012] [Indexed: 05/18/2023]
Abstract
Despite differences in cell wall composition between the type I cell walls of dicots and most monocots and the type II walls of commelinid monocots, all flowering plants respond to the same classes of growth regulators in the same tissue-specific way and exhibit the same growth physics. Substantial progress has been made in defining gene families and identifying mutants in cell wall-related genes, but our understanding of the biochemical basis of wall extensibility during growth is still rudimentary. In this review, we highlight insights into the physiological control of cell expansion emerging from genetic functional analyses, mostly in Arabidopsis and other dicots, and a few examples of genes of potential orthologous function in grass species. We discuss examples of cell wall architectural features that impact growth independent of composition, and progress in identifying proteins involved in transduction of growth signals and integrating their outputs in the molecular machinery of wall expansion.
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Affiliation(s)
- Matheus R. Benatti
- Department of Biological Sciences, Purdue UniversityWest Lafayette, IN, USA
- Bindley Bioscience Center, Purdue UniversityWest Lafayette, IN, USA
| | - Bryan W. Penning
- Department of Biological Sciences, Purdue UniversityWest Lafayette, IN, USA
- Bindley Bioscience Center, Purdue UniversityWest Lafayette, IN, USA
| | - Nicholas C. Carpita
- Department of Biological Sciences, Purdue UniversityWest Lafayette, IN, USA
- Bindley Bioscience Center, Purdue UniversityWest Lafayette, IN, USA
- Department of Botany and Plant Pathology, Purdue UniversityWest Lafayette, IN, USA
| | - Maureen C. McCann
- Department of Biological Sciences, Purdue UniversityWest Lafayette, IN, USA
- Bindley Bioscience Center, Purdue UniversityWest Lafayette, IN, USA
- *Correspondence: Maureen C. McCann, Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN, USA. e-mail:
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Carpita NC, McCann MC. The maize mixed-linkage (1->3),(1->4)-beta-D-glucan polysaccharide is synthesized at the golgi membrane. Plant Physiol 2010; 153:1362-71. [PMID: 20488897 PMCID: PMC2899932 DOI: 10.1104/pp.110.156158] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2010] [Accepted: 05/19/2010] [Indexed: 05/18/2023]
Abstract
With the exception of cellulose and callose, the cell wall polysaccharides are synthesized in Golgi membranes, packaged into vesicles, and exported to the plasma membrane where they are integrated into the microfibrillar structure. Consistent with this paradigm, several published reports have shown that the maize (Zea mays) mixed-linkage (1-->3),(1-->4)-beta-D-glucan, a polysaccharide that among angiosperms is unique to the grasses and related Poales species, is synthesized in vitro with isolated maize coleoptile Golgi membranes and the nucleotide-sugar substrate, UDP-glucose. However, a recent study reported the inability to detect the beta-glucan immunocytochemically at the Golgi, resulting in a hypothesis that the mixed-linkage beta-glucan oligomers may be initiated at the Golgi but are polymerized at the plasma membrane surface. Here, we demonstrate that (1-->3),(1-->4)-beta-D-glucans are detected immunocytochemically at the Golgi of the developing maize coleoptiles. Further, when maize seedlings at the third-leaf stage were pulse labeled with [(14)C]O(2) and Golgi membranes were isolated from elongating cells at the base of the developing leaves, (1-->3),(1-->4)-beta-D-glucans of an average molecular mass of 250 kD and higher were detected in isolated Golgi membranes. When the pulse was followed by a chase period, the labeled polysaccharides of the Golgi membrane diminished with subsequent transfer to the cell wall. (1-->3),(1-->4)-beta-D-Glucans of at least 250 kD were isolated from cell walls, but much larger aggregates were also detected, indicating a potential for intermolecular interactions with glucuronoarabinoxylans or intermolecular grafting in muro.
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Affiliation(s)
- Nicholas C Carpita
- Department of Botany and Plant Pathology, Bindley Biosciences Center, Purdue University, West Lafayette, Indiana 47907-2054, USA.
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Penning BW, Hunter CT, Tayengwa R, Eveland AL, Dugard CK, Olek AT, Vermerris W, Koch KE, McCarty DR, Davis MF, Thomas SR, McCann MC, Carpita NC. Genetic resources for maize cell wall biology. Plant Physiol 2009; 151:1703-28. [PMID: 19926802 PMCID: PMC2785990 DOI: 10.1104/pp.109.136804] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Grass species represent a major source of food, feed, and fiber crops and potential feedstocks for biofuel production. Most of the biomass is contributed by cell walls that are distinct in composition from all other flowering plants. Identifying cell wall-related genes and their functions underpins a fundamental understanding of growth and development in these species. Toward this goal, we are building a knowledge base of the maize (Zea mays) genes involved in cell wall biology, their expression profiles, and the phenotypic consequences of mutation. Over 750 maize genes were annotated and assembled into gene families predicted to function in cell wall biogenesis. Comparative genomics of maize, rice (Oryza sativa), and Arabidopsis (Arabidopsis thaliana) sequences reveal differences in gene family structure between grass species and a reference eudicot species. Analysis of transcript profile data for cell wall genes in developing maize ovaries revealed that expression within families differed by up to 100-fold. When transcriptional analyses of developing ovaries before pollination from Arabidopsis, rice, and maize were contrasted, distinct sets of cell wall genes were expressed in grasses. These differences in gene family structure and expression between Arabidopsis and the grasses underscore the requirement for a grass-specific genetic model for functional analyses. A UniformMu population proved to be an important resource in both forward- and reverse-genetics approaches to identify hundreds of mutants in cell wall genes. A forward screen of field-grown lines by near-infrared spectroscopic screen of mature leaves yielded several dozen lines with heritable spectroscopic phenotypes. Pyrolysis-molecular beam mass spectrometry confirmed that several nir mutants had altered carbohydrate-lignin compositions.
