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Faria NT, Marques S, Fonseca C, Ferreira FC. Direct xylan conversion into glycolipid biosurfactants, mannosylerythritol lipids, by Pseudozyma antarctica PYCC 5048T. Enzyme Microb Technol 2015; 71:58-65. [DOI: 10.1016/j.enzmictec.2014.10.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Revised: 10/27/2014] [Accepted: 10/28/2014] [Indexed: 10/24/2022]
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Boock JT, King BC, Taw MN, Conrado RJ, Siu KH, Stark JC, Walker LP, Gibson DM, DeLisa MP. Repurposing a bacterial quality control mechanism to enhance enzyme production in living cells. J Mol Biol 2015; 427:1451-1463. [PMID: 25591491 DOI: 10.1016/j.jmb.2015.01.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 12/30/2014] [Accepted: 01/05/2015] [Indexed: 11/25/2022]
Abstract
Heterologous expression of many proteins in bacteria, yeasts, and plants is often limited by low titers of functional protein. To address this problem, we have created a two-tiered directed evolution strategy in Escherichia coli that enables optimization of protein production while maintaining high biological activity. The first tier involves a genetic selection for intracellular protein stability that is based on the folding quality control mechanism inherent to the twin-arginine translocation pathway, while the second is a semi-high-throughput screen for protein function. To demonstrate the utility of this strategy, we isolated variants of the endoglucanase Cel5A, from the plant-pathogenic fungus Fusarium graminearum, whose production was increased by as much as 30-fold over the parental enzyme. This gain in production was attributed to just two amino acid substitutions, and it was isolated after two iterations through the two-tiered approach. There was no significant tradeoff in activity on soluble or insoluble cellulose substrates. Importantly, by combining the folding filter afforded by the twin-arginine translocation quality control mechanism with a function-based screen, we show enrichment for variants with increased protein abundance in a manner that does not compromise catalytic activity, providing a highly soluble parent for engineering of improved or new function.
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Affiliation(s)
- Jason T Boock
- School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Brian C King
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA
| | - May N Taw
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
| | - Robert J Conrado
- School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Ka-Hei Siu
- School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Jessica C Stark
- School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Larry P Walker
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Donna M Gibson
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA; Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, United States Department of Agriculture, Ithaca, NY 14853, USA
| | - Matthew P DeLisa
- School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA.
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Engineering Neurospora crassa for improved cellobiose and cellobionate production. Appl Environ Microbiol 2014; 81:597-603. [PMID: 25381238 DOI: 10.1128/aem.02885-14] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
We report engineering Neurospora crassa to improve the yield of cellobiose and cellobionate from cellulose. A previously engineered strain of N. crassa (F5) with six of seven β-glucosidase (bgl) genes knocked out was shown to produce cellobiose and cellobionate directly from cellulose without the addition of exogenous cellulases. In this study, the F5 strain was further modified to improve the yield of cellobiose and cellobionate from cellulose by increasing cellulase production and decreasing product consumption. The effects of two catabolite repression genes, cre-1 and ace-1, on cellulase production were investigated. The F5 Δace-1 mutant showed no improvement over the wild type. The F5 Δcre-1 and F5 Δace-1 Δcre-1 strains showed improved cellobiose dehydrogenase and exoglucanase expression. However, this improvement in cellulase expression did not lead to an improvement in cellobiose or cellobionate production. The cellobionate phosphorylase gene (ndvB) was deleted from the genome of F5 Δace-1 Δcre-1 to prevent the consumption of cellobiose and cellobionate. Despite a slightly reduced hydrolysis rate, the F5 Δace-1 Δcre-1 ΔndvB strain converted 75% of the cellulose consumed to the desired products, cellobiose and cellobionate, compared to 18% converted by the strain F5 Δace-1 Δcre-1.
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Faria NT, Santos M, Ferreira C, Marques S, Ferreira FC, Fonseca C. Conversion of cellulosic materials into glycolipid biosurfactants, mannosylerythritol lipids, by Pseudozyma spp. under SHF and SSF processes. Microb Cell Fact 2014; 13:155. [PMID: 25366184 PMCID: PMC4226859 DOI: 10.1186/s12934-014-0155-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 10/20/2014] [Indexed: 01/28/2023] Open
Abstract
Background Mannosylerythritol lipids (MEL) are glycolipids with unique biosurfactant properties and are produced by Pseudozyma spp. from different substrates, preferably vegetable oils, but also sugars, glycerol or hydrocarbons. However, solvent intensive downstream processing and the relatively high prices of raw materials currently used for MEL production are drawbacks in its sustainable commercial deployment. The present work aims to demonstrate MEL production from cellulosic materials and investigate the requirements and consequences of combining commercial cellulolytic enzymes and Pseudozyma spp. under separate hydrolysis and fermentation (SHF) and simultaneous saccharification and fermentation (SSF) processes. Results MEL was produced from cellulosic substrates, Avicel® as reference (>99% cellulose) and hydrothermally pretreated wheat straw, using commercial cellulolytic enzymes (Celluclast 1.5 L® and Novozyme 188®) and Pseudozyma antarctica PYCC 5048T or Pseudozyma aphidis PYCC 5535T. The strategies included SHF, SSF and fed-batch SSF with pre-hydrolysis. While SSF was isothermal at 28°C, in SHF and fed-batch SSF, yeast fermentation was preceded by an enzymatic (pre-)hydrolysis step at 50°C for 48 h. Pseudozyma antarctica showed the highest MEL yields from both cellulosic substrates, reaching titres of 4.0 and 1.4 g/l by SHF of Avicel® and wheat straw (40 g/l glucan), respectively, using enzymes at low dosage (3.6 and 8.5 FPU/gglucan at 28°C and 50°C, respectively) with prior dialysis. Higher MEL titres were obtained by fed-batch SSF with pre-hydrolysis, reaching 4.5 and 2.5 g/l from Avicel® and wheat straw (80 g/l glucan), respectively. Conclusions This work reports for the first time MEL production from cellulosic materials. The process was successfully performed through SHF, SSF or Fed-batch SSF, requiring, for maximal performance, dialysed commercial cellulolytic enzymes. The use of inexpensive lignocellulosic substrates associated to straightforward downstream processing from sugary broths is expected to have a great impact in the economy of MEL production for the biosurfactant market, inasmuch as low enzyme dosage is sufficient for good systems performance.
