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Happs RM, Addison B, Doeppke C, Donohoe BS, Davis MF, Harman-Ware AE. Comparison of methodologies used to determine aromatic lignin unit ratios in lignocellulosic biomass. Biotechnol Biofuels 2021; 14:58. [PMID: 33676549 PMCID: PMC7936455 DOI: 10.1186/s13068-021-01897-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 02/08/2021] [Indexed: 05/04/2023]
Abstract
BACKGROUND Multiple analytical methods have been developed to determine the ratios of aromatic lignin units, particularly the syringyl/guaiacyl (S/G) ratio, of lignin biopolymers in plant cell walls. Chemical degradation methods such as thioacidolysis produce aromatic lignin units that are released from certain linkages and may induce chemical changes rendering it difficult to distinguish and determine the source of specific aromatic lignin units released, as is the case with nitrobenzene oxidation methodology. NMR methods provide powerful tools used to analyze cell walls for lignin composition and linkage information. Pyrolysis-mass spectrometry methods are also widely used, particularly as high-throughput methodologies. However, the different techniques used to analyze aromatic lignin unit ratios frequently yield different results within and across particular studies, making it difficult to interpret and compare results. This also makes it difficult to obtain meaningful insights relating these measurements to other characteristics of plant cell walls that may impact biomass sustainability and conversion metrics for the production of bio-derived fuels and chemicals. RESULTS The authors compared the S/G lignin unit ratios obtained from thioacidolysis, pyrolysis-molecular beam mass spectrometry (py-MBMS), HSQC liquid-state NMR and solid-state (ss) NMR methodologies of pine, several genotypes of poplar, and corn stover biomass. An underutilized approach to deconvolute ssNMR spectra was implemented to derive S/G ratios. The S/G ratios obtained for the samples did not agree across the different methods, but trends were similar with the most agreement among the py-MBMS, HSQC NMR and deconvoluted ssNMR methods. The relationship between S/G, thioacidolysis yields, and linkage analysis determined by HSQC is also addressed. CONCLUSIONS This work demonstrates that different methods using chemical, thermal, and non-destructive NMR techniques to determine native lignin S/G ratios in plant cell walls may yield different results depending on species and linkage abundances. Spectral deconvolution can be applied to many hardwoods with lignin dominated by S and G units, but the results may not be reliable for some woody and grassy species of more diverse lignin composition. HSQC may be a better method for analyzing lignin in those species given the wealth of information provided on additional aromatic moieties and bond linkages. Additionally, trends or correlations in lignin characteristics such as S/G ratios and lignin linkages within the same species such as poplar may not necessarily exhibit the same trends or correlations made across different biomass types. Careful consideration is required when choosing a method to measure S/G ratios and the benefits and shortcomings of each method discussed here are summarized.
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Affiliation(s)
- Renee M Happs
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Bennett Addison
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Crissa Doeppke
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Bryon S Donohoe
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Mark F Davis
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Anne E Harman-Ware
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA.
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2
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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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3
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Bose E, Leal JH, Hoover AN, Zeng Y, Li C, Ray AE, Semelsberger TA, Donohoe BS. Impacts of Biological Heating and Degradation during Bale Storage on the Surface Properties of Corn Stover. ACS Sustain Chem Eng 2020; 8:13973-13983. [PMID: 38434216 PMCID: PMC10906940 DOI: 10.1021/acssuschemeng.0c03356] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 03/05/2024]
Abstract
The variability of chemical, physical, and mechanical properties of lignocellulosic biomass feedstocks has a major impact on the efficiency of biomass processing and conversion to fuels and chemicals. Storage conditions represent a key source of variability that may contribute to biomass quality variations from the time of harvest until delivery to the biorefinery. In some cases, substantial microbial degradation can take place during storage. In this work, we investigate how degradation during storage affects the surface texture, surface energy, and porosity of different corn stover anatomical fractions (e.g., leaf, stalk, and cob). Understanding any potential changes in surface properties is important because interparticle interactions during bioprocessing cause aggregation and blockages that lead to at least process inefficiency and at most complete equipment failure. The surface roughness and texture parameters of corn stover with variable degrees of microbial degradation were calculated directly from stereomicroscopy and scanning electron microscopy micrographs. Surface energy and porosity were measured by inverse gas chromatography. The results show differing trends in the impact of increasing biological heating and degradation depending on the specific corn stover tissue type that was analyzed. These results also indicate that biomass surface properties are scale-dependent and that the scale, which is most industrially relevant, may depend on the specific unit operation within the biorefinery being considered.
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Affiliation(s)
- Elizabeth Bose
- Bioenergy
Center, National Renewable Energy Laboratory
(NREL), 15013 Denver West Parkway, Golden, Colorado 80401, United
States
| | - Juan H. Leal
- Material
Physics Applications Division, Los Alamos
National Laboratory, P.O. Box 1663, Los Alamos, New Mexico 87545, United States
| | - Amber N. Hoover
- Energy
& Environment Science & Technology, Idaho National Laboratory, 1955 N. Fremont Avenue, Idaho Falls, Idaho 83415, United States
| | - Yining Zeng
- Bioenergy
Center, National Renewable Energy Laboratory
(NREL), 15013 Denver West Parkway, Golden, Colorado 80401, United
States
| | - Chenlin Li
- Energy
& Environment Science & Technology, Idaho National Laboratory, 1955 N. Fremont Avenue, Idaho Falls, Idaho 83415, United States
| | - Allison E. Ray
- Energy
& Environment Science & Technology, Idaho National Laboratory, 1955 N. Fremont Avenue, Idaho Falls, Idaho 83415, United States
| | - Troy A. Semelsberger
- Material
Physics Applications Division, Los Alamos
National Laboratory, P.O. Box 1663, Los Alamos, New Mexico 87545, United States
| | - Bryon S. Donohoe
- Bioenergy
Center, National Renewable Energy Laboratory
(NREL), 15013 Denver West Parkway, Golden, Colorado 80401, United
States
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Thornburg NE, Pecha MB, Brandner DG, Reed ML, Vermaas JV, Michener WE, Katahira R, Vinzant TB, Foust TD, Donohoe BS, Román-Leshkov Y, Ciesielski PN, Beckham GT. Mesoscale Reaction-Diffusion Phenomena Governing Lignin-First Biomass Fractionation. ChemSusChem 2020; 13:4495-4509. [PMID: 32246557 DOI: 10.1002/cssc.202000558] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Indexed: 05/21/2023]
Abstract
Lignin solvolysis from the plant cell wall is the critical first step in lignin depolymerization processes involving whole biomass feedstocks. However, little is known about the coupled reaction kinetics and transport phenomena that govern the effective rates of lignin extraction. Here, we report a validated simulation framework that determines intrinsic, transport-independent kinetic parameters for the solvolysis of lignin, hemicellulose, and cellulose upon incorporation of feedstock characteristics for the methanol-based extraction of poplar as an example fractionation process. Lignin fragment diffusion is predicted to compete on the same time and length scales as reactions of lignin within cell walls and longitudinal pores of typical milled particle sizes, and mass transfer resistances are predicted to dominate the solvolysis of poplar particles that exceed approximately 2 mm in length. Beyond the approximately 2 mm threshold, effectiveness factors are predicted to be below 0.25, which implies that pore diffusion resistances may attenuate observable kinetic rate measurements by at least 75 % in such cases. Thus, researchers are recommended to conduct kinetic evaluations of lignin-first catalysts using biomass particles smaller than approximately 0.2 mm in length to avoid feedstock-specific mass transfer limitations in lignin conversion studies. Overall, this work highlights opportunities to improve lignin solvolysis by genetic engineering and provides actionable kinetic information to guide the design and scale-up of emerging biorefinery strategies.
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Affiliation(s)
- Nicholas E Thornburg
- National Bioenergy Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
| | - M Brennan Pecha
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
| | - David G Brandner
- National Bioenergy Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
| | - Michelle L Reed
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
| | - Josh V Vermaas
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
| | - William E Michener
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
| | - Rui Katahira
- National Bioenergy Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
| | - Todd B Vinzant
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
| | - Thomas D Foust
- National Bioenergy Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
| | - Bryon S Donohoe
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
| | - Yuriy Román-Leshkov
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Peter N Ciesielski
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
| | - Gregg T Beckham
- National Bioenergy Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
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5
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Nagle NJ, Donohoe BS, Wolfrum EJ, Kuhn EM, Haas TJ, Ray AE, Wendt LM, Delwiche ME, Weiss ND, Radtke C. Chemical and Structural Changes in Corn Stover After Ensiling: Influence on Bioconversion. Front Bioeng Biotechnol 2020; 8:739. [PMID: 32923429 PMCID: PMC7457055 DOI: 10.3389/fbioe.2020.00739] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 01/17/2020] [Accepted: 06/10/2020] [Indexed: 11/23/2022] Open
Abstract
Production of biofuels, bioproducts, and bioenergy requires a well-characterized, stable, and reasonably uniform biomass supply and well-established supply chains for shipping biomass from farm fields to biorefineries, while achieving year-round production targets. Preserving and stabilizing biomass feedstock during storage is a necessity for cost-effective and sustainable biofuel production. Ensiling is a common storage method used to preserve and even improve forage quality; however, the impact of ensiling on biomass physical and chemical properties that influence bioconversion processes has been variable. Our objective in this work was to determine the effects of ensiling on lignocellulosic feedstock physicochemical properties and how that influences bioconversion requirements. We observed statistically significant decreases (p < 0.05) in the content of two major structural carbohydrates (glucan and xylan) of 5 and 8%, respectively, between the ensiled and non-ensiled materials. We were unable to detect differences in sugar yields from structural carbohydrates after pretreatment and enzymatic hydrolysis of the ensiled materials compared to non-ensiled controls. Based on this work, we conclude that ensiling the corn stover did not change the bioconversion requirements compared to the control samples and incurred losses of structural carbohydrates. At the light microscopy level, ensiled corn stover exhibited little structural change or relocation of cell wall components as detected by immunocytochemistry. However, more subtle structural changes were revealed by electron microscopy, as ensiled cell walls exhibit ultrastructural characteristics such as wall delimitation intermediate between non-ensiled and dilute-acid-pretreated cell walls. These findings suggest that alternative methods of conversion, such as deacetylation and mechanical refining, could take advantage of lamellar defects and may be more effective than dilute acid or hot water pretreatment for biomass conversion of ensiled materials.
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Affiliation(s)
- Nick J Nagle
- National Renewable Energy Laboratory, Golden, CO, United States
| | - Bryon S Donohoe
- National Renewable Energy Laboratory, Golden, CO, United States
| | | | - Erik M Kuhn
- National Renewable Energy Laboratory, Golden, CO, United States
| | - Thomas J Haas
- National Renewable Energy Laboratory, Golden, CO, United States
| | - Allison E Ray
- Idaho National Laboratory, Idaho Falls, ID, United States
| | - Lynn M Wendt
- Idaho National Laboratory, Idaho Falls, ID, United States
| | | | - Noah D Weiss
- Department of Chemical Engineering, Lund University, Lund, Sweden
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6
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Wei H, Wang W, Ciesielski PN, Donohoe BS, Zhang M, Himmel ME, Chen X, Tucker MP. Ferrous and Ferric Ion-Facilitated Dilute Acid Pretreatment of Lignocellulosic Biomass under Anaerobic or Aerobic Conditions: Observations of Fe Valence Interchange and the Role of Fenton Reaction. Molecules 2020; 25:E1427. [PMID: 32245102 PMCID: PMC7144374 DOI: 10.3390/molecules25061427] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 03/17/2020] [Accepted: 03/18/2020] [Indexed: 11/16/2022] Open
Abstract
Ferrous ion co-catalyst enhancement of dilute-acid (DA) pretreatment of biomass is a promising technology for increasing the release of sugars from recalcitrant lignocellulosic biomass. However, due to the reductive status of ferrous ion and its susceptibility to oxidation with exposure to atmosphere, its effective application presumably requires anaerobic aqueous conditions created by nitrogen gas-purging, which adds extra costs. The objective of this study was to assess the effectiveness of oxidative iron ion, (i.e., ferric ion) as a co-catalyst in DA pretreatment of biomass, using an anaerobic chamber to strictly control exposure to oxygen during setup and post-pretreatment analyses. Remarkably, the ferric ions were found to be as efficient as ferrous ions in enhancing sugar release during DA pretreatment of biomass, which may be attributed to the observation that a major portion of the initial ferric ions were converted to ferrous during pretreatment. Furthermore, the detection of hydrogen peroxide in the liquors after DA/Fe ion pretreatment suggests that Fenton reaction chemistry was likely involved in DA/Fe ion pretreatments of biomass, contributing to the observed ferric and ferrous interchanges during pretreatment. These results help define the extent and specification requirements for applying iron ions as co-catalysts in DA pretreatments of biomass.