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Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves TA, Minx P, Reily AD, Courtney L, Kruchowski SS, Tomlinson C, Strong C, Delehaunty K, Fronick C, Courtney B, Rock SM, Belter E, Du F, Kim K, Abbott RM, Cotton M, Levy A, Marchetto P, Ochoa K, Jackson SM, Gillam B, Chen W, Yan L, Higginbotham J, Cardenas M, Waligorski J, Applebaum E, Phelps L, Falcone J, Kanchi K, Thane T, Scimone A, Thane N, Henke J, Wang T, Ruppert J, Shah N, Rotter K, Hodges J, Ingenthron E, Cordes M, Kohlberg S, Sgro J, Delgado B, Mead K, Chinwalla A, Leonard S, Crouse K, Collura K, Kudrna D, Currie J, He R, Angelova A, Rajasekar S, Mueller T, Lomeli R, Scara G, Ko A, Delaney K, Wissotski M, Lopez G, Campos D, Braidotti M, Ashley E, Golser W, Kim H, Lee S, Lin J, Dujmic Z, Kim W, Talag J, Zuccolo A, Fan C, Sebastian A, Kramer M, Spiegel L, Nascimento L, Zutavern T, Miller B, Ambroise C, Muller S, Spooner W, Narechania A, Ren L, Wei S, Kumari S, Faga B, Levy MJ, McMahan L, Van Buren P, Vaughn MW, Ying K, Yeh CT, Emrich SJ, Jia Y, Kalyanaraman A, Hsia AP, Barbazuk WB, Baucom RS, Brutnell TP, Carpita NC, Chaparro C, Chia JM, Deragon JM, Estill JC, Fu Y, Jeddeloh JA, Han Y, Lee H, Li P, Lisch DR, Liu S, Liu Z, Nagel DH, McCann MC, SanMiguel P, Myers AM, Nettleton D, Nguyen J, Penning BW, Ponnala L, Schneider KL, Schwartz DC, Sharma A, Soderlund C, Springer NM, Sun Q, Wang H, Waterman M, Westerman R, Wolfgruber TK, Yang L, Yu Y, Zhang L, Zhou S, Zhu Q, Bennetzen JL, Dawe RK, Jiang J, Jiang N, Presting GG, Wessler SR, Aluru S, Martienssen RA, Clifton SW, McCombie WR, Wing RA, Wilson RK. The B73 Maize Genome: Complexity, Diversity, and Dynamics. Science 2009; 326:1112-5. [PMID: 19965430 DOI: 10.1126/science.1178534] [Citation(s) in RCA: 2467] [Impact Index Per Article: 164.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Arsovski AA, Popma TM, Haughn GW, Carpita NC, McCann MC, Western TL. AtBXL1 encodes a bifunctional beta-D-xylosidase/alpha-L-arabinofuranosidase required for pectic arabinan modification in Arabidopsis mucilage secretory cells. Plant Physiol 2009; 150:1219-34. [PMID: 19458117 PMCID: PMC2705025 DOI: 10.1104/pp.109.138388] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2009] [Accepted: 05/14/2009] [Indexed: 05/17/2023]
Abstract
Following pollination, the epidermal cells of the Arabidopsis (Arabidopsis thaliana) ovule undergo a complex differentiation process that includes the synthesis and polar secretion of pectinaceous mucilage followed by the production of a secondary cell wall. Wetting of mature seeds leads to the rapid bursting of these mucilage secretory cells to release a hydrophilic gel that surrounds the seed and is believed to aid in seed hydration and germination. A novel mutant is identified where mucilage release is both patchy and slow and whose seeds display delayed germination. While developmental analysis of mutant seeds reveals no change in mucilage secretory cell morphology, changes in monosaccharide quantities are detected, suggesting the mucilage release defect results from altered mucilage composition. Plasmid rescue and cloning of the mutant locus revealed a T-DNA insertion in AtBXL1, which encodes a putative bifunctional beta-d-xylosidase/alpha-l-arabinofuranosidase that has been implicated as a beta-d-xylosidase acting during vascular development. Chemical and immunological analyses of mucilage extracted from bxl1 mutant seeds and antibody staining of developing seed coats reveal an increase in (1-->5)-linked arabinans, suggesting that BXL1 is acting as an alpha-l-arabinofuranosidase in the seed coat. This implication is supported by the ability to rescue mucilage release through treatment of bxl1 seeds with exogenous alpha-l-arabinofuranosidases. Together, these results suggest that trimming of rhamnogalacturonan I arabinan side chains is required for correct mucilage release and reveal a new role for BXL1 as an alpha-l-arabinofuranosidase acting in seed coat development.