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Affiliation(s)
- Nuno Torres Faria
- Department of Bioengineering and IBB - Institute for Bioengineering and Bioscience, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisboa, Portugal. .,MIT-Portugal Program, 77 Massachusetts Avenue, E40-221, Cambridge, MA, 02139, USA. .,Laboratório Nacional de Energia e Geologia, I.P, Unidade de Bioenergia, Estrada do Paço do Lumiar 22, 1649-038, Lisboa, Portugal.
| | - Marisa Santos
- Department of Bioengineering and IBB - Institute for Bioengineering and Bioscience, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisboa, Portugal. .,MIT-Portugal Program, 77 Massachusetts Avenue, E40-221, Cambridge, MA, 02139, USA.
| | - Carla Ferreira
- Laboratório Nacional de Energia e Geologia, I.P, Unidade de Bioenergia, Estrada do Paço do Lumiar 22, 1649-038, Lisboa, Portugal.
| | - Susana Marques
- Laboratório Nacional de Energia e Geologia, I.P, Unidade de Bioenergia, Estrada do Paço do Lumiar 22, 1649-038, Lisboa, Portugal.
| | - Frederico Castelo Ferreira
- Department of Bioengineering and IBB - Institute for Bioengineering and Bioscience, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisboa, Portugal.
| | - César Fonseca
- Laboratório Nacional de Energia e Geologia, I.P, Unidade de Bioenergia, Estrada do Paço do Lumiar 22, 1649-038, Lisboa, Portugal.
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55
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Ohm RA, Riley R, Salamov A, Min B, Choi IG, Grigoriev IV. Genomics of wood-degrading fungi. Fungal Genet Biol 2014; 72:82-90. [DOI: 10.1016/j.fgb.2014.05.001] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 05/08/2014] [Accepted: 05/10/2014] [Indexed: 01/01/2023]
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Shirley D, Oppert C, Reynolds TB, Miracle B, Oppert B, Klingeman WE, Jurat-Fuentes JL. Expression of an endoglucanase from Tribolium castaneum (TcEG1) in Saccharomyces cerevisiae. INSECT SCIENCE 2014; 21:609-618. [PMID: 24318365 DOI: 10.1111/1744-7917.12069] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/10/2013] [Indexed: 05/28/2023]
Abstract
Insects are a largely unexploited resource in prospecting for novel cellulolytic enzymes to improve the production of ethanol fuel from lignocellulosic biomass. The cost of lignocellulosic ethanol production is expected to decrease by the combination of cellulose degradation (saccharification) and fermentation of the resulting glucose to ethanol in a single process, catalyzed by the yeast Saccharomyces cerevisiae transformed to express efficient cellulases. While S. cerevisiae is an established heterologous expression system, there are no available data on the functional expression of insect cellulolytic enzymes for this species. To address this knowledge gap, S. cerevisiae was transformed to express the full-length cDNA encoding an endoglucanase from the red flour beetle, Tribolium castaneum (TcEG1), and evaluated the activity of the transgenic product (rTcEG1). Expression of the TcEG1 cDNA in S. cerevisiae was under control of the strong glyceraldehyde-3 phosphate dehydrogenase promoter. Cultured transformed yeast secreted rTcEG1 protein as a functional β-1,4-endoglucanase, which allowed transformants to survive on selective media containing cellulose as the only available carbon source. Evaluation of substrate specificity for secreted rTcEG1 demonstrated endoglucanase activity, although some activity was also detected against complex cellulose substrates. Potentially relevant to uses in biofuel production rTcEG1 activity increased with pH conditions, with the highest activity detected at pH 12. Our results demonstrate the potential for functional production of an insect cellulase in S. cerevisiae and confirm the stability of rTcEG1 activity in strong alkaline environments.
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Affiliation(s)
- Derek Shirley
- Department of Entomology and Plant Pathology, University of Tennessee
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57
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Luterbacher JS, Moran-Mirabal JM, Burkholder EW, Walker LP. Modeling enzymatic hydrolysis of lignocellulosic substrates using confocal fluorescence microscopy I: Filter paper cellulose. Biotechnol Bioeng 2014; 112:21-31. [DOI: 10.1002/bit.25329] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 05/08/2014] [Accepted: 06/30/2014] [Indexed: 11/09/2022]
Affiliation(s)
- Jeremy S. Luterbacher
- Department of Chemical and Biomolecular Engineering; Olin Hall; Cornell University; Ithaca New York
| | - Jose M. Moran-Mirabal
- Department of Chemistry and Chemical Biology; Arthur N. Bourns Science Building; McMaster University; Hamilton Ontario, Canada L8S4M1
| | - Eric W. Burkholder
- Department of Chemical and Biomolecular Engineering; Olin Hall; Cornell University; Ithaca New York
| | - Larry P. Walker
- Department of Biological and Environmental Engineering; Riley-Robb Hall; Cornell University; Ithaca New York 14850
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58
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Condezo-Hoyos L, Mohanty IP, Noratto GD. Assessing non-digestible compounds in apple cultivars and their potential as modulators of obese faecal microbiota in vitro. Food Chem 2014; 161:208-15. [PMID: 24837942 DOI: 10.1016/j.foodchem.2014.03.122] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Revised: 02/14/2014] [Accepted: 03/26/2014] [Indexed: 01/07/2023]
Abstract
The health benefits of apple bioactive compounds have been extensively reported. However, only few studies have focused on bioactive compounds that are not absorbed and metabolised during gastrointestinal digestion and can induce changes in microbial populations of faeces. We have characterised Braeburn, Fuji, Gala, Golden Delicious, Granny Smith, McIntosh and Red Delicious cultivars and found significant differences for extractable phenolics (1.08-9.2mg/g) non-extractable proanthocyanidins (3.28-5.7mg/g), and dietary fibre (20.6-32.2%) among cultivars with Granny Smith having the highest contents. Granny Smith was used after in vitro digestion for fermentation of faeces from diet-induced obese mice. Results showed that relative abundances of Firmicutes, Bacteroidetes, Enterococcus, Enterobacteriaceae, Escherichia coli, and Bifidobacterium in apple cultured faeces tended to resemble the abundance in faeces from lean mice with increased trend in the production of butyric acid. These results suggest that apple non-digestible compounds might help to re-establish a disturbed microbiota balance in obesity.