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Affiliation(s)
- Hui Wei
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA; (W.W.); (P.N.C.); (B.S.D.); (M.Z.); (M.E.H.)
| | - Wei Wang
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA; (W.W.); (P.N.C.); (B.S.D.); (M.Z.); (M.E.H.)
| | - Peter N. Ciesielski
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA; (W.W.); (P.N.C.); (B.S.D.); (M.Z.); (M.E.H.)
| | - Bryon S. Donohoe
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA; (W.W.); (P.N.C.); (B.S.D.); (M.Z.); (M.E.H.)
| | - Min Zhang
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA; (W.W.); (P.N.C.); (B.S.D.); (M.Z.); (M.E.H.)
| | - Michael E. Himmel
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA; (W.W.); (P.N.C.); (B.S.D.); (M.Z.); (M.E.H.)
| | - Xiaowen Chen
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Melvin P. Tucker
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
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7
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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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8
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Gergely ZR, Martinez DE, Donohoe BS, Mogelsvang S, Herder R, Staehelin LA. 3D electron tomographic and biochemical analysis of ER, Golgi and trans Golgi network membrane systems in stimulated Venus flytrap ( Dionaea muscipula) glandular cells. J Biol Res (Thessalon) 2018; 25:15. [PMID: 30116723 PMCID: PMC6083566 DOI: 10.1186/s40709-018-0086-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 07/28/2018] [Indexed: 11/10/2022]
Abstract
BACKGROUND The insect-trapping leaves of Dionaea muscipula provide a model for studying the secretory pathway of an inducible plant secretory system. The leaf glands were induced with bovine serum albumin to secrete proteases that were characterized via zymogram activity gels over a 6-day period. The accompanying morphological changes of the endoplasmic reticulum (ER) and Golgi were analyzed using 3D electron tomography of glands preserved by high-pressure freezing/freeze substitution methods. RESULTS Secretion of multiple cysteine and aspartic proteases occurred biphasically. The majority of the Golgi was organized in clusters consisting of 3-6 stacks surrounded by a cage-like system of ER cisternae. In these clusters, all Golgi stacks were oriented with their cis-most C1 cisterna facing an ER export site. The C1 Golgi cisternae varied in size and shape consistent with the hypothesis that they form de novo. Following induction, the number of ER-bound polysomes doubled, but no increase in COPII vesicles was observed. Golgi changes included a reduction in the number of cisternae per stack and a doubling of cisternal volume without increased surface area. Polysaccharide molecules that form the sticky slime cause swelling of the trans and trans Golgi network (TGN) cisternae. Peeling of the trans-most cisternae gives rise to free TGN cisternae. One day after gland stimulation, the free TGNs were frequently associated with loose groups of oriented actin-like filaments which were not seen in any other samples. CONCLUSIONS These findings suggest that the secretory apparatus of resting gland cells is "overbuilt" to enable the cells to rapidly up-regulate lytic enzyme production and secretion in response to prey trapping.
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Affiliation(s)
- Zachary R. Gergely
- MCD Biology, University of Colorado at Boulder, Campus Box 347, Boulder, CO 80309 USA
| | - Dana E. Martinez
- Instituto de Fisiología Vegetal (INFIVE), Universidad Nacional de La Plata–CONICET CC 327, La Plata, Argentina
| | - Bryon S. Donohoe
- National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401 USA
| | - Soren Mogelsvang
- Exxel Pharma, Inc, 12635 E Montview Blvd, Suite 100, Aurora, CO 80045 USA
| | - Rachel Herder
- Wilson Sonsini Goodrich & Rosati, One Market Plaza, Spear Tower, Ste 3300, San Francisco, CA 94105 USA
| | - L. Andrew Staehelin
- MCD Biology, University of Colorado at Boulder, Campus Box 347, Boulder, CO 80309 USA
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9
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He Q, Yang Y, Yang S, Donohoe BS, Van Wychen S, Zhang M, Himmel ME, Knoshaug EP. Oleaginicity of the yeast strain Saccharomyces cerevisiae D5A. Biotechnol Biofuels 2018; 11:258. [PMID: 30258492 PMCID: PMC6151946 DOI: 10.1186/s13068-018-1256-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 09/10/2018] [Indexed: 05/28/2023]
Abstract
BACKGROUND The model yeast, Saccharomyces cerevisiae, is not known to be oleaginous. However, an industrial wild-type strain, D5A, was shown to accumulate over 20% storage lipids from glucose when growth is nitrogen-limited compared to no more than 7% lipid accumulation without nitrogen stress. METHODS AND RESULTS To elucidate the mechanisms of S. cerevisiae D5A oleaginicity, we compared physiological and metabolic changes; as well as the transcriptional profiles of the oleaginous industrial strain, D5A, and a non-oleaginous laboratory strain, BY4741, under normal and nitrogen-limited conditions using analytic techniques and next-generation sequencing-based RNA-Seq transcriptomics. Transcriptional levels for genes associated with fatty acid biosynthesis, nitrogen metabolism, amino acid catabolism, as well as the pentose phosphate pathway and ethanol oxidation in central carbon (C) metabolism, were up-regulated in D5A during nitrogen deprivation. Despite increased carbon flux to lipids, most gene-encoding enzymes involved in triacylglycerol (TAG) assembly were expressed at similar levels regardless of the varying nitrogen concentrations in the growth media and strain backgrounds. Phospholipid turnover also contributed to TAG accumulation through increased precursor production with the down-regulation of subsequent phospholipid synthesis steps. Our results also demonstrated that nitrogen assimilation via the glutamate-glutamine pathway and amino acid metabolism, as well as the fluxes of carbon and reductants from central C metabolism, are integral to the general oleaginicity of D5A, which resulted in the enhanced lipid storage during nitrogen deprivation. CONCLUSION This work demonstrated the disequilibrium and rebalance of carbon and nitrogen contribution to the accumulation of lipids in the oleaginous yeast S. cerevisiae D5A. Rather than TAG assembly from acyl groups, the major switches for the enhanced lipid accumulation of D5A (i.e., fatty acid biosynthesis) are the increases of cytosolic pools of acetyl-CoA and NADPH, as well as alternative nitrogen assimilation.
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Affiliation(s)
- Qiaoning He
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, 430062 China
| | - Yongfu Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, 430062 China
| | - Shihui Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, 430062 China
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, 80401 USA
| | - Bryon S. Donohoe
- Biosciences Center, National Renewable Energy Laboratory, Golden, 80401 USA
| | | | - Min Zhang
- Biosciences Center, National Renewable Energy Laboratory, Golden, 80401 USA
| | - Michael E. Himmel
- Biosciences Center, National Renewable Energy Laboratory, Golden, 80401 USA
| | - Eric P. Knoshaug
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, 80401 USA
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10
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Sammond DW, Kastelowitz N, Donohoe BS, Alahuhta M, Lunin VV, Chung D, Sarai NS, Yin H, Mittal A, Himmel ME, Guss AM, Bomble YJ. An iterative computational design approach to increase the thermal endurance of a mesophilic enzyme. Biotechnol Biofuels 2018; 11:189. [PMID: 30002729 PMCID: PMC6036693 DOI: 10.1186/s13068-018-1178-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 06/18/2018] [Indexed: 05/26/2023]
Abstract
BACKGROUND Strategies for maximizing the microbial production of bio-based chemicals and fuels include eliminating branched points to streamline metabolic pathways. While this is often achieved by removing key enzymes, the introduction of nonnative enzymes can provide metabolic shortcuts, bypassing branched points to decrease the production of undesired side-products. Pyruvate decarboxylase (PDC) can provide such a shortcut in industrially promising thermophilic organisms; yet to date, this enzyme has not been found in any thermophilic organism. Incorporating nonnative enzymes into host organisms can be challenging in cases such as this, where the enzyme has evolved in a very different environment from that of the host. RESULTS In this study, we use computational protein design to engineer the Zymomonas mobilis PDC to resist thermal denaturation at the growth temperature of a thermophilic host. We generate thirteen PDC variants using the Rosetta protein design software. We measure thermal stability of the wild-type PDC and PDC variants using circular dichroism. We then measure and compare enzyme endurance for wild-type PDC with the PDC variants at an elevated temperature of 60 °C (thermal endurance) using differential interference contrast imaging. CONCLUSIONS We find that increases in melting temperature (Tm) do not directly correlate with increases in thermal endurance at 60 °C. We also do not find evidence that any individual mutation or design approach is the major contributor to the most thermostable PDC variant. Rather, remarkable cooperativity among sixteen thermostabilizing mutations is key to rationally designing a PDC with significantly enhanced thermal endurance. These results suggest a generalizable iterative computational protein design approach to improve thermal stability and endurance of target enzymes.
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Affiliation(s)
- Deanne W. Sammond
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401 USA
| | - Noah Kastelowitz
- Department of Chemistry & Biochemistry and the BioFrontiers Institute, University of Colorado, Boulder, CO 80309 USA
| | - Bryon S. Donohoe
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401 USA
| | - Markus Alahuhta
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401 USA
| | - Vladimir V. Lunin
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401 USA
| | - Daehwan Chung
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401 USA
| | - Nicholas S. Sarai
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401 USA
| | - Hang Yin
- Department of Chemistry & Biochemistry and the BioFrontiers Institute, University of Colorado, Boulder, CO 80309 USA
| | - Ashutosh Mittal
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401 USA
| | - Michael E. Himmel
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401 USA
| | - Adam M. Guss
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Yannick J. Bomble
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401 USA
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11
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Belteton SA, Sawchuk MG, Donohoe BS, Scarpella E, Szymanski DB. Reassessing the Roles of PIN Proteins and Anticlinal Microtubules during Pavement Cell Morphogenesis. Plant Physiol 2018; 176:432-449. [PMID: 29192026 PMCID: PMC5761804 DOI: 10.1104/pp.17.01554] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 11/22/2017] [Indexed: 05/03/2023]
Abstract
The leaf epidermis is a biomechanical shell that influences the size and shape of the organ. Its morphogenesis is a multiscale process in which nanometer-scale cytoskeletal protein complexes, individual cells, and groups of cells pattern growth and define macroscopic leaf traits. Interdigitated growth of neighboring cells is an evolutionarily conserved developmental strategy. Understanding how signaling pathways and cytoskeletal proteins pattern cell walls during this form of tissue morphogenesis is an important research challenge. The cellular and molecular control of a lobed cell morphology is currently thought to involve PIN-FORMED (PIN)-type plasma membrane efflux carriers that generate subcellular auxin gradients. Auxin gradients were proposed to function across cell boundaries to encode stable offset patterns of cortical microtubules and actin filaments between adjacent cells. Many models suggest that long-lived microtubules along the anticlinal cell wall generate local cell wall heterogeneities that restrict local growth and specify the timing and location of lobe formation. Here, we used Arabidopsis (Arabidopsis thaliana) reverse genetics and multivariate long-term time-lapse imaging to test current cell shape control models. We found that neither PIN proteins nor long-lived microtubules along the anticlinal wall predict the patterns of lobe formation. In fields of lobing cells, anticlinal microtubules are not correlated with cell shape and are unstable at the time scales of cell expansion. Our analyses indicate that anticlinal microtubules have multiple functions in pavement cells and that lobe initiation is likely controlled by complex interactions among cell geometry, cell wall stress patterns, and transient microtubule networks that span the anticlinal and periclinal walls.