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Affiliation(s)
- Andrej A Arsovski
- Biology Department, McGill University, Montreal, Quebec, Canada H3A 1B1
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Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten U, Mitros T, Poliakov A, Schmutz J, Spannagl M, Tang H, Wang X, Wicker T, Bharti AK, Chapman J, Feltus FA, Gowik U, Grigoriev IV, Lyons E, Maher CA, Martis M, Narechania A, Otillar RP, Penning BW, Salamov AA, Wang Y, Zhang L, Carpita NC, Freeling M, Gingle AR, Hash CT, Keller B, Klein P, Kresovich S, McCann MC, Ming R, Peterson DG, Mehboob-ur-Rahman, Ware D, Westhoff P, Mayer KFX, Messing J, Rokhsar DS. The Sorghum bicolor genome and the diversification of grasses. Nature 2009; 457:551-6. [PMID: 19189423 DOI: 10.1038/nature07723] [Citation(s) in RCA: 1628] [Impact Index Per Article: 108.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Sorghum, an African grass related to sugar cane and maize, is grown for food, feed, fibre and fuel. We present an initial analysis of the approximately 730-megabase Sorghum bicolor (L.) Moench genome, placing approximately 98% of genes in their chromosomal context using whole-genome shotgun sequence validated by genetic, physical and syntenic information. Genetic recombination is largely confined to about one-third of the sorghum genome with gene order and density similar to those of rice. Retrotransposon accumulation in recombinationally recalcitrant heterochromatin explains the approximately 75% larger genome size of sorghum compared with rice. Although gene and repetitive DNA distributions have been preserved since palaeopolyploidization approximately 70 million years ago, most duplicated gene sets lost one member before the sorghum-rice divergence. Concerted evolution makes one duplicated chromosomal segment appear to be only a few million years old. About 24% of genes are grass-specific and 7% are sorghum-specific. Recent gene and microRNA duplications may contribute to sorghum's drought tolerance.
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Affiliation(s)
- Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA.
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Daras G, Rigas S, Penning B, Milioni D, McCann MC, Carpita NC, Fasseas C, Hatzopoulos P. The thanatos mutation in Arabidopsis thaliana cellulose synthase 3 (AtCesA3) has a dominant-negative effect on cellulose synthesis and plant growth. New Phytol 2009; 184:114-126. [PMID: 19645738 DOI: 10.1111/j.1469-8137.2009.02960.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Genetic functional analyses of mutants in plant genes encoding cellulose synthases (CesAs) have suggested that cellulose deposition requires the activity of multiple CesA proteins. Here, a genetic screen has led to the identification of thanatos (than), a semi-dominant mutant of Arabidopsis thaliana with impaired growth of seedlings. Homozygous seedlings of than germinate and grow but do not survive. In contrast to other CesA mutants, heterozygous plants are dwarfed and display a radially swollen root phenotype. Cellulose content is reduced by approximately one-fifth in heterozygous and by two-fifths in homozygous plants, showing gene-dosage dependence. Map-based cloning revealed an amino acid substitution (P578S) in the catalytic domain of the AtCesA3 gene, indicating a critical role for this residue in the structure and function of the cellulose synthase complex. Ab initio analysis of the AtCesA3 subdomain flanking the conserved proline residue predicted that the amino acid substitution to serine alters protein secondary structure in the catalytic domain. Gene dosage-dependent expression of the AtCesA3 mutant gene in wild-type A. thaliana plants resulted in a than dominant-negative phenotype. We propose that the incorporation of a mis-folded CesA3 subunit into the cellulose synthase complex may stall or prevent the formation of functional rosette complexes.
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Affiliation(s)
- Gerasimos Daras
- Department of Agricultural Biotechnology, Agricultural University of Athens, Iera Odos 75, Athens 118 55, Greece
| | - Stamatis Rigas
- Department of Agricultural Biotechnology, Agricultural University of Athens, Iera Odos 75, Athens 118 55, Greece
| | - Bryan Penning
- Department of Biological Sciences, Purdue University, 915 W. State Street, West Lafayette, IN 47907, USA
| | - Dimitra Milioni
- Department of Agricultural Biotechnology, Agricultural University of Athens, Iera Odos 75, Athens 118 55, Greece
| | - Maureen C McCann
- Department of Biological Sciences, Purdue University, 915 W. State Street, West Lafayette, IN 47907, USA
| | - Nicholas C Carpita
- Department of Botany and Plant Pathology, Purdue University, 915 W. State Street, West Lafayette, IN 47907, USA
| | - Constantinos Fasseas
- Department of Agricultural Biotechnology, Agricultural University of Athens, Iera Odos 75, Athens 118 55, Greece
| | - Polydefkis Hatzopoulos
- Department of Agricultural Biotechnology, Agricultural University of Athens, Iera Odos 75, Athens 118 55, Greece
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Carpita NC, McCann MC. Maize and sorghum: genetic resources for bioenergy grasses. Trends Plant Sci 2008; 13:415-20. [PMID: 18650120 DOI: 10.1016/j.tplants.2008.06.002] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2008] [Revised: 06/02/2008] [Accepted: 06/04/2008] [Indexed: 05/18/2023]
Abstract
The highly photosynthetic-efficient C4 grasses, such as switchgrass (Panicum virgatum), Miscanthus (Miscanthusxgiganteus), sorghum (Sorghum bicolor) and maize (Zea mays), are expected to provide abundant and sustainable resources of lignocellulosic biomass for the production of biofuels. A deeper understanding of the synthesis, deposition and hydrolysis of the distinctive cell walls of grasses is crucial to gain genetic control of traits that contribute to biomass yield and quality. With a century of genetic investigations and breeding success, recently completed genome sequences, well-characterized cell wall compositions, and a close evolutionary relationship with future bioenergy perennial grasses, we propose that maize and sorghum are key model systems for gene discovery relating to biomass yield and quality in the bioenergy grasses.