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Affiliation(s)
- Luis Condezo-Hoyos
- School of Food Science, Washington State University/University of Idaho, USA
| | - Indira P Mohanty
- School of Food Science, Washington State University/University of Idaho, USA
| | - Giuliana D Noratto
- School of Food Science, Washington State University/University of Idaho, USA.
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59
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Ortiz GE, Guitart ME, Albertó E, Fernández Lahore HM, Blasco M. Microplate assay for endo-polygalacturonase activity determination based on ruthenium red method. Anal Biochem 2014; 454:33-5. [PMID: 24613259 DOI: 10.1016/j.ab.2014.02.028] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Revised: 02/23/2014] [Accepted: 02/26/2014] [Indexed: 11/18/2022]
Abstract
Endo-polygalacturonase (endo-PGase) activity determinations generally rely on viscosity changes or reducing sugar ends produced by this activity over polygalacturonic acid. Torres and coworkers [Enzyme Microb. Technol. 48 (2011) 123-128] showed that ruthenium red (RR) is useful for endo-PGase determination. In this article, we present a high-throughput liquid-based endo-PGase assay based on the RR method and compare it with the viscosity determination method. The reduced assay uses a small volume of enzyme solution, 40 μg of polygalacturonic acid, and 45 μg of RR for each sample determination. Furthermore, we obtained an interconversion factor for RR and viscosity activities.
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Affiliation(s)
- Gastón E Ortiz
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico Chascomús (IIB-INTECH, UNSAM-CONICET), Universidad de San Martín, San Martín, Buenos Aires 1650, Argentina
| | - María E Guitart
- Downstream Processing Laboratory, Jacobs University Bremen, D-28759 Bremen, Germany
| | - Edgardo Albertó
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico Chascomús (IIB-INTECH, UNSAM-CONICET), Universidad de San Martín, San Martín, Buenos Aires 1650, Argentina
| | | | - Martin Blasco
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico Chascomús (IIB-INTECH, UNSAM-CONICET), Universidad de San Martín, San Martín, Buenos Aires 1650, Argentina.
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Expeditious quantification of lignocellulolytic enzymes from indigenous wood rot and litter degrading fungi from tropical dry evergreen forests of Tamil Nadu. BIOTECHNOLOGY RESEARCH INTERNATIONAL 2014; 2014:127848. [PMID: 24719770 PMCID: PMC3955672 DOI: 10.1155/2014/127848] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Accepted: 12/31/2013] [Indexed: 11/17/2022]
Abstract
In this study thirty wood rotting and litter degrading basidiomycetes were screened for the production of lignocellulolytic enzymes such as, laccase, peroxidase, and cellulase using rapid micro quantification assay. Out of the 30 indigenous isolates Trametes gibbosa was identified to be a potential lignocellulolytic enzyme producer, producing a maximum amount of cellulase (299.66 ± 1.59 IU/L) and laccase (257.94 ± 1.79 U/L). Moreover, it is the second leading producer of peroxidase enzyme (170.19 ± 1.98 U/L). Tricholomopsis sp. a wood rot basidiomycete was found to be the leading lignin decomposer with maximum peroxidase activity (287.84 ± 2 U/L) and second maximum laccase activity (250.19 ± 1.83 U/L). However, its cellulolytic potential was found to be moderate (100.04 ± 1.13 U/L). A higher level of lignocellulolytic enzymes was recorded in wood rotting basidiomycetes, whereas very low levels of lignolytic enzymes were found in litter inhabiting basidiomycetes. However, their cellulolytic potential was found to be moderate.
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61
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Chang C, Sustarich J, Bharadwaj R, Chandrasekaran A, Adams PD, Singh AK. Droplet-based microfluidic platform for heterogeneous enzymatic assays. LAB ON A CHIP 2013; 13:1817-22. [PMID: 23507976 DOI: 10.1039/c3lc41418c] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Heterogeneous enzymatic reactions are used in many industrial processes including pulp and paper, food, and biofuel production. Industrially-relevant optimization of the enzymes used in these processes requires assaying them with insoluble substrates. However, platforms for high throughput heterogeneous assays do not exist thereby severely increasing the cost and time of enzyme optimization, or leading to the use of assays with soluble substrates for convenient, but non-ideal, optimization. We present an innovative approach to perform heterogeneous reactions in a high throughput fashion using droplet microfluidics. Droplets provide a facile platform for heterogeneous reactions as internal recirculation allows rapid mixing of insoluble substrates with soluble enzymes. Moreover, it is easy to generate hundreds or thousands of picoliter droplets in a small footprint chip allowing many parallel reactions. We validate our approach by screening combinations of cellulases with real-world insoluble substrates, and demonstrate that the chip-based screening is in excellent agreement with the conventional screening methods, while offering advantages of throughput, speed and lower reagent consumption. We believe that our approach, while demonstrated for a biofuel application, provides a generic platform for high throughput monitoring of heterogeneous reactions.