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Affiliation(s)
- Samuel A Belteton
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907
| | - Megan G Sawchuk
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada T6G 2R3
| | - Bryon S Donohoe
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401
| | - Enrico Scarpella
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada T6G 2R3
| | - Daniel B Szymanski
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907
- Department of Agronomy, Purdue University, West Lafayette, Indiana 47907
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12
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de Assis T, Huang S, Driemeier CE, Donohoe BS, Kim C, Kim SH, Gonzalez R, Jameel H, Park S. Toward an understanding of the increase in enzymatic hydrolysis by mechanical refining. Biotechnol Biofuels 2018; 11:289. [PMID: 30386426 PMCID: PMC6201573 DOI: 10.1186/s13068-018-1289-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 10/09/2018] [Indexed: 05/11/2023]
Abstract
BACKGROUND Mechanical refining is a low-capital and well-established technology used in pulp and paper industry to improve fiber bonding for product strength. Refining can also be applied in a biorefinery context to overcome the recalcitrance of pretreated biomass by opening up the biomass structure and modifying substrate properties (e.g., morphology, particle size, porosity, crystallinity), which increases enzyme accessibility to substrate and improves carbohydrate conversion. Although several characterization methods have been used to identify the changes in substrate properties, there is no systematic approach to evaluate the extent of fiber cell wall disruption and what physical properties can explain the improvement in enzymatic digestibility when pretreated lignocellulosic biomass is mechanically refined. This is because the fiber cell wall is complex across multiple scales, including the molecular scale, nano- and meso-scale (microfibril), and microscale (tissue level). A combination of advanced characterization tools is used in this study to better understand the effect of mechanical refining on the meso-scale microfibril assembly and the relationship between those meso-scale modifications and enzymatic hydrolysis. RESULTS Enzymatic conversion of autohydrolysis sugarcane bagasse was improved from 69.6 to 77.2% (11% relative increase) after applying mechanical refining and an increase in enzymatic digestibility is observed with an increase in refining intensity. Based on a combination of advanced characterizations employed in this study, it was found that the refining action caused fiber size reduction, internal delamination, and increase in pores and swellability. CONCLUSIONS A higher level of delamination and higher increase in porosity, analyzed by TEM and DSC, were clearly demonstrated, which explain the faster digestibility rate during the first 72 h of enzymatic hydrolysis for disc-refined samples when compared to the PFI-refined samples. In addition, an increased inter-fibrillar distance between cellulose microfibrils at the nano-meso-scale was also revealed by SFG analysis, while no evidence was found for a change in crystalline structure by XRD and solid-state NMR analysis.
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Affiliation(s)
- Tiago de Assis
- Department of Forest Biomaterials, College of Natural Reseources, NC State University, Raleigh, NC USA
| | - Shixin Huang
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA USA
| | - Carlos Eduardo Driemeier
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP Brazil
| | - Bryon S. Donohoe
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO USA
| | - Chaehoon Kim
- Department of Forest Biomaterials, College of Natural Reseources, NC State University, Raleigh, NC USA
| | - Seong H. Kim
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA USA
| | - Ronalds Gonzalez
- Department of Forest Biomaterials, College of Natural Reseources, NC State University, Raleigh, NC USA
| | - Hasan Jameel
- Department of Forest Biomaterials, College of Natural Reseources, NC State University, Raleigh, NC USA
| | - Sunkyu Park
- Department of Forest Biomaterials, College of Natural Reseources, NC State University, Raleigh, NC USA
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13
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Lin CY, Donohoe BS, Ahuja N, Garrity DM, Qu R, Tucker MP, Himmel ME, Wei H. Evaluation of parameters affecting switchgrass tissue culture: toward a consolidated procedure for Agrobacterium-mediated transformation of switchgrass ( Panicum virgatum). Plant Methods 2017; 13:113. [PMID: 29270209 PMCID: PMC5735814 DOI: 10.1186/s13007-017-0263-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 12/06/2017] [Indexed: 05/21/2023]
Abstract
BACKGROUND Switchgrass (Panicum virgatum), a robust perennial C4-type grass, has been evaluated and designated as a model bioenergy crop by the U.S. DOE and USDA. Conventional breeding of switchgrass biomass is difficult because it displays self-incompatible hindrance. Therefore, direct genetic modifications of switchgrass have been considered the more effective approach to tailor switchgrass with traits of interest. Successful transformations have demonstrated increased biomass yields, reduction in the recalcitrance of cell walls and enhanced saccharification efficiency. Several tissue culture protocols have been previously described to produce transgenic switchgrass lines using different nutrient-based media, co-cultivation approaches, and antibiotic strengths for selection. RESULTS After evaluating the published protocols, we consolidated these approaches and optimized the process to develop a more efficient protocol for producing transgenic switchgrass. First, seed sterilization was optimized, which led to a 20% increase in yield of induced calluses. Second, we have selected a N6 macronutrient/B5 micronutrient (NB)-based medium for callus induction from mature seeds of the Alamo cultivar, and chose a Murashige and Skoog-based medium to regenerate both Type I and Type II calluses. Third, Agrobacterium-mediated transformation was adopted that resulted in 50-100% positive regenerated transformants after three rounds (2 weeks/round) of selection with antibiotic. Genomic DNA PCR, RT-PCR, Southern blot, visualization of the red fluorescent protein and histochemical β-glucuronidase (GUS) staining were conducted to confirm the positive switchgrass transformants. The optimized methods developed here provide an improved strategy to promote the production and selection of callus and generation of transgenic switchgrass lines. CONCLUSION The process for switchgrass transformation has been evaluated and consolidated to devise an improved approach for transgenic switchgrass production. With the optimization of seed sterilization, callus induction, and regeneration steps, a reliable and effective protocol is established to facilitate switchgrass engineering.
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Affiliation(s)
- Chien-Yuan Lin
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Bryon S. Donohoe
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Neha Ahuja
- Department of Biology, Colorado State University, Fort Collins, CO 80523 USA
| | - Deborah M. Garrity
- Department of Biology, Colorado State University, Fort Collins, CO 80523 USA
| | - Rongda Qu
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC 27695-7287 USA
| | - Melvin P. Tucker
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO USA
| | - Michael E. Himmel
- Biosciences 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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14
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Bomble YJ, Lin CY, Amore A, Wei H, Holwerda EK, Ciesielski PN, Donohoe BS, Decker SR, Lynd LR, Himmel ME. Lignocellulose deconstruction in the biosphere. Curr Opin Chem Biol 2017; 41:61-70. [DOI: 10.1016/j.cbpa.2017.10.013] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 10/09/2017] [Accepted: 10/10/2017] [Indexed: 12/18/2022]
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15
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Thomas VA, Donohoe BS, Li M, Pu Y, Ragauskas AJ, Kumar R, Nguyen TY, Cai CM, Wyman CE. Adding tetrahydrofuran to dilute acid pretreatment provides new insights into substrate changes that greatly enhance biomass deconstruction by Clostridium thermocellum and fungal enzymes. Biotechnol Biofuels 2017; 10:252. [PMID: 29213312 PMCID: PMC5707920 DOI: 10.1186/s13068-017-0937-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 10/19/2017] [Indexed: 05/11/2023]
Abstract
BACKGROUND Consolidated bioprocessing (CBP) by anaerobes, such as Clostridium thermocellum, which combine enzyme production, hydrolysis, and fermentation are promising alternatives to historical economic challenges of using fungal enzymes for biological conversion of lignocellulosic biomass. However, limited research has integrated CBP with real pretreated biomass, and understanding how pretreatment impacts subsequent deconstruction by CBP vs. fungal enzymes can provide valuable insights into CBP and suggest other novel biomass deconstruction strategies. This study focused on determining the effect of pretreatment by dilute sulfuric acid alone (DA) and with tetrahydrofuran (THF) addition via co-solvent-enhanced lignocellulosic fractionation (CELF) on deconstruction of corn stover and Populus with much different recalcitrance by C. thermocellum vs. fungal enzymes and changes in pretreated biomass related to these differences. RESULTS Coupling CELF fractionation of corn stover and Populus with subsequent CBP by the anaerobe C. thermocellum completely solubilized polysaccharides left in the pretreated solids within only 48 h without adding enzymes. These results were better than those from the conventional DA followed by either CBP or fungal enzymes or CELF followed by fungal enzyme hydrolysis, especially at viable enzyme loadings. Enzyme adsorption on CELF-pretreated corn stover and CELF-pretreated Populus solids were virtually equal, while DA improved the enzyme accessibility for corn stover more than Populus. Confocal scanning light microscopy (CSLM), transmission electron microscopy (TEM), and NMR characterization of solids from both pretreatments revealed differences in cell wall structure and lignin composition, location, coalescence, and migration-enhanced digestibility of CELF-pretreated solids. CONCLUSIONS Adding THF to DA pretreatment (CELF) greatly enhanced deconstruction of corn stover and Populus by fungal enzymes and C. thermocellum CBP, and the CELF-CBP tandem was agnostic to feedstock recalcitrance. Composition measurements, material balances, cellulase adsorption, and CSLM and TEM imaging revealed adding THF enhanced the enzyme accessibility, cell wall fractures, and cellular dislocation and cell wall delamination. Overall, enhanced deconstruction of CELF solids by enzymes and particularly by C. thermocellum could be related to lignin removal and alteration, thereby pointing to these factors being key contributors to biomass recalcitrance as a barrier to low-cost biological conversion to sustainable fuels.
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Affiliation(s)
- Vanessa A. Thomas
- Department of Chemical and Environmental Engineering, Bourns College of Engineering, University of California Riverside, Riverside, CA USA
- Center for Environmental Research and Technology (CE-CERT), Bourns College of Engineering, University of California Riverside, Riverside, CA USA
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Bryon S. Donohoe
- National Renewable Energy Laboratory, Golden, CO USA
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Mi Li
- Joint Institute of Biological Science, Biosciences Division, Oak Ridge National Laboratory (ORNL), Oak Ridge, TN USA
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Yunqiao Pu
- Joint Institute of Biological Science, Biosciences Division, Oak Ridge National Laboratory (ORNL), Oak Ridge, TN USA
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Arthur J. Ragauskas
- Joint Institute of Biological Science, Biosciences Division, Oak Ridge National Laboratory (ORNL), Oak Ridge, TN USA
- Department of Chemical & Bimolecular Engineering, Center for Renewable Carbon and Department of Forestry, Wildlife, and Fisheries, University of Tennessee Knoxville, Knoxville, TN USA
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Rajeev Kumar
- Center for Environmental Research and Technology (CE-CERT), Bourns College of Engineering, University of California Riverside, Riverside, CA USA
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Thanh Yen Nguyen
- Center for Environmental Research and Technology (CE-CERT), Bourns College of Engineering, University of California Riverside, Riverside, CA USA
- Department of Bioengineering, Bourns College of Engineering, University of California Riverside, Riverside, CA USA
| | - Charles M. Cai
- Center for Environmental Research and Technology (CE-CERT), Bourns College of Engineering, University of California Riverside, Riverside, CA USA
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Charles E. Wyman
- Department of Chemical and Environmental Engineering, Bourns College of Engineering, University of California Riverside, Riverside, CA USA
- Center for Environmental Research and Technology (CE-CERT), Bourns College of Engineering, University of California Riverside, Riverside, CA USA
- Department of Bioengineering, Bourns College of Engineering, University of California Riverside, Riverside, CA USA
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN USA
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16
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Donohoe BS, Wei H, Mittal A, Shollenberger T, Lunin VV, Himmel ME, Brunecky R. Towards an Understanding of Enhanced Biomass Digestibility by In Planta Expression of a Family 5 Glycoside Hydrolase. Sci Rep 2017; 7:4389. [PMID: 28663545 PMCID: PMC5491509 DOI: 10.1038/s41598-017-04502-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 05/17/2017] [Indexed: 12/21/2022] Open
Abstract
In planta expression of a thermophilic endoglucanase (AcCel5A) reduces recalcitrance by creating voids and other irregularities in cell walls of Arabidopsis thaliana that increase enzyme accessibility without negative impacts on plant growth or cell wall composition. Our results suggest that cellulose β-1-4 linkages can be cut sparingly in the assembling wall and that these minimal changes, made at the proper time, have an impact on plant cell wall recalcitrance without negative effects on overall plant development.