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Affiliation(s)
- Nicholas C Carpita
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907-2054, USA.
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McCann MC, Carpita NC. Designing the deconstruction of plant cell walls. Curr Opin Plant Biol 2008; 11:314-20. [PMID: 18486537 DOI: 10.1016/j.pbi.2008.04.001] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2007] [Revised: 03/25/2008] [Accepted: 04/02/2008] [Indexed: 05/18/2023]
Abstract
Cell wall architecture plays a key role in the regulation of plant cell growth and differentiation into specific cell types. Gaining genetic control of the amount, composition, and structure of cell walls in different cell types will impact both the quantity and yield of fermentable sugars from biomass for biofuels production. The recalcitrance of plant biomass to degradation is a function of how polymers crosslink and aggregate within walls. Novel imaging technologies provide an opportunity to probe these higher order structures in their native state. If cell walls are to be efficiently deconstructed enzymatically to release fermentable sugars, then we require a detailed understanding of their structural organization in future bioenergy crops.
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Affiliation(s)
- Maureen C McCann
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA.
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Dean GH, Zheng H, Tewari J, Huang J, Young DS, Hwang YT, Western TL, Carpita NC, McCann MC, Mansfield SD, Haughn GW. The Arabidopsis MUM2 gene encodes a beta-galactosidase required for the production of seed coat mucilage with correct hydration properties. Plant Cell 2007; 19:4007-21. [PMID: 18165329 PMCID: PMC2217648 DOI: 10.1105/tpc.107.050609] [Citation(s) in RCA: 120] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2007] [Revised: 12/10/2007] [Accepted: 12/12/2007] [Indexed: 05/17/2023]
Abstract
Seed coat development in Arabidopsis thaliana involves a complex pathway where cells of the outer integument differentiate into a highly specialized cell type after fertilization. One aspect of this developmental process involves the secretion of a large amount of pectinaceous mucilage into the apoplast. When the mature seed coat is exposed to water, this mucilage expands to break the primary cell wall and encapsulate the seed. The mucilage-modified2 (mum2) mutant is characterized by a failure to extrude mucilage on hydration, although mucilage is produced as normal during development. The defect in mum2 appears to reside in the mucilage itself, as mucilage fails to expand even when the barrier of the primary cell wall is removed. We have cloned the MUM2 gene and expressed recombinant MUM2 protein, which has beta-galactosidase activity. Biochemical analysis of the mum2 mucilage reveals alterations in pectins that are consistent with a defect in beta-galactosidase activity, and we have demonstrated that MUM2 is localized to the cell wall. We propose that MUM2 is involved in modifying mucilage to allow it to expand upon hydration, establishing a link between the galactosyl side-chain structure of pectin and its physical properties.
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Affiliation(s)
- Gillian H Dean
- Department of Botany, University of British Columbia, Vancouver, Canada V6T 1Z4
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Sindhu A, Langewisch T, Olek A, Multani DS, McCann MC, Vermerris W, Carpita NC, Johal G. Maize Brittle stalk2 encodes a COBRA-like protein expressed in early organ development but required for tissue flexibility at maturity. Plant Physiol 2007; 145:1444-59. [PMID: 17932309 PMCID: PMC2151699 DOI: 10.1104/pp.107.102582] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2007] [Accepted: 10/01/2007] [Indexed: 05/18/2023]
Abstract
The maize (Zea mays) brittle stalk2 (bk2) is a recessive mutant, the aerial parts of which are easily broken. The bk2 phenotype is developmentally regulated and appears 4 weeks after planting, at about the fifth-leaf stage. Before this time, mutants are indistinguishable from wild-type siblings. Afterward, all organs of the bk2 mutants turn brittle, even the preexisting ones, and they remain brittle throughout the life of the plant. Leaf tension assays and bend tests of the internodes show that the brittle phenotype does not result from loss of tensile strength but from loss in flexibility that causes the tissues to snap instead of bend. The Bk2 gene was cloned by a combination of transposon tagging and a candidate gene approach and found to encode a COBRA-like protein similar to rice (Oryza sativa) BC1 and Arabidopsis (Arabidopsis thaliana) COBRA-LIKE4. The outer periphery of the stalk has fewer vascular bundles, and the sclerids underlying the epidermis possess thinner secondary walls. Relative cellulose content is not strictly correlated with the brittle phenotype. Cellulose content in mature zones of bk2 mature stems is lowered by 40% but is about the same as wild type in developing stems. Although relative cellulose content is lowered in leaves after the onset of the brittle phenotype, total wall mass as a proportion of dry mass is either unchanged or slightly increased, indicating a compensatory increase in noncellulosic carbohydrate mass. Fourier transform infrared spectra indicated an increase in phenolic ester content in the walls of bk2 leaves and stems. Total content of lignin is unaffected in bk2 juvenile leaves before or after appearance of the brittle phenotype, but bk2 mature and developing stems are markedly enriched in lignin compared to wild-type stems. Despite increased lignin in bk2 stems, loss of staining with phloroglucinol and ultraviolet autofluorescence is observed in vascular bundles and sclerid layers. Consistent with the infrared analyses, levels of saponifiable hydroxycinnamates are elevated in bk2 leaves and stems. As Bk2 is highly expressed during early development, well before the onset of the brittle phenotype, we propose that Bk2 functions in a patterning of lignin-cellulosic interactions that maintain organ flexibility rather than having a direct role in cellulose biosynthesis.