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Affiliation(s)
- Chieh Chang
- Technology Division, Joint BioEnergy Institute, Emeryville, California 94608, United States
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62
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Kalita D, Jayanty SS. Reduction of acrylamide formation by vanadium salt in potato French fries and chips. Food Chem 2013; 138:644-9. [DOI: 10.1016/j.foodchem.2012.09.123] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2012] [Revised: 08/29/2012] [Accepted: 09/25/2012] [Indexed: 10/27/2022]
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63
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Blifernez-Klassen O, Klassen V, Doebbe A, Kersting K, Grimm P, Wobbe L, Kruse O. Cellulose degradation and assimilation by the unicellular phototrophic eukaryote Chlamydomonas reinhardtii. Nat Commun 2013; 3:1214. [PMID: 23169055 DOI: 10.1038/ncomms2210] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Accepted: 10/15/2012] [Indexed: 12/29/2022] Open
Abstract
Plants convert sunlight to biomass, which is primarily composed of lignocellulose, the most abundant natural biopolymer and a potential feedstock for fuel and chemical production. Cellulose assimilation has so far only been described for heterotrophic organisms that rely on photosynthetically active primary producers of organic compounds. Among phototrophs, the unicellular green microalga Chlamydomonas reinhardtii is widely known as one of the best established model organisms. It occupies many habitats, including aquatic and soil ecosystems. This ubiquity underscores the versatile metabolic properties of this microorganism. Here we present yet another paradigm of adaptation for C. reinhardtii, highlighting its photoheterotrophic ability to utilize cellulose for growth in the absence of other carbon sources. When grown under CO(2)-limiting conditions in the light, secretion of endo-β-1,4-glucanases by the cell causes digestion of exogenous cellulose, followed by cellobiose uptake and assimilation. Phototrophic microbes like C. reinhardtii may thus serve as biocatalysts for cellulosic biofuel production.
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Affiliation(s)
- Olga Blifernez-Klassen
- Department of Biology, Algae Biotechnology and Bioenergy-Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany
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Romano N, Gioffré A, Sede SM, Campos E, Cataldi A, Talia P. Characterization of Cellulolytic Activities of Environmental Bacterial Consortia from an Argentinian Native Forest. Curr Microbiol 2013; 67:138-47. [DOI: 10.1007/s00284-013-0345-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Accepted: 02/21/2013] [Indexed: 11/29/2022]
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65
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Lucena SA, Moraes CS, Costa SG, de Souza W, Azambuja P, Garcia ES, Genta FA. Miniaturization of hydrolase assays in thermocyclers. Anal Biochem 2012; 434:39-43. [PMID: 23123426 DOI: 10.1016/j.ab.2012.10.032] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Revised: 10/12/2012] [Accepted: 10/22/2012] [Indexed: 11/25/2022]
Abstract
We adapted the protocols of reducing sugar measurements with dinitrosalicylic acid and bicinchoninic acid for thermocyclers and their use in enzymatic assays for hydrolases such as amylase and β-1,3-glucanase. The use of thermocyclers for these enzymatic assays resulted in a 10 times reduction in the amount of reagent and volume of the sample needed when compared with conventional microplate protocols. We standardized absorbance readings from the polymerase chain reaction plates, which allowed us to make direct readings of the techniques above, and a β-glycosidase assay was also established under the same conditions. Standardization of the enzymatic reaction in thermocyclers resulted in less time-consuming temperature calibrations and without loss of volume through leakage or evaporation from the microplate. Kinetic parameters were successfully obtained, and the use of the thermocycler allowed the measurement of enzymatic activities in biological samples from the field with a limited amount of protein.
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Affiliation(s)
- Severino A Lucena
- National Institute of Metrology, Quality, and Technology (INMETRO), Rio de Janeiro 20261-232, Brazil; Oswaldo Cruz Institute (IOC, FIOCRUZ), Rio de Janeiro 21040-900, Brazil
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Luterbacher JS, Parlange JY, Walker LP. A pore-hindered diffusion and reaction model can help explain the importance of pore size distribution in enzymatic hydrolysis of biomass. Biotechnol Bioeng 2012; 110:127-36. [PMID: 22811319 DOI: 10.1002/bit.24614] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Revised: 06/08/2012] [Accepted: 07/09/2012] [Indexed: 11/06/2022]
Abstract
Until now, most efforts to improve monosaccharide production from biomass through pretreatment and enzymatic hydrolysis have used empirical optimization rather than employing a rational design process guided by a theory-based modeling framework. For such an approach to be successful a modeling framework that captures the key mechanisms governing the relationship between pretreatment and enzymatic hydrolysis must be developed. In this study, we propose a pore-hindered diffusion and kinetic model for enzymatic hydrolysis of biomass. When compared to data available in the literature, this model accurately predicts the well-known dependence of initial cellulose hydrolysis rates on surface area available to a cellulase-size molecule. Modeling results suggest that, for particles smaller than 5 × 10(-3) cm, a key rate-limiting step is the exposure of previously unexposed cellulose occurring after cellulose on the surface has hydrolyzed, rather than binding or diffusion. However, for larger particles, according to the model, diffusion plays a more significant role. Therefore, the proposed model can be used to design experiments that produce results that are either affected or unaffected by diffusion. Finally, by using pore size distribution data to predict the biomass fraction that is accessible to degradation, this model can be used to predict cellulose hydrolysis with time using only pore size distribution and initial composition data.