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Affiliation(s)
- Bryon S Donohoe
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado, 80401, United States
| | - Hui Wei
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado, 80401, United States
| | - Ashutosh Mittal
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado, 80401, United States
| | - Todd Shollenberger
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado, 80401, United States
| | - Vladimir V Lunin
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado, 80401, United States
| | - Michael E Himmel
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado, 80401, United States
| | - Roman Brunecky
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado, 80401, United States.
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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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19
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Xu Q, Resch MG, Podkaminer K, Yang S, Baker JO, Donohoe BS, Wilson C, Klingeman DM, Olson DG, Decker SR, Giannone RJ, Hettich RL, Brown SD, Lynd LR, Bayer EA, Himmel ME, Bomble YJ. Dramatic performance of Clostridium thermocellum explained by its wide range of cellulase modalities. Sci Adv 2016; 2:e1501254. [PMID: 26989779 PMCID: PMC4788478 DOI: 10.1126/sciadv.1501254] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 11/30/2015] [Indexed: 05/18/2023]
Abstract
Clostridium thermocellum is the most efficient microorganism for solubilizing lignocellulosic biomass known to date. Its high cellulose digestion capability is attributed to efficient cellulases consisting of both a free-enzyme system and a tethered cellulosomal system wherein carbohydrate active enzymes (CAZymes) are organized by primary and secondary scaffoldin proteins to generate large protein complexes attached to the bacterial cell wall. This study demonstrates that C. thermocellum also uses a type of cellulosomal system not bound to the bacterial cell wall, called the "cell-free" cellulosomal system. The cell-free cellulosome complex can be seen as a "long range cellulosome" because it can diffuse away from the cell and degrade polysaccharide substrates remotely from the bacterial cell. The contribution of these two types of cellulosomal systems in C. thermocellum was elucidated by characterization of mutants with different combinations of scaffoldin gene deletions. The primary scaffoldin, CipA, was found to play the most important role in cellulose degradation by C. thermocellum, whereas the secondary scaffoldins have less important roles. Additionally, the distinct and efficient mode of action of the C. thermocellum exoproteome, wherein the cellulosomes splay or divide biomass particles, changes when either the primary or secondary scaffolds are removed, showing that the intact wild-type cellulosomal system is necessary for this essential mode of action. This new transcriptional and proteomic evidence shows that a functional primary scaffoldin plays a more important role compared to secondary scaffoldins in the proper regulation of CAZyme genes, cellodextrin transport, and other cellular functions.
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Affiliation(s)
- Qi Xu
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
- BioEnergy Science Center, Oak Ridge, TN 37831, USA
| | - Michael G. Resch
- BioEnergy Science Center, Oak Ridge, TN 37831, USA
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Kara Podkaminer
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
- BioEnergy Science Center, Oak Ridge, TN 37831, USA
| | - Shihui Yang
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - John O. Baker
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
- BioEnergy Science Center, Oak Ridge, TN 37831, USA
| | - Bryon S. Donohoe
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
- BioEnergy Science Center, Oak Ridge, TN 37831, USA
| | - Charlotte Wilson
- BioEnergy Science Center, Oak Ridge, TN 37831, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Dawn M. Klingeman
- BioEnergy Science Center, Oak Ridge, TN 37831, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Daniel G. Olson
- BioEnergy Science Center, Oak Ridge, TN 37831, USA
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA
| | - Stephen R. Decker
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
- BioEnergy Science Center, Oak Ridge, TN 37831, USA
| | - Richard J. Giannone
- BioEnergy Science Center, Oak Ridge, TN 37831, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Robert L. Hettich
- BioEnergy Science Center, Oak Ridge, TN 37831, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Steven D. Brown
- BioEnergy Science Center, Oak Ridge, TN 37831, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Lee R. Lynd
- BioEnergy Science Center, Oak Ridge, TN 37831, USA
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA
| | | | - Michael E. Himmel
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
- BioEnergy Science Center, Oak Ridge, TN 37831, USA
| | - Yannick J. Bomble
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
- BioEnergy Science Center, Oak Ridge, TN 37831, USA
- Corresponding author. E-mail:
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20
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Paye JMD, Guseva A, Hammer SK, Gjersing E, Davis MF, Davison BH, Olstad J, Donohoe BS, Nguyen TY, Wyman CE, Pattathil S, Hahn MG, Lynd LR. Biological lignocellulose solubilization: comparative evaluation of biocatalysts and enhancement via cotreatment. Biotechnol Biofuels 2016; 9:8. [PMID: 26759604 PMCID: PMC4709877 DOI: 10.1186/s13068-015-0412-y] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 12/04/2015] [Indexed: 05/19/2023]
Abstract
BACKGROUND Feedstock recalcitrance is the most important barrier impeding cost-effective production of cellulosic biofuels. Pioneer commercial cellulosic ethanol facilities employ thermochemical pretreatment and addition of fungal cellulase, reflecting the main research emphasis in the field. However, it has been suggested that it may be possible to process cellulosic biomass without thermochemical pretreatment using thermophilic, cellulolytic bacteria. To further explore this idea, we examine the ability of various biocatalysts to solubilize autoclaved but otherwise unpretreated cellulosic biomass under controlled but not industrial conditions. RESULTS Carbohydrate solubilization of mid-season harvested switchgrass after 5 days ranged from 24 % for Caldicellulosiruptor bescii to 65 % for Clostridium thermocellum, with intermediate values for a thermophilic horse manure enrichment, Clostridium clariflavum, Clostridium cellulolyticum, and simultaneous saccharification and fermentation (SSF) featuring a fungal cellulase cocktail and yeast. Under a variety of conditions, solubilization yields were about twice as high for C. thermocellum compared to fungal cellulase. Solubilization of mid-season harvested switchgrass was about twice that of senescent switchgrass. Lower yields and greater dependence on particle size were observed for Populus as compared to switchgrass. Trends observed from data drawn from six conversion systems and three substrates, including both time course and end-point data, were (1) equal fractional solubilization of glucan and xylan, (2) no biological solubilization of the non-carbohydrate fraction of biomass, and (3) higher solubilization for three of the four bacterial cultures tested as compared to the fungal cellulase system. Brief (5 min) ball milling of solids remaining after fermentation of senescent switchgrass by C. thermocellum nearly doubled carbohydrate solubilization upon reinnoculation as compared to a control without milling. Greater particle size reduction and solubilization were observed for milling of partially fermented solids than for unfermented solids. Physical disruption of cellulosic feedstocks after initiation of fermentation, termed cotreatment, warrants further study. CONCLUSIONS While the ability to achieve significant solubilization of minimally pretreated switchgrass is widespread, a fivefold difference between the most and least effective biocatalyst-feedstock combinations was observed. Starting with nature's best biomass-solubilizing systems may enable a reduction in the amount of non-biological processing required, and in particular substitution of cotreatment for pretreatment.
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Affiliation(s)
- Julie M. D. Paye
- />Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH 03755 USA
- />BioEnergy Science Center Oak Ridge National Laboratory Oak Ridge, Oak Ridge, TN USA
| | - Anna Guseva
- />Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH 03755 USA
- />BioEnergy Science Center Oak Ridge National Laboratory Oak Ridge, Oak Ridge, TN USA
| | - Sarah K. Hammer
- />Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH 03755 USA
- />BioEnergy Science Center Oak Ridge National Laboratory Oak Ridge, Oak Ridge, TN USA
| | - Erica Gjersing
- />BioEnergy Science Center Oak Ridge National Laboratory Oak Ridge, Oak Ridge, TN USA
- />National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401 USA
| | - Mark F. Davis
- />BioEnergy Science Center Oak Ridge National Laboratory Oak Ridge, Oak Ridge, TN USA
- />National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401 USA
| | - Brian H. Davison
- />BioEnergy Science Center Oak Ridge National Laboratory Oak Ridge, Oak Ridge, TN USA
- />Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Jessica Olstad
- />BioEnergy Science Center Oak Ridge National Laboratory Oak Ridge, Oak Ridge, TN USA
- />National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401 USA
| | - Bryon S. Donohoe
- />BioEnergy Science Center Oak Ridge National Laboratory Oak Ridge, Oak Ridge, TN USA
- />National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401 USA
| | - Thanh Yen Nguyen
- />BioEnergy Science Center Oak Ridge National Laboratory Oak Ridge, Oak Ridge, TN USA
- />Center for Environmental Research and Technology (CE-CERT), Bourns College of Engineering, University of California, Riverside, 1084 Columbia Ave, Riverside, CA USA
| | - Charles E. Wyman
- />BioEnergy Science Center Oak Ridge National Laboratory Oak Ridge, Oak Ridge, TN USA
- />Center for Environmental Research and Technology (CE-CERT), Bourns College of Engineering, University of California, Riverside, 1084 Columbia Ave, Riverside, CA USA
| | - Sivakumar Pattathil
- />BioEnergy Science Center Oak Ridge National Laboratory Oak Ridge, Oak Ridge, TN USA
- />Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens GA, 30602 USA
| | - Michael G. Hahn
- />BioEnergy Science Center Oak Ridge National Laboratory Oak Ridge, Oak Ridge, TN USA
- />Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens GA, 30602 USA
| | - Lee R. Lynd
- />Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH 03755 USA
- />BioEnergy Science Center Oak Ridge National Laboratory Oak Ridge, Oak Ridge, TN USA
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21
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Anderson NA, Tobimatsu Y, Ciesielski PN, Ximenes E, Ralph J, Donohoe BS, Ladisch M, Chapple C. Manipulation of Guaiacyl and Syringyl Monomer Biosynthesis in an Arabidopsis Cinnamyl Alcohol Dehydrogenase Mutant Results in Atypical Lignin Biosynthesis and Modified Cell Wall Structure. Plant Cell 2015; 27:2195-209. [PMID: 26265762 PMCID: PMC4568507 DOI: 10.1105/tpc.15.00373] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 07/13/2015] [Accepted: 07/25/2015] [Indexed: 05/17/2023]
Abstract
Modifying lignin composition and structure is a key strategy to increase plant cell wall digestibility for biofuel production. Disruption of the genes encoding both cinnamyl alcohol dehydrogenases (CADs), including CADC and CADD, in Arabidopsis thaliana results in the atypical incorporation of hydroxycinnamaldehydes into lignin. Another strategy to change lignin composition is downregulation or overexpression of ferulate 5-hydroxylase (F5H), which results in lignins enriched in guaiacyl or syringyl units, respectively. Here, we combined these approaches to generate plants enriched in coniferaldehyde-derived lignin units or lignins derived primarily from sinapaldehyde. The cadc cadd and ferulic acid hydroxylase1 (fah1) cadc cadd plants are similar in growth to wild-type plants even though their lignin compositions are drastically altered. In contrast, disruption of CAD in the F5H-overexpressing background results in dwarfism. The dwarfed phenotype observed in these plants does not appear to be related to collapsed xylem, a hallmark of many other lignin-deficient dwarf mutants. cadc cadd, fah1 cadc cadd, and cadd F5H-overexpressing plants have increased enzyme-catalyzed cell wall digestibility. Given that these CAD-deficient plants have similar total lignin contents and only differ in the amounts of hydroxycinnamaldehyde monomer incorporation, these results suggest that hydroxycinnamaldehyde content is a more important determinant of digestibility than lignin content.