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Affiliation(s)
- Anoop Sindhu
- Department of Botany and Plant Pathology , Purdue University, West Lafayette, Indiana 47907-2054, USA
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Derbyshire P, McCann MC, Roberts K. Restricted cell elongation in Arabidopsis hypocotyls is associated with a reduced average pectin esterification level. BMC Plant Biol 2007; 7:31. [PMID: 17572910 PMCID: PMC1913053 DOI: 10.1186/1471-2229-7-31] [Citation(s) in RCA: 135] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2007] [Accepted: 06/17/2007] [Indexed: 05/15/2023]
Abstract
BACKGROUND Cell elongation is mainly limited by the extensibility of the cell wall. Dicotyledonous primary (growing) cell walls contain cellulose, xyloglucan, pectin and proteins, but little is known about how each polymer class contributes to the cell wall mechanical properties that control extensibility. RESULTS We present evidence that the degree of pectin methyl-esterification (DE%) limits cell growth, and that a minimum level of about 60% DE is required for normal cell elongation in Arabidopsis hypocotyls. When the average DE% falls below this level, as in two gibberellic acid (GA) mutants ga1-3 and gai, and plants expressing pectin methyl-esterase (PME1) from Aspergillus aculeatus, then hypocotyl elongation is reduced. CONCLUSION Low average levels of pectin DE% are associated with reduced cell elongation, implicating PMEs, the enzymes that regulate DE%, in the cell elongation process and in responses to GA. At high average DE% other components of the cell wall limit GA-induced growth.
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Affiliation(s)
- Paul Derbyshire
- Department of Metabolic Biology, John Innes Centre, Colney Lane, Norwich, NR4 7UH, UK
| | - Maureen C McCann
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Keith Roberts
- Department of Cell and Developmental Biology, John Innes Centre, Colney Lane, Norwich, NR4 7UH, UK
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McCann MC, Defernez M, Urbanowicz BR, Tewari JC, Langewisch T, Olek A, Wells B, Wilson RH, Carpita NC. Neural network analyses of infrared spectra for classifying cell wall architectures. Plant Physiol 2007; 143:1314-26. [PMID: 17220361 PMCID: PMC1820913 DOI: 10.1104/pp.106.093054] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2006] [Accepted: 12/11/2006] [Indexed: 05/13/2023]
Abstract
About 10% of plant genomes are devoted to cell wall biogenesis. Our goal is to establish methodologies that identify and classify cell wall phenotypes of mutants on a genome-wide scale. Toward this goal, we have used a model system, the elongating maize (Zea mays) coleoptile system, in which cell wall changes are well characterized, to develop a paradigm for classification of a comprehensive range of cell wall architectures altered during development, by environmental perturbation, or by mutation. Dynamic changes in cell walls of etiolated maize coleoptiles, sampled at one-half-d intervals of growth, were analyzed by chemical and enzymatic assays and Fourier transform infrared spectroscopy. The primary walls of grasses are composed of cellulose microfibrils, glucuronoarabinoxylans, and mixed-linkage (1 --> 3),(1 --> 4)-beta-D-glucans, together with smaller amounts of glucomannans, xyloglucans, pectins, and a network of polyphenolic substances. During coleoptile development, changes in cell wall composition included a transient appearance of the (1 --> 3),(1 --> 4)-beta-D-glucans, a gradual loss of arabinose from glucuronoarabinoxylans, and an increase in the relative proportion of cellulose. Infrared spectra reflected these dynamic changes in composition. Although infrared spectra of walls from embryonic, elongating, and senescent coleoptiles were broadly discriminated from each other by exploratory principal components analysis, neural network algorithms (both genetic and Kohonen) could correctly classify infrared spectra from cell walls harvested from individuals differing at one-half-d interval of growth. We tested the predictive capabilities of the model with a maize inbred line, Wisconsin 22, and found it to be accurate in classifying cell walls representing developmental stage. The ability of artificial neural networks to classify infrared spectra from cell walls provides a means to identify many possible classes of cell wall phenotypes. This classification can be broadened to phenotypes resulting from mutations in genes encoding proteins for which a function is yet to be described.
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Affiliation(s)
- Maureen C McCann
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA
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Derbyshire P, Findlay K, McCann MC, Roberts K. Cell elongation in Arabidopsis hypocotyls involves dynamic changes in cell wall thickness. J Exp Bot 2007; 58:2079-89. [PMID: 17470442 DOI: 10.1093/jxb/erm074] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Field-emission scanning electron microscopy was used to measure wall thicknesses of different cell types in freeze-fractured hypocotyls of Arabidopsis thaliana. Measurements of uronic acid content, wall mass, and wall volume suggest that cell wall biosynthesis in this organ does not always keep pace with, and is not always tightly coupled to, elongation. In light-grown hypocotyls, walls thicken, maintain a constant thickness, or become thinner during elongation, depending upon the cell type and the stage of growth. In light-grown hypocotyls, exogenous gibberellic acid represses the extent of thickening and promotes cell elongation by both wall thinning and increased anisotropy during the early stages of hypocotyl elongation, and by increased wall deposition in the latter stages. Dark-grown hypocotyls, in the 48 h period between cold imbibition and seedling emergence, deposit very thick walls that subsequently thin in a narrow developmental window as the hypocotyl rapidly elongates. The rate of wall deposition is then maintained and keeps pace with cell elongation. The outer epidermal wall is always the thickest ( approximately 1 mum) whereas the thinnest walls, about 50 nm, are found in inner cell layers. It is concluded that control of wall thickness in different cell types is tightly regulated during hypocotyl development, and that wall deposition and cell elongation are not invariably coupled.