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Affiliation(s)
- Jeremy S Luterbacher
- Department of Chemical and Biomolecular Engineering, Olin Hall, Cornell University, Ithaca, New York 14850, USA
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67
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Davison BH. The Increasing Importance and Capabilities of Biomass Characterization. Ind Biotechnol (New Rochelle N Y) 2012. [DOI: 10.1089/ind.2012.1527] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Brian H. Davison
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN
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68
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Cianchetta S, Galletti S, Burzi PL, Cerato C. Hydrolytic potential of Trichoderma sp. strains evaluated by microplate-based screening followed by switchgrass saccharification. Enzyme Microb Technol 2012; 50:304-10. [DOI: 10.1016/j.enzmictec.2012.02.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Revised: 11/28/2011] [Accepted: 02/22/2012] [Indexed: 11/26/2022]
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69
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Chu D, Deng H, Zhang X, Zhang J, Bao J. A Simplified Filter Paper Assay Method of Cellulase Enzymes Based on HPLC Analysis. Appl Biochem Biotechnol 2012; 167:190-6. [DOI: 10.1007/s12010-012-9673-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2012] [Accepted: 04/09/2012] [Indexed: 11/29/2022]
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70
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Goacher RE, Edwards EA, Yakunin AF, Mims CA, Master ER. Application of Time-of-Flight-Secondary Ion Mass Spectrometry for the Detection of Enzyme Activity on Solid Wood Substrates. Anal Chem 2012; 84:4443-51. [DOI: 10.1021/ac3005346] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Robyn E. Goacher
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto,
Ontario, Canada M5S 3E5
| | - Elizabeth A. Edwards
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto,
Ontario, Canada M5S 3E5
| | - Alexander F. Yakunin
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto,
Ontario, Canada M5S 3E5
| | - Charles A. Mims
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto,
Ontario, Canada M5S 3E5
| | - Emma R. Master
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto,
Ontario, Canada M5S 3E5
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71
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Suryanarayanan TS, Thirunavukkarasu N, Govindarajulu MB, Gopalan V. Fungal endophytes: an untapped source of biocatalysts. FUNGAL DIVERS 2012. [DOI: 10.1007/s13225-012-0168-7] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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72
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Cabero K, Pozzo T, Lidén G, Karlsson EN. A cellulolytic Hypocrea strain isolated from South American brave straw produces a modular xylanase. Carbohydr Res 2012; 356:215-23. [PMID: 22609439 DOI: 10.1016/j.carres.2012.03.030] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Revised: 03/20/2012] [Accepted: 03/23/2012] [Indexed: 11/28/2022]
Abstract
Cellulase-producing fungi from the Andean regions in Bolivia, an ecosystem characterized as an extreme arid highland, were studied. Thirty-two isolates were screened for presence of cellulase activity using carboxymethyl cellulose (CMC) as carbon source, and activity was confirmed using a filter paper assay. One isolate, denoted as BLT1C was selected from this screening, and sequence analysis of the internal transcribed spacer (ITS) classified the strain as Hypocrea lixii. The secretome of BLT1C showed high xylanase activity (compared to that of two reference Trichoderma reesei strains) when cultivated using brave straw, an abundant native grass from the area, as carbon source. SDS-PAGE analysis revealed three main protein-bands (18, 32 and 65 kDa) and in-gel digestion and mass spectrometry combined with activity analysis showed that these proteins were active xylanases with molecular masses corresponding to (I) a single glycoside hydrolase family 11 catalytic module (18 kDa), and (II, III) modular enzymes, with the GH11 catalytic domain connected to a module of unknown function (32 kDa) or putatively connected to a GH7 catalytic module (65 kDa). The N-terminal sequence of the 65 kDa xylanase did not show significant sequence similarities to deposited sequences. The collected data on xylanase activity, molecular mass, GH11-sequence conservation, combined with lack of sequence similarities in the N-terminus show that the 65 kDa band corresponds to a novel modular xylanase.
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Affiliation(s)
- Karen Cabero
- Department of Chemical Engineering, Lund University, SE-221 00 Lund, Sweden
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73
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Medium-throughput profiling method for screening polysaccharide-degrading enzymes in complex bacterial extracts. J Microbiol Methods 2012; 89:222-9. [PMID: 22465222 DOI: 10.1016/j.mimet.2012.03.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Revised: 03/06/2012] [Accepted: 03/06/2012] [Indexed: 01/26/2023]
Abstract
Polysaccharides are the most abundant and the most diverse renewable materials found on earth. Due to the stereochemical variability of carbohydrates, polysaccharide-degrading enzymes - i.e. glycoside hydrolases and polysaccharide lyases - are essential tools for resolving the structure of these complex macromolecules. The exponential increase of genomic and metagenomic data contrasts sharply with the low number of proteins that have ascribed functions. To help fill this gap, we designed and implemented a medium-throughput profiling method to screen for polysaccharide-degrading enzymes in crude bacterial extracts. Our strategy was based on a series of filtrations, which are absolutely necessary to eliminate any reducing sugars not directly generated by enzyme degradation. In contrast with other protocols already available in the literature, our method can be applied to any panel of polysaccharides having known and unknown structures because no chemical modifications are required. We applied this approach to screen for enzymes that occur in Pseudoalteromonas carrageenovora grown in two culture conditions.
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74
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Perla V, Holm DG, Jayanty SS. Effects of cooking methods on polyphenols, pigments and antioxidant activity in potato tubers. Lebensm Wiss Technol 2012. [DOI: 10.1016/j.lwt.2011.08.005] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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75
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Riedlberger P, Weuster-Botz D. New miniature stirred-tank bioreactors for parallel study of enzymatic biomass hydrolysis. BIORESOURCE TECHNOLOGY 2012; 106:138-146. [PMID: 22206921 DOI: 10.1016/j.biortech.2011.12.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2011] [Revised: 12/02/2011] [Accepted: 12/03/2011] [Indexed: 05/31/2023]
Abstract
Many factors strongly influence the enzymatic hydrolysis of biomass to fermentable sugars (feedstock composition, pretreatment, enzymes and enzyme loading). In order to optimize the reaction conditions for the hydrolysis of biomass, an accurate high-throughput bioprocess development tool is mandatory, which enables a parallelization and an easy scale-up. New S-shaped impellers were developed for magnetically inductive driven stirred-tank bioreactors at a 10mL-scale. An efficient and reproducible homogenization was shown at 20% w/w solids loading of microcrystalline cellulose and at, 4-10% with wheat straw in 48 parallel operated stirred-tank bioreactors. The scale-up was successfully validated for the enzymatic hydrolysis of wheat straw suspensions and microcrystalline cellulose mixtures by application of a cellulase complex at a milliliter- and liter-scale. As an example, the parallel stirred-tank bioreactor system was applied for the evaluation of enzymatic batch hydrolyses of plant materials with varying pretreatments.