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Affiliation(s)
- Nickolas A Anderson
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907 Heartland Plant Innovations, Manhattan, Kansas 66502
| | - Yuki Tobimatsu
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706 DOE Great Lakes Bioenergy Research Center and Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, Wisconsin 53726 Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Peter N Ciesielski
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401
| | - Eduardo Ximenes
- Department of Agricultural and Biological Engineering and the Laboratory of Renewable Resources Engineering, Purdue University, West Lafayette, Indiana 47907
| | - John Ralph
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706 DOE Great Lakes Bioenergy Research Center and Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, Wisconsin 53726 Department of Biological Systems Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Bryon S Donohoe
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401
| | - Michael Ladisch
- Department of Agricultural and Biological Engineering and the Laboratory of Renewable Resources Engineering, Purdue University, West Lafayette, Indiana 47907 Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana 47907
| | - Clint Chapple
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907
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22
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Wei H, Brunecky R, Donohoe BS, Ding SY, Ciesielski PN, Yang S, Tucker MP, Himmel ME. Identifying the ionically bound cell wall and intracellular glycoside hydrolases in late growth stage Arabidopsis stems: implications for the genetic engineering of bioenergy crops. Front Plant Sci 2015; 6:315. [PMID: 26029221 PMCID: PMC4429552 DOI: 10.3389/fpls.2015.00315] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2014] [Accepted: 04/21/2015] [Indexed: 05/07/2023]
Abstract
Identifying the cell wall-ionically bound glycoside hydrolases (GHs) in Arabidopsis stems is important for understanding the regulation of cell wall integrity. For cell wall proteomics studies, the preparation of clean cell wall fractions is a challenge since cell walls constitute an open compartment, which is more likely to contain a mixture of intracellular and extracellular proteins due to cell leakage at the late growth stage. Here, we utilize a CaCl2-extraction procedure to isolate non-structural proteins from Arabidopsis whole stems, followed by the in-solution and in-gel digestion methods coupled with Nano-LC-MS/MS, bioinformatics and literature analyses. This has led to the identification of 75 proteins identified using the in-solution method and 236 proteins identified by the in-gel method, among which about 10% of proteins predicted to be secreted. Together, eight cell wall proteins, namely AT1G75040, AT5G26000, AT3G57260, AT4G21650, AT3G52960, AT3G49120, AT5G49360, and AT3G14067, were identified by the in-solution method; among them, three were the GHs (AT5G26000, myrosinase 1, GH1; AT3G57260, β-1,3-glucanase 2, GH17; AT5G49360, bifunctional XYL 1/α-L-arabinofuranosidase, GH3). Moreover, four more GHs: AT4G30270 (xyloglucan endotransferase, GH16), AT1G68560 (bifunctional α-l-arabinofuranosidase/XYL, GH31), AT1G12240 (invertase, GH32) and AT2G28470 (β-galactosidase 8, GH35), were identified by the in-gel solution method only. Notably, more than half of above identified GHs are xylan- or hemicellulose-modifying enzymes, and will likely have an impact on cellulose accessibility, which is a critical factor for downstream enzymatic hydrolysis of plant tissues for biofuels production. The implications of these cell wall proteins identified at the late growth stage for the genetic engineering of bioenergy crops are discussed.
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Affiliation(s)
- Hui Wei
- Biosciences Center, National Renewable Energy LaboratoryGolden, CO, USA
- *Correspondence: Hui Wei and Michael E. Himmel, Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA ;
| | - Roman Brunecky
- Biosciences Center, National Renewable Energy LaboratoryGolden, CO, USA
| | - Bryon S. Donohoe
- Biosciences Center, National Renewable Energy LaboratoryGolden, CO, USA
| | - Shi-You Ding
- Biosciences Center, National Renewable Energy LaboratoryGolden, CO, USA
- Department of Plant Biology, Michigan State UniversityEast Lansing, MI, USA
| | | | - Shihui Yang
- National Bioenergy Center, National Renewable Energy LaboratoryGolden, CO, USA
| | - Melvin P. Tucker
- National Bioenergy Center, National Renewable Energy LaboratoryGolden, CO, USA
| | - Michael E. Himmel
- Biosciences Center, National Renewable Energy LaboratoryGolden, CO, USA
- *Correspondence: Hui Wei and Michael E. Himmel, Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA ;
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23
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Hinkle JD, Ciesielski PN, Gruchalla K, Munch KR, Donohoe BS. Biomass accessibility analysis using electron tomography. Biotechnol Biofuels 2015; 8:212. [PMID: 26709354 PMCID: PMC4691013 DOI: 10.1186/s13068-015-0395-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 11/24/2015] [Indexed: 05/09/2023]
Abstract
BACKGROUND Substrate accessibility to catalysts has been a dominant theme in theories of biomass deconstruction. However, current methods of quantifying accessibility do not elucidate mechanisms for increased accessibility due to changes in microstructure following pretreatment. RESULTS We introduce methods for characterization of surface accessibility based on fine-scale microstructure of the plant cell wall as revealed by 3D electron tomography. These methods comprise a general framework, enabling analysis of image-based cell wall architecture using a flexible model of accessibility. We analyze corn stover cell walls, both native and after undergoing dilute acid pretreatment with and without a steam explosion process, as well as AFEX pretreatment. CONCLUSION Image-based measures provide useful information about how much pretreatments are able to increase biomass surface accessibility to a wide range of catalyst sizes. We find a strong dependence on probe size when measuring surface accessibility, with a substantial decrease in biomass surface accessibility to probe sizes above 5-10 nm radius compared to smaller probes.
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Affiliation(s)
- Jacob D. Hinkle
- />Computational Science Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401 USA
| | - Peter N. Ciesielski
- />Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401 USA
| | - Kenny Gruchalla
- />Computational Science Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401 USA
| | - Kristin R. Munch
- />Computational Science Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401 USA
| | - Bryon S. Donohoe
- />Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401 USA
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24
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Brunecky R, Alahuhta M, Xu Q, Donohoe BS, Crowley MF, Kataeva IA, Yang SJ, Resch MG, Adams MWW, Lunin VV, Himmel ME, Bomble YJ. Response to Comment on "Revealing nature's cellulase diversity: the digestion mechanism of Caldicellulosiruptor bescii CelA". Science 2014; 344:578. [PMID: 24812382 DOI: 10.1126/science.1251701] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Gusakov critiques our methodology for comparing the cellulolytic activity of the bacterial cellulase CelA with the fungal cellulase Cel7A. We address his concerns by clarifying some misconceptions, carefully referencing the literature, and justifying our approach to point out that the results from our study still stand.
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Affiliation(s)
- Roman Brunecky
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA
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25
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Kim JI, Ciesielski PN, Donohoe BS, Chapple C, Li X. Chemically induced conditional rescue of the reduced epidermal fluorescence8 mutant of Arabidopsis reveals rapid restoration of growth and selective turnover of secondary metabolite pools. Plant Physiol 2014; 164:584-95. [PMID: 24381065 PMCID: PMC3912091 DOI: 10.1104/pp.113.229393] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The phenylpropanoid pathway is responsible for the biosynthesis of diverse and important secondary metabolites including lignin and flavonoids. The reduced epidermal fluorescence8 (ref8) mutant of Arabidopsis (Arabidopsis thaliana), which is defective in a lignin biosynthetic enzyme p-coumaroyl shikimate 3'-hydroxylase (C3'H), exhibits severe dwarfism and sterility. To better understand the impact of perturbation of phenylpropanoid metabolism on plant growth, we generated a chemically inducible C3'H expression construct and transformed it into the ref8 mutant. Application of dexamethasone to these plants greatly alleviates the dwarfism and sterility and substantially reverses the biochemical phenotypes of ref8 plants, including the reduction of lignin content and hyperaccumulation of flavonoids and p-coumarate esters. Induction of C3'H expression at different developmental stages has distinct impacts on plant growth. Although early induction effectively restored the elongation of primary inflorescence stem, application to 7-week-old plants enabled them to produce new rosette inflorescence stems. Examination of hypocotyls of these plants revealed normal vasculature in the newly formed secondary xylem, presumably restoring water transport in the mutant. The ref8 mutant accumulates higher levels of salicylic acid than the wild type, but depletion of this compound in ref8 did not relieve the mutant's growth defects, suggesting that the hyperaccumulation of salicylic acid is unlikely to be responsible for dwarfism in this mutant.
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Affiliation(s)
| | | | | | | | - Xu Li
- Address correspondence to
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26
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Wang W, Chen X, Donohoe BS, Ciesielski PN, Katahira R, Kuhn EM, Kafle K, Lee CM, Park S, Kim SH, Tucker MP, Himmel ME, Johnson DK. Effect of mechanical disruption on the effectiveness of three reactors used for dilute acid pretreatment of corn stover Part 1: chemical and physical substrate analysis. Biotechnol Biofuels 2014; 7:57. [PMID: 24713111 PMCID: PMC3999883 DOI: 10.1186/1754-6834-7-57] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 03/17/2014] [Indexed: 05/07/2023]
Abstract
BACKGROUND There is considerable interest in the conversion of lignocellulosic biomass to liquid fuels to provide substitutes for fossil fuels. Pretreatments, conducted to reduce biomass recalcitrance, usually remove at least some of the hemicellulose and/or lignin in cell walls. The hypothesis that led to this research was that reactor type could have a profound effect on the properties of pretreated materials and impact subsequent cellulose hydrolysis. RESULTS Corn stover was dilute-acid pretreated using commercially relevant reactor types (ZipperClave(®) (ZC), Steam Gun (SG) and Horizontal Screw (HS)) under the same nominal conditions. Samples produced in the SG and HS achieved much higher cellulose digestibilities (88% and 95%, respectively), compared to the ZC sample (68%). Characterization, by chemical, physical, spectroscopic and electron microscopy methods, was used to gain an understanding of the effects causing the digestibility differences. Chemical differences were small; however, particle size differences appeared significant. Sum-frequency generation vibrational spectra indicated larger inter-fibrillar spacing or randomization of cellulose microfibrils in the HS sample. Simons' staining indicated increased cellulose accessibility for the SG and HS samples. Electron microscopy showed that the SG and HS samples were more porous and fibrillated because of mechanical grinding and explosive depressurization occurring with these two reactors. These structural changes most likely permitted increased cellulose accessibility to enzymes, enhancing saccharification. CONCLUSIONS Dilute-acid pretreatment of corn stover using three different reactors under the same nominal conditions gave samples with very different digestibilities, although chemical differences in the pretreated substrates were small. The results of the physical and chemical analyses of the samples indicate that the explosive depressurization and mechanical grinding with these reactors increased enzyme accessibility. Pretreatment reactors using physical force to disrupt cell walls increase the effectiveness of the pretreatment process.
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Affiliation(s)
- Wei Wang
- National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA
| | - Xiaowen Chen
- National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA
| | - Bryon S Donohoe
- National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA
| | - Peter N Ciesielski
- National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA
| | - Rui Katahira
- National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA
| | - Erik M Kuhn
- National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA
| | - Kabindra Kafle
- Department of Chemical Engineering and Materials Research Institute, Pennsylvania State University, University Park, PA 16802, USA
| | - Christopher M Lee
- Department of Chemical Engineering and Materials Research Institute, Pennsylvania State University, University Park, PA 16802, USA
| | - Sunkyu Park
- Department of Forest Biomaterials, North Carolina State University, Raleigh NC 27695, USA
| | - Seong H Kim
- Department of Chemical Engineering and Materials Research Institute, Pennsylvania State University, University Park, PA 16802, USA
| | - Melvin P Tucker
- National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA
| | - Michael E Himmel
- National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA
| | - David K Johnson
- National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA
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Ciesielski PN, Wang W, Chen X, Vinzant TB, Tucker MP, Decker SR, Himmel ME, Johnson DK, Donohoe BS. Effect of mechanical disruption on the effectiveness of three reactors used for dilute acid pretreatment of corn stover Part 2: morphological and structural substrate analysis. Biotechnol Biofuels 2014; 7:47. [PMID: 24690534 PMCID: PMC4022059 DOI: 10.1186/1754-6834-7-47] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 03/17/2014] [Indexed: 05/18/2023]
Abstract
BACKGROUND Lignocellulosic biomass is a renewable, naturally mass-produced form of stored solar energy. Thermochemical pretreatment processes have been developed to address the challenge of biomass recalcitrance, however the optimization, cost reduction, and scalability of these processes remain as obstacles to the adoption of biofuel production processes at the industrial scale. In this study, we demonstrate that the type of reactor in which pretreatment is carried out can profoundly alter the micro- and nanostructure of the pretreated materials and dramatically affect the subsequent efficiency, and thus cost, of enzymatic conversion of cellulose. RESULTS Multi-scale microscopy and quantitative image analysis was used to investigate the impact of different biomass pretreatment reactor configurations on plant cell wall structure. We identify correlations between enzymatic digestibility and geometric descriptors derived from the image data. Corn stover feedstock was pretreated under the same nominal conditions for dilute acid pretreatment (2.0 wt% H2SO4, 160°C, 5 min) using three representative types of reactors: ZipperClave® (ZC), steam gun (SG), and horizontal screw (HS) reactors. After 96 h of enzymatic digestion, biomass treated in the SG and HS reactors achieved much higher cellulose conversions, 88% and 95%, respectively, compared to the conversion obtained using the ZC reactor (68%). Imaging at the micro- and nanoscales revealed that the superior performance of the SG and HS reactors could be explained by reduced particle size, cellular dislocation, increased surface roughness, delamination, and nanofibrillation generated within the biomass particles during pretreatment. CONCLUSIONS Increased cellular dislocation, surface roughness, delamination, and nanofibrillation revealed by direct observation of the micro- and nanoscale change in accessibility explains the superior performance of reactors that augment pretreatment with physical energy.