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Affiliation(s)
- Paul Derbyshire
- Department of Cell and Developmental Biology, John Innes Centre, Colney, Norwich NR4 7UH, UK
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MacKinnon IM, Sturcová A, Sugimoto-Shirasu K, His I, McCann MC, Jarvis MC. Cell-wall structure and anisotropy in procuste, a cellulose synthase mutant of Arabidopsis thaliana. Planta 2006; 224:438-48. [PMID: 16404578 DOI: 10.1007/s00425-005-0208-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2005] [Accepted: 12/12/2005] [Indexed: 05/06/2023]
Abstract
In dark-grown hypocotyls of the Arabidopsis procuste mutant, a mutation in the CesA6 gene encoding a cellulose synthase reduces cellulose synthesis and severely inhibits elongation growth. Previous studies had left it uncertain why growth was inhibited, because cellulose synthesis was affected before, not during, the main phase of elongation. We characterised the quantity, structure and orientation of the cellulose remaining in the walls of affected cells. Solid-state NMR spectroscopy and infrared microscopy showed that the residual cellulose did not differ in structure from that of the wild type, but the cellulose content of the prc-1 cell walls was reduced by 28%. The total mass of cell-wall polymers per hypocotyl was reduced in prc-1 by about 20%. Therefore, the fourfold inhibition of elongation growth in prc-1 does not result from aberrant cellulose structure, nor from uniform reduction in the dimensions of the cell-wall network due to reduced cellulose or cell-wall mass. Cellulose orientation was quantified by two quantitative methods. First, the orientation of newly synthesised microfibrils was measured in field-emission scanning electron micrographs of the cytoplasmic face of the inner epidermal cell wall. The ordered transverse orientation of microfibrils at the inner face of the cell wall was severely disrupted in prc-1 hypocotyls, particularly in the early growth phase. Second, cellulose orientation distributions across the whole cell-wall thickness, measured by polarised infrared microscopy, were much broader. Analysis of the microfibril orientations according to the theory of composite materials showed that during the initial growth phase, their anisotropy at the plasma membrane was sufficient to explain the anisotropy of subsequent growth.
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Affiliation(s)
- Iain M MacKinnon
- Chemistry Department, Glasgow University, G12 8QQ Glasgow, Scotland, UK
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Dahiya P, Findlay K, Roberts K, McCann MC. A fasciclin-domain containing gene, ZeFLA11, is expressed exclusively in xylem elements that have reticulate wall thickenings in the stem vascular system of Zinnia elegans cv Envy. Planta 2006; 223:1281-91. [PMID: 16328545 DOI: 10.1007/s00425-005-0177-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2005] [Accepted: 11/04/2005] [Indexed: 05/05/2023]
Abstract
The vascular cylinder of the mature stem of Zinnia elegans cv Envy contains two anatomically distinct sets of vascular bundles, stem bundles and leaf-trace bundles. We isolated a full-length cDNA of ZeFLA11, a fasciclin-domain-containing gene, from a zinnia cDNA library derived from in vitro cultures of mesophyll cells induced to form tracheary elements. Using RNA in situ hybridization, we show that ZeFLA11 is expressed in the differentiating xylem vessels with reticulate type wall thickenings and adjacent parenchyma cells of zinnia stem bundles, but not in the leaf-trace bundles that deposit spiral thickenings. Our results suggest a function for this cell-surface GPI-anchored glycoprotein in secondary wall deposition during differentiation of metaxylem tissue with reticulate vessels.
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Affiliation(s)
- Preeti Dahiya
- Department of Cell and Developmental Biology, John Innes Centre, Colney Lane, NR4 7UH Norwich, UK
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Sugimoto-Shirasu K, Roberts GR, Stacey NJ, McCann MC, Maxwell A, Roberts K. RHL1 is an essential component of the plant DNA topoisomerase VI complex and is required for ploidy-dependent cell growth. Proc Natl Acad Sci U S A 2005; 102:18736-41. [PMID: 16339310 PMCID: PMC1309048 DOI: 10.1073/pnas.0505883102] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
How cells achieve their final sizes is a pervasive biological question. One strategy to increase cell size is for the cell to amplify its chromosomal DNA content through endoreduplication cycles. Although endoreduplication is widespread in eukaryotes, we know very little about its molecular mechanisms. Successful progression of the endoreduplication cycle in Arabidopsis requires a plant homologue of archaeal DNA topoisomerase (topo) VI. To further understand how DNA is endoreduplicated and how this process is regulated, we isolated a dwarf Arabidopsis mutant, hyp7 (hypocotyl 7), in which various large cell types that in the wild type normally endoreduplicate multiple times complete only the first two rounds of endoreduplication and stall at 8C. HYP7 encodes the RHL1 (ROOT HAIRLESS 1) protein, and sequence analysis reveals that RHL1 has similarity to the C-terminal domain of mammalian DNA topo IIalpha, another type II topo that shares little sequence homology with topo VI. RHL1 shows DNA binding activity in vitro, and we present both genetic and in vivo evidence that RHL1 forms a multiprotein complex with plant topo VI. We propose that RHL1 plays an essential role in the topo VI complex to modulate its function and that the two distantly related topos, topo II and topo VI, have evolved a common domain that extends their function. Our data suggest that plant topo II and topo VI play distinct but overlapping roles during the mitotic cell cycle and endoreduplication cycle.