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Affiliation(s)
- Peter Riedlberger
- Lehrstuhl für Bioverfahrenstechnik, Technische Universität München, Boltzmannstr. 15, 85748 Garching, Germany
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76
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Chancharoonpong C, Hsieh PC, Sheu SC. Effect of Different Combinations of Soybean and Wheat Bran on Enzyme Production from Aspergillus oryzae S. ACTA ACUST UNITED AC 2012. [DOI: 10.1016/j.apcbee.2012.06.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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77
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Wang D, Sun J, Yu HL, Li CX, Bao J, Xu JH. Maximum Saccharification of Cellulose Complex by an Enzyme Cocktail Supplemented with Cellulase from Newly Isolated Aspergillus fumigatus ECU0811. Appl Biochem Biotechnol 2011; 166:176-86. [DOI: 10.1007/s12010-011-9414-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Accepted: 10/18/2011] [Indexed: 11/30/2022]
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78
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Glycoside hydrolase activities of thermophilic bacterial consortia adapted to switchgrass. Appl Environ Microbiol 2011; 77:5804-12. [PMID: 21724886 DOI: 10.1128/aem.00032-11] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Industrial-scale biofuel production requires robust enzymatic cocktails to produce fermentable sugars from lignocellulosic biomass. Thermophilic bacterial consortia are a potential source of cellulases and hemicellulases adapted to harsher reaction conditions than commercial fungal enzymes. Compost-derived microbial consortia were adapted to switchgrass at 60°C to develop thermophilic biomass-degrading consortia for detailed studies. Microbial community analysis using small-subunit rRNA gene amplicon pyrosequencing and short-read metagenomic sequencing demonstrated that thermophilic adaptation to switchgrass resulted in low-diversity bacterial consortia with a high abundance of bacteria related to thermophilic paenibacilli, Rhodothermus marinus, and Thermus thermophilus. At lower abundance, thermophilic Chloroflexi and an uncultivated lineage of the Gemmatimonadetes phylum were observed. Supernatants isolated from these consortia had high levels of xylanase and endoglucanase activities. Compared to commercial enzyme preparations, the endoglucanase enzymes had a higher thermotolerance and were more stable in the presence of 1-ethyl-3-methylimidazolium acetate ([C2mim][OAc]), an ionic liquid used for biomass pretreatment. The supernatants were used to saccharify [C2mim][OAc]-pretreated switchgrass at elevated temperatures (up to 80°C), demonstrating that these consortia are an excellent source of enzymes for the development of enzymatic cocktails tailored to more extreme reaction conditions.
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79
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Gibson DM, King BC, Hayes ML, Bergstrom GC. Plant pathogens as a source of diverse enzymes for lignocellulose digestion. Curr Opin Microbiol 2011; 14:264-70. [DOI: 10.1016/j.mib.2011.04.002] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2011] [Accepted: 04/07/2011] [Indexed: 01/09/2023]
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80
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Mellitzer A, Glieder A, Weis R, Reisinger C, Flicker K. Sensitive high-throughput screening for the detection of reducing sugars. Biotechnol J 2011; 7:155-62. [DOI: 10.1002/biot.201100001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2011] [Revised: 02/04/2011] [Accepted: 02/20/2011] [Indexed: 11/09/2022]
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81
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King BC, Waxman KD, Nenni NV, Walker LP, Bergstrom GC, Gibson DM. Arsenal of plant cell wall degrading enzymes reflects host preference among plant pathogenic fungi. BIOTECHNOLOGY FOR BIOFUELS 2011; 4:4. [PMID: 21324176 PMCID: PMC3051899 DOI: 10.1186/1754-6834-4-4] [Citation(s) in RCA: 139] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2010] [Accepted: 02/16/2011] [Indexed: 05/06/2023]
Abstract
BACKGROUND The discovery and development of novel plant cell wall degrading enzymes is a key step towards more efficient depolymerization of polysaccharides to fermentable sugars for the production of liquid transportation biofuels and other bioproducts. The industrial fungus Trichoderma reesei is known to be highly cellulolytic and is a major industrial microbial source for commercial cellulases, xylanases and other cell wall degrading enzymes. However, enzyme-prospecting research continues to identify opportunities to enhance the activity of T. reesei enzyme preparations by supplementing with enzymatic diversity from other microbes. The goal of this study was to evaluate the enzymatic potential of a broad range of plant pathogenic and non-pathogenic fungi for their ability to degrade plant biomass and isolated polysaccharides. RESULTS Large-scale screening identified a range of hydrolytic activities among 348 unique isolates representing 156 species of plant pathogenic and non-pathogenic fungi. Hierarchical clustering was used to identify groups of species with similar hydrolytic profiles. Among moderately and highly active species, plant pathogenic species were found to be more active than non-pathogens on six of eight substrates tested, with no significant difference seen on the other two substrates. Among the pathogenic fungi, greater hydrolysis was seen when they were tested on biomass and hemicellulose derived from their host plants (commelinoid monocot or dicot). Although T. reesei has a hydrolytic profile that is highly active on cellulose and pretreated biomass, it was less active than some natural isolates of fungi when tested on xylans and untreated biomass. CONCLUSIONS Several highly active isolates of plant pathogenic fungi were identified, particularly when tested on xylans and untreated biomass. There were statistically significant preferences for biomass type reflecting the monocot or dicot host preference of the pathogen tested. These highly active fungi are promising targets for identification and characterization of novel cell wall degrading enzymes for industrial applications.