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Affiliation(s)
- Peter N Ciesielski
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
| | - Wei Wang
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
| | - Xiaowen Chen
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, USA
| | - Todd B Vinzant
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
| | - Melvin P Tucker
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, USA
| | - Stephen R Decker
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
| | - Michael E Himmel
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
| | - David K Johnson
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
| | - Bryon S Donohoe
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
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Brunecky R, Alahuhta M, Xu Q, Donohoe BS, Crowley MF, Kataeva IA, Yang SJ, Resch MG, Adams MWW, Lunin VV, Himmel ME, Bomble YJ. Revealing Nature's Cellulase Diversity: The Digestion Mechanism of Caldicellulosiruptor bescii CelA. Science 2013; 342:1513-6. [PMID: 24357319 DOI: 10.1126/science.1244273] [Citation(s) in RCA: 229] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Roman Brunecky
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA
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29
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Ciesielski PN, Matthews JF, Tucker MP, Beckham GT, Crowley MF, Himmel ME, Donohoe BS. 3D electron tomography of pretreated biomass informs atomic modeling of cellulose microfibrils. ACS Nano 2013; 7:8011-9. [PMID: 23988022 DOI: 10.1021/nn4031542] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Fundamental insights into the macromolecular architecture of plant cell walls will elucidate new structure-property relationships and facilitate optimization of catalytic processes that produce fuels and chemicals from biomass. Here we introduce computational methodology to extract nanoscale geometry of cellulose microfibrils within thermochemically treated biomass directly from electron tomographic data sets. We quantitatively compare the cell wall nanostructure in corn stover following two leading pretreatment strategies: dilute acid with iron sulfate co-catalyst and ammonia fiber expansion (AFEX). Computational analysis of the tomographic data is used to extract mathematical descriptions for longitudinal axes of cellulose microfibrils from which we calculate their nanoscale curvature. These nanostructural measurements are used to inform the construction of atomistic models that exhibit features of cellulose within real, process-relevant biomass. By computational evaluation of these atomic models, we propose relationships between the crystal structure of cellulose Iβ and the nanoscale geometry of cellulose microfibrils.
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Affiliation(s)
- Peter N Ciesielski
- Biosciences Center, National Renewable Energy Laboratory , 15013 Denver West Parkway, Golden, Colorado 80401, United States
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30
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Donohoe BS, Kang BH, Gerl MJ, Gergely ZR, McMichael CM, Bednarek SY, Staehelin LA. Cis-Golgi cisternal assembly and biosynthetic activation occur sequentially in plants and algae. Traffic 2013; 14:551-67. [PMID: 23369235 DOI: 10.1111/tra.12052] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Revised: 01/28/2013] [Accepted: 01/31/2013] [Indexed: 12/18/2022]
Abstract
The cisternal progression/maturation model of Golgi trafficking predicts that cis-Golgi cisternae are formed de novo on the cis-side of the Golgi. Here we describe structural and functional intermediates of the cis cisterna assembly process in high-pressure frozen algae (Scherffelia dubia, Chlamydomonas reinhardtii) and plants (Arabidopsis thaliana, Dionaea muscipula; Venus flytrap) as determined by electron microscopy, electron tomography and immuno-electron microscopy techniques. Our findings are as follows: (i) The cis-most (C1) Golgi cisternae are generated de novo from cisterna initiators produced by the fusion of 3-5 COPII vesicles in contact with a C2 cis cisterna. (ii) COPII vesicles fuel the growth of the initiators, which then merge into a coherent C1 cisterna. (iii) When a C1 cisterna nucleates its first cisterna initiator it becomes a C2 cisterna. (iv) C2-Cn cis cisternae grow through COPII vesicle fusion. (v) ER-resident proteins are recycled from cis cisternae to the ER via COPIa-type vesicles. (vi) In S. dubia the C2 cisternae are capable of mediating the self-assembly of scale protein complexes. (vii) In plants, ∼90% of native α-mannosidase I localizes to medial Golgi cisternae. (viii) Biochemical activation of cis cisternae appears to coincide with their conversion to medial cisternae via recycling of medial cisterna enzymes. We propose how the different cis cisterna assembly intermediates of plants and algae may actually be related to those present in the ERGIC and in the pre-cis Golgi cisterna layer in mammalian cells.
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Affiliation(s)
- Bryon S Donohoe
- Molecular Cellular and Developmental Biology, University of Colorado at Boulder, Boulder, CO 80306, USA.
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31
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van der Lelie D, Taghavi S, McCorkle SM, Li LL, Malfatti SA, Monteleone D, Donohoe BS, Ding SY, Adney WS, Himmel ME, Tringe SG. The metagenome of an anaerobic microbial community decomposing poplar wood chips. PLoS One 2012; 7:e36740. [PMID: 22629327 PMCID: PMC3357426 DOI: 10.1371/journal.pone.0036740] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2011] [Accepted: 04/11/2012] [Indexed: 02/01/2023] Open
Abstract
This study describes the composition and metabolic potential of a lignocellulosic biomass degrading community that decays poplar wood chips under anaerobic conditions. We examined the community that developed on poplar biomass in a non-aerated bioreactor over the course of a year, with no microbial inoculation other than the naturally occurring organisms on the woody material. The composition of this community contrasts in important ways with biomass-degrading communities associated with higher organisms, which have evolved over millions of years into a symbiotic relationship. Both mammalian and insect hosts provide partial size reduction, chemical treatments (low or high pH environments), and complex enzymatic ‘secretomes’ that improve microbial access to cell wall polymers. We hypothesized that in order to efficiently degrade coarse untreated biomass, a spontaneously assembled free-living community must both employ alternative strategies, such as enzymatic lignin depolymerization, for accessing hemicellulose and cellulose and have a much broader metabolic potential than host-associated communities. This would suggest that such a community would make a valuable resource for finding new catalytic functions involved in biomass decomposition and gaining new insight into the poorly understood process of anaerobic lignin depolymerization. Therefore, in addition to determining the major players in this community, our work specifically aimed at identifying functions potentially involved in the depolymerization of cellulose, hemicelluloses, and lignin, and to assign specific roles to the prevalent community members in the collaborative process of biomass decomposition. A bacterium similar to Magnetospirillum was identified among the dominant community members, which could play a key role in the anaerobic breakdown of aromatic compounds. We suggest that these compounds are released from the lignin fraction in poplar hardwood during the decay process, which would point to lignin-modification or depolymerization under anaerobic conditions.
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Affiliation(s)
- Daniel van der Lelie
- Biology Department, Brookhaven National Laboratory, Upton, New York, United States of America.
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32
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Donohoe BS, Ciesielski PN, Vinzant TB. Preservation and preparation of lignocellulosic biomass samples for multi-scale microscopy analysis. Methods Mol Biol 2012; 908:31-47. [PMID: 22843387 DOI: 10.1007/978-1-61779-956-3_4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Biomass exhibits structural and chemical complexity over multiple size scales, presenting many challenges to the effective characterization of these materials. The macroscopic nature of plants requires that some form of size reduction, such as dissection and microtomy, be performed to prepare samples and reveal features of interest for any microscopic and nanoscopic analyses. These size reduction techniques, particularly sectioning and microtomy, are complicated by the inherent porosity of plant tissue that often necessitates fixation and embedding in a supporting matrix to preserve structural integrity. The chemical structure of plant cell walls is vastly different from that of the membrane bound organelles and protein macromolecular complexes within the cytosol, which are the focus of many traditional transmission electron microscopy (TEM) investigations in structural biology; thus, staining procedures developed for the latter are not optimized for biomass. While the moisture content of biomass is dramatically reduced compared to the living plant tissue, the residual water is still problematic for microscopic techniques conducted under vacuum such as scanning electron microscopy (SEM). This requires that samples must be carefully dehydrated or that the instrument must be operated in an environmental mode to accommodate the presence of water. In this chapter we highlight tools and techniques that have been successfully used to address these challenges and present procedural details regarding the preparation of biomass samples that enable effective and accurate multi-scale microscopic analysis.
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Affiliation(s)
- Bryon S Donohoe
- National Renewable Energy Laboratory, Biosciences Center, Golden, CO, USA.
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33
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Donohoe BS, Vinzant TB, Elander RT, Pallapolu VR, Lee YY, Garlock RJ, Balan V, Dale BE, Kim Y, Mosier NS, Ladisch MR, Falls M, Holtzapple MT, Sierra-Ramirez R, Shi J, Ebrik MA, Redmond T, Yang B, Wyman CE, Hames B, Thomas S, Warner RE. Surface and ultrastructural characterization of raw and pretreated switchgrass. Bioresour Technol 2011; 102:11097-104. [PMID: 21571527 DOI: 10.1016/j.biortech.2011.03.092] [Citation(s) in RCA: 9] [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: 01/13/2011] [Revised: 03/25/2011] [Accepted: 03/29/2011] [Indexed: 05/03/2023]
Abstract
The US Department of Energy-funded Biomass Refining CAFI (Consortium for Applied Fundamentals and Innovation) project has developed leading pretreatment technologies for application to switchgrass and has evaluated their effectiveness in recovering sugars from the coupled operations of pretreatment and enzymatic hydrolysis. Key chemical and physical characteristics have been determined for pretreated switchgrass samples. Several analytical microscopy approaches utilizing instruments in the Biomass Surface Characterization Laboratory (BSCL) at the National Renewable Energy Laboratory (NREL) have been applied to untreated and CAFI-pretreated switchgrass samples. The results of this work have shown that each of the CAFI pretreatment approaches on switchgrass result in different structural impacts at the plant tissue, cellular, and cell wall levels. Some of these structural changes can be related to changes in chemical composition upon pretreatment. There are also apparently different structural mechanisms that are responsible for achieving the highest enzymatic hydrolysis sugar yields.
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Affiliation(s)
- Bryon S Donohoe
- Chemical and Biosciences Center, National Renewable Energy Laboratory, 1617 Cole Blvd., Golden, CO 80401, USA
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Shi J, Ebrik MA, Yang B, Garlock RJ, Balan V, Dale BE, Pallapolu VR, Lee YY, Kim Y, Mosier NS, Ladisch MR, Holtzapple MT, Falls M, Sierra-Ramirez R, Donohoe BS, Vinzant TB, Elander RT, Hames B, Thomas S, Warner RE, Wyman CE. Application of cellulase and hemicellulase to pure xylan, pure cellulose, and switchgrass solids from leading pretreatments. Bioresour Technol 2011; 102:11080-8. [PMID: 21596559 DOI: 10.1016/j.biortech.2011.04.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2011] [Revised: 04/02/2011] [Accepted: 04/02/2011] [Indexed: 05/14/2023]
Abstract
Accellerase 1000 cellulase, Spezyme CP cellulase, β-glucosidase, Multifect xylanase, and beta-xylosidase were evaluated for hydrolysis of pure cellulose, pure xylan, and switchgrass solids from leading pretreatments of dilute sulfuric acid, sulfur dioxide, liquid hot water, lime, soaking in aqueous ammonia, and ammonia fiber expansion. Distinctive sugar release patterns were observed from Avicel, phosphoric acid swollen cellulose (PASC), xylan, and pretreated switchgrass solids, with accumulation of significant amounts of xylooligomers during xylan hydrolysis. The strong inhibition of cellulose hydrolysis by xylooligomers could be partially attributed to the negative impact of xylooligomers on cellulase adsorption. The digestibility of pretreated switchgrass varied with pretreatment but could not be consistently correlated to xylan, lignin, or acetyl removal. Initial hydrolysis rates did correlate well with cellulase adsorption capacities for all pretreatments except lime, but more investigation is needed to relate this behavior to physical and compositional properties of pretreated switchgrass.