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Affiliation(s)
- Keiko Sugimoto-Shirasu
- Department of Cell and Developmental Biology, John Innes Centre, Colney, Norwich NR4 7UH, United Kingdom.
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Yong W, Link B, O'Malley R, Tewari J, Hunter CT, Lu CA, Li X, Bleecker AB, Koch KE, McCann MC, McCarty DR, Patterson SE, Reiter WD, Staiger C, Thomas SR, Vermerris W, Carpita NC. Genomics of plant cell wall biogenesis. Planta 2005; 221:747-51. [PMID: 15981004 DOI: 10.1007/s00425-005-1563-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2004] [Accepted: 04/01/2005] [Indexed: 05/03/2023]
Affiliation(s)
- Weidong Yong
- Department of Botany and Plant Pathology, Purdue University, 915 West State Street, West Lafayette, Indiana, 47907-2054, USA
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Dahiya P, Milioni D, Wells B, Stacey N, Roberts K, McCann MC. A RING domain gene is expressed in different cell types of leaf trace, stem, and juvenile bundles in the stem vascular system of zinnia. Plant Physiol 2005; 138:1383-95. [PMID: 15965022 PMCID: PMC1176411 DOI: 10.1104/pp.104.057901] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The in vitro zinnia (Zinnia elegans) mesophyll cell system, in which leaf mesophyll cells are induced to transdifferentiate into tracheary elements with high synchrony, has become an established model for studying xylogenesis. The architecture of the stem vascular system of zinnia cv Envy contains three anatomically distinct vascular bundles at different stages of development. Juvenile vascular strands of the subapical region develop into mature vascular strands with leaf trace segments and stem segments. Characteristic patterns of gene expression in juvenile, leaf trace, and stem bundles are revealed by a molecular marker, a RING domain-encoding gene, ZeRH2.1, originally isolated from a zinnia cDNA library derived from differentiating in vitro cultures. Using RNA in situ hybridization, we show that ZeRH2.1 is expressed preferentially in two specific cell types in mature zinnia stems. In leaf trace bundles, ZeRH2.1 transcript is abundant in xylem parenchyma cells, while in stem bundles it is abundant in phloem companion cells. Both of these cell types show wall ingrowths characteristic of transfer cells. In addition, ZeRH2.1 transcript is abundant in some phloem cells of juvenile bundles and in leaf palisade parenchyma. The complex and developmentally regulated expression pattern of ZeRH2.1 reveals heterogeneity in the vascular anatomy of the zinnia stem. We discuss a potential function for this gene in intercellular transport processes.
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Affiliation(s)
- Preeti Dahiya
- Department of Cell and Developmental Biology, John Innes Centre, Colney, Norwich NR4 7UH, United Kingdom
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Jones L, Milne JL, Ashford D, McCann MC, McQueen-Mason SJ. A conserved functional role of pectic polymers in stomatal guard cells from a range of plant species. Planta 2005; 221:255-64. [PMID: 15578215 DOI: 10.1007/s00425-004-1432-1] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2004] [Accepted: 10/12/2004] [Indexed: 05/18/2023]
Abstract
Guard cell walls combine exceptional strength and flexibility in order to accommodate the turgor pressure-driven changes in size and shape that underlie the opening and closing of stomatal pores. To investigate the molecular basis of these exceptional qualities, we have used a combination of compositional and functional analyses in three different plant species. We show that comparisons of FTIR spectra from stomatal guard cells and those of other epidermal cells indicate a number of clear differences in cell-wall composition. The most obvious characteristics are that stomatal guard cells are enriched in phenolic esters of pectins. This enrichment is apparent in guard cells from Vicia faba (possessing a type I cell wall) and Commelina communis and Zea mays (having a type II wall). We further show that these common defining elements of guard cell walls have conserved functional roles. As previously reported in C. communis, we show that enzymatic modification of the pectin network in guard cell walls in both V. faba and Z. mays has profound effects on stomatal function. In all three species, incubation of epidermal strips with a combination of pectin methyl esterase and endopolygalacturonase (EPG) caused an increase in stomatal aperture on opening. This effect was not seen when strips were incubated with EPG alone indicating that the methyl-esterified fraction of homogalacturonan is key to this effect. In contrast, arabinanase treatment, and incubation with feruloyl esterase both impeded stomatal opening. It therefore appears that pectins and phenolic esters have a conserved functional role in guard cell walls even in grass species with type II walls, which characteristically are composed of low levels of pectins.
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Affiliation(s)
- Louise Jones
- CNAP, Biology Department, University of York, P.O. Box 373, York, YO10 5YW, UK.