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Affiliation(s)
- Brian C King
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Plant Science Building, Ithaca, NY 14853, USA
| | - Katrina D Waxman
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Plant Science Building, Ithaca, NY 14853, USA
| | - Nicholas V Nenni
- Department of Biology, SUNY Geneseo, Geneseo, NY 14454, USA
- BioWorks Inc, Victor, NY 14564, USA
| | - Larry P Walker
- Department of Biological and Environmental Engineering, Cornell University, Riley-Robb Hall, Ithaca, NY 14853, USA
| | - Gary C Bergstrom
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Plant Science Building, Ithaca, NY 14853, USA
| | - Donna M Gibson
- USDA Agricultural Research Service, Robert W Holley Center for Agriculture and Health, Ithaca, NY 14853, USA
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82
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Abstract
Switchgrass (Panicum virgatum L.) is a warm-season grass that is native to the prairies of North America that is being developed into a biomass energy crop. It has been used in the Great Plains and Midwest USA as a forage and pasture grass for over 50 years and since the early 1990s research has been conducted on it for bioenergy because of several principal attributes. Switchgrass can be grown on marginal land that is not suitable for intensive cultivation on which it can produce high biomass yields with good management. It is a long lived perennial that has low establishment and production costs and it can harvested and handled with conventional forage equipment. There is substantial potential for genetic improvement of switchgrass for biomass energy production by increasing biomass yield and altering cell wall composition to increase liquid energy yields in biorefineries.
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Affiliation(s)
- Kenneth P. Vogel
- Grain, Forage, and Bioenergy Research Unit, Agricultural Research Service U. S. Department of Agriculture Keim Hall Rm 317 P.O. Box 830937 University of Nebraska Lincoln NE 68583 USA
| | - Gautam Sarath
- Grain, Forage, and Bioenergy Research Unit, Agricultural Research Service U. S. Department of Agriculture Keim Hall Rm 317 P.O. Box 830937 University of Nebraska Lincoln NE 68583 USA
| | - Aaron J. Saathoff
- Grain, Forage, and Bioenergy Research Unit, Agricultural Research Service U. S. Department of Agriculture Keim Hall Rm 317 P.O. Box 830937 University of Nebraska Lincoln NE 68583 USA
| | - Robert B. Mitchell
- Grain, Forage, and Bioenergy Research Unit, Agricultural Research Service U. S. Department of Agriculture Keim Hall Rm 317 P.O. Box 830937 University of Nebraska Lincoln NE 68583 USA
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83
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Cianchetta S, Galletti S, Burzi PL, Cerato C. A novel microplate-based screening strategy to assess the cellulolytic potential of Trichoderma strains. Biotechnol Bioeng 2010; 107:461-8. [PMID: 20517987 DOI: 10.1002/bit.22816] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Bioconversion of lignocellulosic biomass to fuel requires a hydrolysis step to obtain fermentable sugars, generally accomplished by fungal enzymes. An assorted library of cellulolytic microbial strains should facilitate the development of optimal enzyme cocktails specific for locally available feedstocks. Only a limited number of strains can be simultaneously assayed in screening based on large volume cultivation methods, as in shake flasks. This study describes a miniaturization strategy aimed at allowing parallel assessment of large numbers of fungal strains. Trichoderma strains were cultivated stationary on microcrystalline cellulose using flat bottom 24-well plates containing an agarized medium. Supernatants obtained by a rapid centrifugation step of the whole culture plates were evaluated for extracellular total cellulase activity, measured as filter paper activity, using a microplate-based assay. The results obtained were consistent with those observed in shake-flask experiments and more than 300 Trichoderma strains were accordingly characterized for cellulase production. Five strains, displaying on shake-flasks at least 80% of the activity shown by the hyper-cellulolytic mutant Trichoderma Rut-C30, were correctly recognized by the screening on 24-well plates, demonstrating the feasibility of this approach. Cellulase activity distribution for the entire Trichoderma collection is also reported. One strain (T. harzianum Ba8/86) displayed the closest profile to the reference strain Rut-C30 in time course experiments. The method is scalable and addresses a major bottleneck in screening programs, allowing small-scale parallel cultivation and rapid supernatant extraction. It can also be easily integrated with high-throughput enzyme assays and could be suitable for automation.
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Affiliation(s)
- Stefano Cianchetta
- Research Centre for Industrial Crops, Agriculture Research Council, Bologna, Italy.
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84
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Badel S, Laroche C, Gardarin C, Petit E, Bernardi T, Michaud P. A new method to screen polysaccharide cleavage enzymes. Enzyme Microb Technol 2010; 48:248-52. [PMID: 22112907 DOI: 10.1016/j.enzmictec.2010.11.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2010] [Revised: 11/09/2010] [Accepted: 11/11/2010] [Indexed: 11/17/2022]
Abstract
The activity of polysaccharide cleavage enzymes has usually been evaluated by qualitative plate screening methods and quantitative colorimetric or chromatographic assays. The recent development of protein engineering has shown the limits of these techniques when applied to high throughput screening. Here we propose a microplate method to measure the activity of polysaccharide cleavage enzymes through small variations in viscosity. Polysaccharide solutions are co-incubated with magnetic particles in enzyme buffers. The cleavage action of polymer-degrading enzymes increases the mobility of the particles in a magnetic field, even at low levels of enzyme activities. This reproducible, sensitive technique was used to evaluate enzymatic specificity towards substrates. BioFilm indices (BFI) determined by associated software were used to follow enzyme kinetics and measure the usual variables.