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Affiliation(s)
- Jian Shi
- Center for Environmental Research and Technology, Bourns College of Engineering, University of California at Riverside, 1084 Columbia Avenue, Riverside, CA 92507, USA
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Pallapolu VR, Lee YY, Garlock RJ, Balan V, Dale BE, Kim Y, Mosier NS, Ladisch MR, Falls M, Holtzapple MT, Sierra-Ramirez R, Shi J, Ebrik MA, Redmond T, Yang B, Wyman CE, Donohoe BS, Vinzant TB, Elander RT, Hames B, Thomas S, Warner RE. Effects of enzyme loading and β-glucosidase supplementation on enzymatic hydrolysis of switchgrass processed by leading pretreatment technologies. Bioresour Technol 2011; 102:11115-20. [PMID: 21507624 DOI: 10.1016/j.biortech.2011.03.085] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2011] [Revised: 03/23/2011] [Accepted: 03/25/2011] [Indexed: 05/02/2023]
Abstract
The objective of this work is to investigate the effects of cellulase loading and β-glucosidase supplementation on enzymatic hydrolysis of pretreated Dacotah switchgrass. To assess the difference among various pretreatment methods, the profiles of sugars and intermediates were determined for differently treated substrates. For all pretreatments, 72 h glucan/xylan digestibilities increased sharply with enzyme loading up to 25mg protein/g-glucan, after which the response varied depending on the pretreatment method. For a fixed level of enzyme loading, dilute sulfuric acid (DA), SO(2), and Lime pretreatments exhibited higher digestibility than the soaking in aqueous ammonia (SAA) and ammonia fiber expansion (AFEX). Supplementation of Novozyme-188 to Spezyme-CP improved the 72 h glucan digestibility only for the SAA treated samples. The effect of β-glucosidase supplementation was discernible only at the early phase of hydrolysis where accumulation of cellobiose and oligomers is significant. Addition of β-glucosidase increased the xylan digestibility of alkaline treated samples due to the β-xylosidase activity present in Novozyme-188.
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Kim Y, Mosier NS, Ladisch MR, Pallapolu VR, Lee YY, Garlock R, Balan V, Dale BE, Donohoe BS, Vinzant TB, Elander RT, Falls M, Sierra R, Holtzapple MT, Shi J, Ebrik MA, Redmond T, Yang B, Wyman CE, Warner RE. Comparative study on enzymatic digestibility of switchgrass varieties and harvests processed by leading pretreatment technologies. Bioresour Technol 2011; 102:11089-96. [PMID: 21741233 DOI: 10.1016/j.biortech.2011.06.054] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2011] [Accepted: 06/12/2011] [Indexed: 05/09/2023]
Abstract
Feedstock quality of switchgrass for biofuel production depends on many factors such as morphological types, geographic origins, maturity, environmental and cultivation parameters, and storage. We report variability in compositions and enzymatic digestion efficiencies for three cultivars of switchgrass (Alamo, Dacotah and Shawnee), grown and harvested at different locations and seasons. Saccharification yields of switchgrass processed by different pretreatment technologies (AFEX, dilute sulfuric acid, liquid hot water, lime, and soaking in aqueous ammonia) are compared in regards to switchgrass genotypes and harvest seasons. Despite its higher cellulose content per dry mass, Dacotah switchgrass harvested after wintering consistently gave a lower saccharification yield than the other two varieties harvested in the fall. The recalcitrance of upland cultivars and over-wintered switchgrass may require more severe pretreatment conditions. We discuss the key features of different pretreatment technologies and differences in switchgrass cultivars and harvest seasons on hydrolysis performance for the applied pretreatment methods.
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Affiliation(s)
- Youngmi Kim
- Laboratory of Renewable Resources Engineering, Potter Engineering Center, 500 Central Drive, Purdue University, West Lafayette, IN 47907-2022, USA
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Garlock RJ, Balan V, Dale BE, Pallapolu VR, Lee YY, Kim Y, Mosier NS, Ladisch MR, Holtzapple MT, Falls M, Sierra-Ramirez R, Shi J, Ebrik MA, Redmond T, Yang B, Wyman CE, Donohoe BS, Vinzant TB, Elander RT, Hames B, Thomas S, Warner RE. Comparative material balances around pretreatment technologies for the conversion of switchgrass to soluble sugars. Bioresour Technol 2011; 102:11063-71. [PMID: 21524908 DOI: 10.1016/j.biortech.2011.04.002] [Citation(s) in RCA: 23] [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: 01/08/2011] [Revised: 04/01/2011] [Accepted: 04/01/2011] [Indexed: 05/02/2023]
Abstract
For this project, six chemical pretreatments were compared for the Consortium for Applied Fundamentals and Innovation (CAFI): ammonia fiber expansion (AFEX), dilute sulfuric acid (DA), lime, liquid hot water (LHW), soaking in aqueous ammonia (SAA), and sulfur dioxide (SO(2)). For each pretreatment, a material balance was analyzed around the pretreatment, optional post-washing step, and enzymatic hydrolysis of Dacotah switchgrass. All pretreatments+enzymatic hydrolysis solubilized over two-thirds of the available glucan and xylan. Lime, post-washed LHW, and SO(2) achieved >83% total glucose yields. Lime, post-washed AFEX, and DA achieved >83% total xylose yields. Alkaline pretreatments, except AFEX, solubilized the most lignin and a portion of the xylan as xylo-oligomers. As pretreatment pH decreased, total solubilized xylan and released monomeric xylose increased. Low temperature-long time or high temperature-short time pretreatments are necessary for high glucose release from late-harvest Dacotah switchgrass but high temperatures may cause xylose degradation.
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Affiliation(s)
- Rebecca J Garlock
- Biomass Conversion Research Laboratory, Department of Chemical Engineering and Materials Science, Michigan State University, 3900 Collins Road, Lansing, MI 48910, USA.
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Falls M, Shi J, Ebrik MA, Redmond T, Yang B, Wyman CE, Garlock R, Balan V, Dale BE, Pallapolu VR, Lee YY, Kim Y, Mosier NS, Ladisch MR, Hames B, Thomas S, Donohoe BS, Vinzant TB, Elander RT, Warner RE, Sierra-Ramirez R, Holtzapple MT. Investigation of enzyme formulation on pretreated switchgrass. Bioresour Technol 2011; 102:11072-9. [PMID: 21478012 DOI: 10.1016/j.biortech.2011.03.035] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2011] [Revised: 03/09/2011] [Accepted: 03/12/2011] [Indexed: 05/25/2023]
Abstract
This work studied the benefits of adding different enzyme cocktails (cellulase, xylanase, β-glucosidase) to pretreated switchgrass. Pretreatment methods included ammonia fiber expansion (AFEX), dilute-acid (DA), liquid hot water (LHW), lime, lime+ball-milling, soaking in aqueous ammonia (SAA), and sulfur dioxide (SO(2)). The compositions of the pretreated materials were analyzed and showed a strong correlation between initial xylan composition and the benefits of xylanase addition. Adding xylanase dramatically improved xylan yields for SAA (+8.4%) and AFEX (+6.3%), and showed negligible improvement (0-2%) for the pretreatments with low xylan content (dilute-acid, SO(2)). Xylanase addition also improved overall yields with lime+ball-milling and SO(2) achieving the highest overall yields from pretreated biomass (98.3% and 93.2%, respectively). Lime+ball-milling obtained an enzymatic yield of 92.3kg of sugar digested/kg of protein loaded.
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Affiliation(s)
- Matthew Falls
- Texas A&M University, College Station, TX 77843, USA.
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Wei H, Donohoe BS, Vinzant TB, Ciesielski PN, Wang W, Gedvilas LM, Zeng Y, Johnson DK, Ding SY, Himmel ME, Tucker MP. Elucidating the role of ferrous ion cocatalyst in enhancing dilute acid pretreatment of lignocellulosic biomass. Biotechnol Biofuels 2011; 4:48. [PMID: 22074910 PMCID: PMC3279309 DOI: 10.1186/1754-6834-4-48] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Accepted: 11/10/2011] [Indexed: 05/07/2023]
Abstract
BACKGROUND Recently developed iron cocatalyst enhancement of dilute acid pretreatment of biomass is a promising approach for enhancing sugar release from recalcitrant lignocellulosic biomass. However, very little is known about the underlying mechanisms of this enhancement. In the current study, our aim was to identify several essential factors that contribute to ferrous ion-enhanced efficiency during dilute acid pretreatment of biomass and to initiate the investigation of the mechanisms that result in this enhancement. RESULTS During dilute acid and ferrous ion cocatalyst pretreatments, we observed concomitant increases in solubilized sugars in the hydrolysate and reducing sugars in the (insoluble) biomass residues. We also observed enhancements in sugar release during subsequent enzymatic saccharification of iron cocatalyst-pretreated biomass. Fourier transform Raman spectroscopy showed that major peaks representing the C-O-C and C-H bonds in cellulose are significantly attenuated by iron cocatalyst pretreatment. Imaging using Prussian blue staining indicated that Fe2+ ions associate with both cellulose/xylan and lignin in untreated as well as dilute acid/Fe2+ ion-pretreated corn stover samples. Analyses by scanning electron microscopy and transmission electron microscopy revealed structural details of biomass after dilute acid/Fe2+ ion pretreatment, in which delamination and fibrillation of the cell wall were observed. CONCLUSIONS By using this multimodal approach, we have revealed that (1) acid-ferrous ion-assisted pretreatment increases solubilization and enzymatic digestion of both cellulose and xylan to monomers and (2) this pretreatment likely targets multiple chemistries in plant cell wall polymer networks, including those represented by the C-O-C and C-H bonds in cellulose.
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Affiliation(s)
- Hui Wei
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Bryon S Donohoe
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Todd B Vinzant
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Peter N Ciesielski
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Wei Wang
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Lynn M Gedvilas
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Yining Zeng
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - David K Johnson
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Shi-You Ding
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, 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
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Brunecky R, Vinzant TB, Porter SE, Donohoe BS, Johnson DK, Himmel ME. Redistribution of xylan in maize cell walls during dilute acid pretreatment. Biotechnol Bioeng 2009; 102:1537-43. [PMID: 19161247 DOI: 10.1002/bit.22211] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Developing processes for the conversion of biomass for use in transportation fuels production is becoming a critically important economic and engineering challenge. Dilute acid pretreatment is a promising technology for increasing the enzymatic digestibility of lignocellulosic biomass. However, a deeper understanding of the pretreatability of biomass is needed so that the rate of formation and yields of sugars can be increased. Xylan is an important hemicellulosic component of the plant cell wall and acts as a barrier to cellulose, essentially blocking cellulase action. To better understand xylan hydrolysis in corn stover, we have studied changes in the distribution of xylan caused by dilute acid pretreatment using correlative microscopy. A dramatic loss of xylan antibody signal from the center of the cell wall and an increase or retention of xylan at the plasma membrane interface and middle lamella of the cell were observed by confocal laser scanning microscopy (CLSM). We also observed a reduction in xylan fluorescence signal by CLSM that is generally consistent with the decrease in xylan content measured experimentally in the bulk sample, however, the compartmentalization of this xylan retention was not anticipated.
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Affiliation(s)
- Roman Brunecky
- Chemical and Biosciences Center, Golden, Colorado 80401, USA.