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McCann MC, Stacey NJ, Roberts K. Targeted cell death in xylogenesis. Symp Soc Exp Biol 2005; 52:193-201. [PMID: 12090008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Affiliation(s)
- M C McCann
- Department of Cell Biology, John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UH, UK
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Mourelatou M, Doonan JH, McCann MC. Transition of G1 to early S phase may be required for zinnia mesophyll cells to trans-differentiate to tracheary elements. Planta 2004; 220:172-176. [PMID: 15365839 DOI: 10.1007/s00425-004-1375-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2004] [Accepted: 08/07/2004] [Indexed: 05/24/2023]
Abstract
We have used the Zinnia elegans mesophyll cell system, in which single isolated leaf mesophyll cells can be induced to trans-differentiate into tracheary elements in vitro, to study the relationship between the cell division cycle and cell differentiation. Almost all cells go through several rounds of division before characteristic features of tracheary element formation are observed. The addition of aphidicolin, a DNA synthesis inhibitor, blocks cell division but not cell differentiation in the zinnia system. Low concentrations of aphidicolin, which possibly delay cells in the early S phase, can significantly enhance levels of tracheary element formation. In contrast, roscovitine, an inhibitor of cyclin-dependent kinase activity, decelerates the cell division cycle and inhibits tracheary element formation with similar dose responses. Cells blocked in S phase and then transferred to roscovitine-containing medium can divide once, indicating that roscovitine may target the G1/S transition, but do not differentiate. Cells inhibited in G1/S in roscovitine-containing medium that are subsequently blocked in S phase by transfer to aphidicolin-containing medium, do not divide but do differentiate. Taken together, our results indicate that cells may be required to transit the G1/S checkpoint and enter early S phase to acquire competence to trans-differentiate to tracheary elements.
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Affiliation(s)
- Maria Mourelatou
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
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Oomen RJFJ, Tzitzikas EN, Bakx EJ, Straatman-Engelen I, Bush MS, McCann MC, Schols HA, Visser RGF, Vincken JP. Modulation of the cellulose content of tuber cell walls by antisense expression of different potato (Solanum tuberosum L.) CesA clones. Phytochemistry 2004; 65:535-46. [PMID: 15003416 DOI: 10.1016/j.phytochem.2003.12.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 12/12/2003] [Accepted: 12/19/2003] [Indexed: 05/21/2023]
Abstract
Four potato cellulose synthase (CesA) homologs (StCesA1, 2, 3 and 4) were isolated by screening a cDNA library made from developing tubers. Based on sequence comparisons and the fact that all four potato cDNAs were isolated from this single cDNA-library, all four StCesA clones are likely to play a role in primary cell wall biosynthesis. Several constructs were generated to modulate cellulose levels in potato plants in which the granule-bound starch synthase promoter was used to target the modification to the tubers. The StCesA3 was used for up- and down-regulation of the cellulose levels by sense (SE-StCesA3) and antisense (AS-StCesA3) expression of the complete cDNA. Additionally, the class-specific regions (CSR) of all four potato cellulose synthase genes were used for specific down-regulation (antisense) of the corresponding CesA genes (csr1, 2, 3 and 4). None of the transformants showed an overt developmental phenotype. Sections of tubers were screened for altered cell wall structure by Fourier Transform Infrared microspectroscopy (FTIR) and exploratory Principal Component Analysis (PCA), and those plants discriminating from WT plants were analysed for cellulose content and monosaccharide composition. Several transgenic lines were obtained with mainly decreased levels of cellulose. These results show that the cellulose content in potato tubers can be reduced down to 40% of the WT level without affecting normal plant development, and that constructs based on the CSR alone are specific and sufficient to down-regulate cellulose biosynthesis.
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Affiliation(s)
- Ronald J F J Oomen
- Graduate School Experimental Plant Sciences, Laboratory of Plant Breeding, Wageningen University, Binnenhaven 5, 6709 PD Wageningen, The Netherlands
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Vincken JP, Schols HA, Oomen RJFJ, McCann MC, Ulvskov P, Voragen AGJ, Visser RGF. If homogalacturonan were a side chain of rhamnogalacturonan I. Implications for cell wall architecture. Plant Physiol 2003; 132:1781-9. [PMID: 12913136 PMCID: PMC1540329 DOI: 10.1104/pp.103.022350] [Citation(s) in RCA: 396] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Affiliation(s)
- Jean-Paul Vincken
- Graduate School Experimental Plant Sciences, Laboratory of Plant Breeding, Wageningen University, Binnenhaven 5, 6709 PD Wageningen, The Netherlands.
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Milioni D, Sado PE, Stacey NJ, Roberts K, McCann MC. Early gene expression associated with the commitment and differentiation of a plant tracheary element is revealed by cDNA-amplified fragment length polymorphism analysis. Plant Cell 2002; 14:2813-24. [PMID: 12417703 PMCID: PMC152729 DOI: 10.1105/tpc.005231] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2002] [Accepted: 08/05/2002] [Indexed: 05/18/2023]
Abstract
Isolated mesophyll cells from Zinnia elegans are induced by auxin and cytokinin to form tracheary elements (TEs) in vitro with high synchrony. To reveal the changing patterns of gene expression during the 48 h of transdifferentiation from mesophyll to TE cell fate, we used a cDNA-amplified fragment length polymorphism approach to generate expression profiles of >30,000 cDNA fragments. Transcriptional changes of 652 cDNA fragments were observed, of which 304 have no previously described function or sequence identity. Sixty-eight genes were upregulated within 30 min of induction and represent key candidates for the processes that underlie the early stages of commitment and differentiation to a TE cell fate.
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Affiliation(s)
- Dimitra Milioni
- Department of Cell and Developmental Biology, John Innes Centre, Colney, Norwich NR4 7UH, United Kingdom
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