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Affiliation(s)
- S Badel
- Clermont Université, Université Blaise Pascal, Laboratoire de Génie Chimique et Biochimique, Polytech' Clermont Ferrand, 24 avenue des Landais BP 206, 63174 Aubière cedex, France
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85
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Dashtban M, Maki M, Leung KT, Mao C, Qin W. Cellulase activities in biomass conversion: measurement methods and comparison. Crit Rev Biotechnol 2010; 30:302-9. [DOI: 10.3109/07388551.2010.490938] [Citation(s) in RCA: 167] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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86
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Chandrasekaran A, Bharadwaj R, Park JI, Sapra R, Adams PD, Singh AK. A Microscale Platform for Integrated Cell-Free Expression and Activity Screening of Cellulases. J Proteome Res 2010; 9:5677-83. [DOI: 10.1021/pr1003938] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Aarthi Chandrasekaran
- Joint BioEnergy Institute, Emeryville, California 94608, Sandia National Laboratories, Livermore, California 94551, and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Rajiv Bharadwaj
- Joint BioEnergy Institute, Emeryville, California 94608, Sandia National Laboratories, Livermore, California 94551, and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Joshua I. Park
- Joint BioEnergy Institute, Emeryville, California 94608, Sandia National Laboratories, Livermore, California 94551, and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Rajat Sapra
- Joint BioEnergy Institute, Emeryville, California 94608, Sandia National Laboratories, Livermore, California 94551, and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Paul D. Adams
- Joint BioEnergy Institute, Emeryville, California 94608, Sandia National Laboratories, Livermore, California 94551, and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Anup K. Singh
- Joint BioEnergy Institute, Emeryville, California 94608, Sandia National Laboratories, Livermore, California 94551, and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
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87
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Navarro D, Couturier M, da Silva GGD, Berrin JG, Rouau X, Asther M, Bignon C. Automated assay for screening the enzymatic release of reducing sugars from micronized biomass. Microb Cell Fact 2010; 9:58. [PMID: 20637080 PMCID: PMC2919459 DOI: 10.1186/1475-2859-9-58] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2010] [Accepted: 07/16/2010] [Indexed: 11/10/2022] Open
Abstract
Background To reduce the production cost of bioethanol obtained from fermentation of the sugars provided by degradation of lignocellulosic biomass (i.e., second generation bioethanol), it is necessary to screen for new enzymes endowed with more efficient biomass degrading properties. This demands the set-up of high-throughput screening methods. Several methods have been devised all using microplates in the industrial SBS format. Although this size reduction and standardization has greatly improved the screening process, the published methods comprise one or more manual steps that seriously decrease throughput. Therefore, we worked to devise a screening method devoid of any manual steps. Results We describe a fully automated assay for measuring the amount of reducing sugars released by biomass-degrading enzymes from wheat-straw and spruce. The method comprises two independent and automated steps. The first step is the making of "substrate plates". It consists of filling 96-well microplates with slurry suspensions of micronized substrate which are then stored frozen until use. The second step is an enzymatic activity assay. After thawing, the substrate plates are supplemented by the robot with cell-wall degrading enzymes where necessary, and the whole process from addition of enzymes to quantification of released sugars is autonomously performed by the robot. We describe how critical parameters (amount of substrate, amount of enzyme, incubation duration and temperature) were selected to fit with our specific use. The ability of this automated small-scale assay to discriminate among different enzymatic activities was validated using a set of commercial enzymes. Conclusions Using an automatic microplate sealer solved three main problems generally encountered during the set-up of methods for measuring the sugar-releasing activity of plant cell wall-degrading enzymes: throughput, automation, and evaporation losses. In its present set-up, the robot can autonomously process 120 triplicate wheat-straw samples per day. This throughput can be doubled if the incubation time is reduced from 24 h to 4 h (for initial rates measurements, for instance). This method can potentially be used with any insoluble substrate that is micronizable. A video illustrating the method can be seen at the following URL: http://www.youtube.com/watch?v=NFg6TxjuMWU
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Affiliation(s)
- David Navarro
- Architecture et Fonction des Macromolécules Biologiques, UMR 6098, CNRS et Université d'Aix-Marseille I et II, 163 Avenue de Luminy CP 925, 13288 Marseille Cedex 09, France
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88
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Current state and perspectives of fungal DNA barcoding and rapid identification procedures. Appl Microbiol Biotechnol 2010; 87:99-108. [PMID: 20405123 DOI: 10.1007/s00253-010-2585-4] [Citation(s) in RCA: 217] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2010] [Revised: 03/24/2010] [Accepted: 03/24/2010] [Indexed: 12/11/2022]
Abstract
Fungal research is experiencing a new wave of methodological improvements that most probably will boost mycology as profoundly as molecular phylogeny has done during the last 15 years. Especially the next generation sequencing technologies can be expected to have a tremendous effect on fungal biodiversity and ecology research. In order to realise the full potential of these exciting techniques by accelerating biodiversity assessments, identification procedures of fungi need to be adapted to the emerging demands of modern large-scale ecological studies. But how should fungal species be identified in the near future? While the answer might seem trivial to most microbiologists, taxonomists working with fungi may have other views. In the present review, we will analyse the state of the art of the so-called barcoding initiatives in the light of fungi, and we will seek to evaluate emerging trends in the field. We will furthermore demonstrate that the usability of DNA barcoding as a major tool for identification of fungi largely depends on the development of high-quality sequence databases that are thoroughly curated by taxonomists and systematists.
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89
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Banerjee G, Car S, Scott-Craig JS, Borrusch MS, Aslam N, Walton JD. Synthetic enzyme mixtures for biomass deconstruction: Production and optimization of a core set. Biotechnol Bioeng 2010; 106:707-20. [DOI: 10.1002/bit.22741] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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90
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Nada A, Mohamed S, Abd El Mongy S, Seoudi R. Preparation, vibrational structure and dielectric properties studies of cotton linter and its derivatives. JOURNAL OF NON-CRYSTALLINE SOLIDS 2009; 355:2544-2549. [DOI: 10.1016/j.jnoncrysol.2009.09.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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