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Donohoe BS, Selig MJ, Viamajala S, Vinzant TB, Adney WS, Himmel ME. Detecting cellulase penetration into corn stover cell walls by immuno-electron microscopy. Biotechnol Bioeng 2009; 103:480-9. [PMID: 19266575 DOI: 10.1002/bit.22281] [Citation(s) in RCA: 44] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
In general, pretreatments are designed to enhance the accessibility of cellulose to enzymes, allowing for more efficient conversion. In this study, we have detected the penetration of major cellulases present in a commercial enzyme preparation (Spezyme CP) into corn stem cell walls following mild-, moderate- and high-severity dilute sulfuric acid pretreatments. The Trichoderma reesei enzymes, Cel7A (CBH I) and Cel7B (EG I), as well as the cell wall matrix components xylan and lignin were visualized within digested corn stover cell walls by immuno transmission electron microscopy (TEM) using enzyme- and polymer-specific antibodies. Low severity dilute-acid pretreatment (20 min at 100 degrees C) enabled <1% of the thickness of secondary cell walls to be penetrated by enzyme, moderate severity pretreatment at (20 min at 120 degrees C) allowed the enzymes to penetrate approximately 20% of the cell wall, and the high severity (20 min pretreatment at 150 degrees C) allowed 100% penetration of even the thickest cell walls. These data allow direct visualization of the dramatic effect dilute-acid pretreatment has on altering the condensed ultrastructure of biomass cell walls. Loosening of plant cell wall structure due to pretreatment and the subsequently improved access by cellulases has been hypothesized by the biomass conversion community for over two decades, and for the first time, this study provides direct visual evidence to verify this hypothesis. Further, the high-resolution enzyme penetration studies presented here provide insight into the mechanisms of cell wall deconstruction by cellulolytic enzymes.
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Affiliation(s)
- Bryon S Donohoe
- Chemical and Biosciences Center, Golden, Colorado 80401, USA.
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Donohoe BS, Decker SR, Tucker MP, Himmel ME, Vinzant TB. Visualizing lignin coalescence and migration through maize cell walls following thermochemical pretreatment. Biotechnol Bioeng 2008; 101:913-25. [PMID: 18781690 DOI: 10.1002/bit.21959] [Citation(s) in RCA: 291] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Plant cell walls are composed primarily of cellulose, hemicelluloses, lignins, and pectins. Of these components, lignins exhibit unique chemistry and physiological functions. Although lignins can be used as a product feedstock or as a fuel, lignins are also generally seen as a barrier to efficient enzymatic breakdown of biomass to sugars. Indeed, many pretreatment strategies focus on removing a significant fraction of lignin from biomass to better enable saccharification. In order to better understand the fate of biomass lignins that remain with the solids following dilute acid pretreatment, we undertook a structural investigation to track lignins on and in biomass cell walls. SEM and TEM imaging revealed a range of droplet morphologies that appear on and within cell walls of pretreated biomass; as well as the specific ultrastructural regions that accumulate the droplets. These droplets were shown to contain lignin by FTIR, NMR, antibody labeling, and cytochemical staining. We provide evidence supporting the idea that thermochemical pretreatments reaching temperatures above the range for lignin phase transition cause lignins to coalesce into larger molten bodies that migrate within and out of the cell wall, and can redeposit on the surface of plant cell walls. This decompartmentalization and relocalization of lignins is likely to be at least as important as lignin removal in the quest to improve the digestibility of biomass for sugars and fuels production.
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Affiliation(s)
- Bryon S Donohoe
- Chemical and Biosciences Center, National Renewable Energy Laboratory, 1617 Cole Boulevard, Golden, Colorado 80401, USA.
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Abstract
Tomographic reconstruction by transmission electron microscopy is used to reveal three-dimensional nanoparticle shapes and the stacking configurations of nanoparticle ensembles. Reconstructions are generated from bright-field image tilt series, with a sample tilt range up to +/- 70 degrees, using single or dual tilt axes. We demonstrate the feasibility of this technique for the analysis of nanomaterials, using appropriate acquisition conditions. Tomography reveals both cubic and hexagonal close-packing configurations in multi-layered arrays of size-selected In nanospheres. By tomography and phase-contrast lattice imaging, we relate the three-dimensional shape of PbSe octahedral nanoparticles to the underlying crystal structure. We also confirm simple-cubic packing in multi-layers of PbSe nanocubes and see evidence that the particle shapes have cubic symmetry. The shapes of TiO(2) nanorod bundles are shown by tomographic reconstruction to resemble flattened ellipsoids.
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Affiliation(s)
- S P Ahrenkiel
- National Renewable Energy Laboratory, 1617 Cole Boulevard, Golden, CO 80401, USA.
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Porter SE, Donohoe BS, Beery KE, Xu Q, Ding SY, Vinzant TB, Abbas CA, Himmel ME. Microscopic analysis of corn fiber using starch- and cellulose-specific molecular probes. Biotechnol Bioeng 2007; 98:123-31. [PMID: 17335065 DOI: 10.1002/bit.21409] [Citation(s) in RCA: 21] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Ethanol is the primary liquid transportation fuel produced from renewable feedstocks in the United States today. The majority of corn grain, the primary feedstock for ethanol production, has been historically processed in wet mills yielding products such as gluten feed, gluten meal, starch, and germ. Starch extracted from the grain is used to produce ethanol in saccharification and fermentation steps; however the extraction of starch is not 100% efficient. To better understand starch extraction during the wet milling process, we have developed fluorescent probes that can be used to visually localize starch and cellulose in samples using confocal microscopy. These probes are based on the binding specificities of two types of carbohydrate binding modules (CBMs), which are small substrate-specific protein domains derived from carbohydrate degrading enzymes. CBMs were fused, using molecular cloning techniques, to a green fluorescent protein (GFP) or to the red fluorescent protein DsRed (RFP). Using these engineered probes, we found that the binding of the starch-specific probe correlates with starch content in corn fiber samples. We also demonstrate that there is starch internally localized in the endosperm that may contribute to the high starch content in corn fiber. We also surprisingly found that the cellulose-specific probe did not bind to most corn fiber samples, but only to corn fiber that had been hydrolyzed using a thermochemical process that removes the residual starch and much of the hemicellulose. Our findings should be of interest to those working to increase the efficiency of the corn grain to ethanol process.
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Affiliation(s)
- Stephanie E Porter
- Chemical and Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, USA.
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Donohoe BS, Kang BH, Staehelin LA. Identification and characterization of COPIa- and COPIb-type vesicle classes associated with plant and algal Golgi. Proc Natl Acad Sci U S A 2006; 104:163-8. [PMID: 17185411 PMCID: PMC1765428 DOI: 10.1073/pnas.0609818104] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.0] [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: 11/18/2022] Open
Abstract
Coat protein I (COPI) vesicles arise from Golgi cisternae and mediate the recycling of proteins from the Golgi back to the endoplasmic reticulum (ER) and the transport of Golgi resident proteins between cisternae. In vitro studies have produced evidence for two distinct types of COPI vesicles, but the in vivo sites of operation of these vesicles remain to be established. We have used a combination of electron tomography and immunolabeling techniques to examine Golgi stacks and associated vesicles in the cells of the scale-producing alga Scherffelia dubia and Arabidopsis preserved by high-pressure freezing/freeze-substitution methods. Five structurally distinct types of vesicles were distinguished. In Arabidopsis, COPI and COPII vesicle coat proteins as well as vesicle cargo molecules (mannosidase I and sialyltransferase-yellow fluorescent protein) were identified by immunogold labeling. In both organisms, the COPI-type vesicles were further characterized by a combination of six structural criteria: coat architecture, coat thickness, membrane structure, cargo staining, cisternal origin, and spatial distribution. Using this multiparameter structural approach, we can distinguish two types of COPI vesicles, COPIa and COPIb. COPIa vesicles bud exclusively from cis cisternae and occupy the space between cis cisternae and ER export sites, whereas the COPIb vesicles bud exclusively from medial- and trans-Golgi cisternae and are confined to the space around these latter cisternae. We conclude that COPIa vesicle-mediated recycling to the ER occurs only from cis cisternae, that retrograde transport of Golgi resident proteins by COPIb vesicles is limited to medial and trans cisternae, and that diffusion of periGolgi vesicles is restricted.
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Affiliation(s)
- Bryon S. Donohoe
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309
| | - Byung-Ho Kang
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309
- To whom correspondence should be addressed. E-mail:
| | - L. Andrew Staehelin
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309
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Abstract
A primary goal of cell biology is to uncover the mechanisms of cellular processes. A detailed structural understanding of the organelles and subcellular structures involved in these processes has often formed the foundation for the elucidation of their function. Electron tomography is a powerful technique for characterizing subcellular architecture and structural details in three dimensions. Electron tomography of cryofixed, freeze-substituted, and plastic-embedded samples allows three-dimensional visualization and display of dynamic, pleiomorphic structures at a resolution of approximately 7 nm in cell volumes up to approximately 25 microm(3). In this review, we describe the electron tomography protocols that we have employed to determine the 3D architecture of complex cellular structures, thereby gaining insights into their functional organization. We stress the need for studying specimens preserved by cryofixation methods to obtain accurate information on the geometry and size of cellular structures. We also discuss some of the challenges associated with the staining of certain types of membranes. Finally, we provide examples of how tomographic data can be analyzed, dissected, and displayed using the tools built into the IMOD software package.
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Affiliation(s)
- Bryon S Donohoe
- University of Colorado at Boulder, MCD Biology, Boulder, CO 80309, USA
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Anandarajah K, Kiefer PM, Donohoe BS, Copley SD. Recruitment of a double bond isomerase to serve as a reductive dehalogenase during biodegradation of pentachlorophenol. Biochemistry 2000; 39:5303-11. [PMID: 10820000 DOI: 10.1021/bi9923813] [Citation(s) in RCA: 81] [Impact Index Per Article: 3.4] [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: 11/29/2022]
Abstract
Tetrachlorohydroquinone dehalogenase catalyzes the replacement of chlorine atoms on tetrachlorohydroquinone and trichlorohydroquinone with hydrogen atoms during the biodegradation of pentachlorophenol by Sphingomonas chlorophenolica. The sequence of the active site region of tetrachlorohydroquinone dehalogenase is very similar to those of the corresponding regions of maleylacetoacetate isomerases, enzymes that catalyze the glutathione-dependent isomerization of a cis double bond in maleylacetoacetate to the trans configuration during the catabolism of phenylalanine and tyrosine. Furthermore, tetrachlorohydroquinone dehalogenase catalyzes the isomerization of maleylacetone (an analogue of maleylacetoacetate) at a rate nearly comparable to that of a bona fide bacterial maleylacetoacetate isomerase. Since maleylacetoacetate isomerase is involved in a common and presumably ancient pathway for catabolism of tyrosine, while tetrachlorohydroquinone dehalogenase catalyzes a more specialized reaction, it is likely that tetrachlorohydroquinone dehalogenase arose from a maleylacetoacetate isomerase. The substrates and overall transformations involved in the dehalogenation and isomerization reactions are strikingly different. This enzyme provides a remarkable example of Nature's ability to recruit an enzyme with a useful structural scaffold and elaborate upon its basic catalytic capabilities to generate a catalyst for a newly needed reaction.
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Affiliation(s)
- K Anandarajah
- Department of Molecular, Cellular and Developmental Biology and Cooperative Institute for Research in Environmental Sciences, University of Colorado at Boulder, Campus Box 216, Boulder, Colorado 80309-0216, USA
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Peterson DG, Stack SM, Healy JL, Donohoe BS, Anderson LK. The relationship between synaptonemal complex length and genome size in four vertebrate classes (Osteicthyes, Reptilia, Aves, Mammalia). Chromosome Res 1994; 2:153-62. [PMID: 8032674 DOI: 10.1007/bf01553494] [Citation(s) in RCA: 36] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
We investigated the relationship between synaptonemal complex (SC) length and genome size in 18 species of vertebrates from the classes Osteicthyes (bony fish), Reptilia (reptiles), Aves (birds), and Mammalia (mammals). When total SC length was plotted against genome size for all 18 vertebrate species, there did not appear to be a correlation between the two variables. However, when birds were excluded from the data and a linear regression analysis was performed, variation in genome size accounted for approximately 50% of the variation in total SC length (r2 = 0.47). Dividing the average total SC length for a species by its 4C DNA amount yields the species' SC/DNA ratio. SC/DNA ratios of birds were approximately twice as high as the SC/DNA ratios of reptiles and mammals. Bony fish showed intraclass divergence in SC/DNA ratios. The sunfish (Centrarchidae) had SC/DNA ratios almost as high as those of birds, while the remaining fish in the study had SC/DNA ratios similar to those of reptiles and mammals. These observations indicate that inter and intraclass divergence in the relationship between total SC length and genome size has occurred in the vertebrates. Coupled with evidence from the literature, our results also suggest that SC/DNA ratios are positively correlated with crossover frequency.
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Affiliation(s)
- D G Peterson
- Department of Biology, Colorado State University, Fort Collins 80523
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