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Joshi NC, Sinha S, Bhatnagar P, Nath Y, Negi B, Kumar V, Gururani P. A concise review on waste biomass valorization through thermochemical conversion. CURRENT RESEARCH IN MICROBIAL SCIENCES 2024; 6:100237. [PMID: 38706494 PMCID: PMC11067365 DOI: 10.1016/j.crmicr.2024.100237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2024] Open
Abstract
Due to an increase in industrialization and urbanization, massive amounts of solid waste biomass are speedily accumulating in our environment, which poses several adverse effects on habitat and human health thus becoming a matter of discussion in the environmental community. With reference to the circular economy, continuous efforts have been put forward for setting up an organised management approach in combination with an efficient treatment technique for increasing the profitable utilization of solid waste. This review aims to provide a systematic discussion on the recent thermochemical technologies employed for converting waste biomass generated from different sources into valuable products like biochar, bio-oil, heat, energy and syngas. The article further focuses on a few important aspects of thermochemical conversion of waste biomass to useful products like technical factors affecting thermochemical processes, applications of by-products of thermochemical conversion, and biological pretreatment of waste biomass. The review assists interesting recent and scientific trends for boosting up the systematic management and valorization of solid waste through low-cost, efficient, environment-friendly and sustainable technologies.
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Affiliation(s)
- Naveen Chandra Joshi
- Division of Research & Innovation, Uttaranchal University, Dehradun, 248007, India
| | - Somya Sinha
- Department of Biotechnology, Graphic Era Deemed to be University, Dehradun, 248002, India
| | - Pooja Bhatnagar
- Algal Research and Bioenergy Laboratory, Department of Food Science & Technology, Graphic Era (Deemed to be University), Dehradun, Uttarakhand, 248002, India
| | - Yogesh Nath
- Department of Biotechnology, Graphic Era Deemed to be University, Dehradun, 248002, India
| | - Bhavya Negi
- Department of Biotechnology, Graphic Era Deemed to be University, Dehradun, 248002, India
| | - Vinod Kumar
- Algal Research and Bioenergy Laboratory, Department of Food Science & Technology, Graphic Era (Deemed to be University), Dehradun, Uttarakhand, 248002, India
| | - Prateek Gururani
- Department of Biotechnology, Graphic Era Deemed to be University, Dehradun, 248002, India
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Influence of Environmental Microbiota on the Activity and Metabolism of Starter Cultures Used in Coffee Beans Fermentation. FERMENTATION 2021. [DOI: 10.3390/fermentation7040278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Microbial activity is an integral part of agricultural ecosystems and can influence the quality of food commodities. During on-farm processing, coffee growers use a traditional method of fermentation to remove the cherry pulp surrounding the beans. Here, we investigated the influence of the coffee farm microbiome and the resulting fermentation process conducted with selected starter cultures (Pichia fermentans YC5.2 and Pediococcus acidilactici LPBC161). The microbiota of the coffee farm (coffee fruits and leaves, over-ripe fruits, cherries before de-pulping, depulped beans, and water used for de-pulping beans) was dominated by Enterobacteriaceae and Saccharomycetales, as determined by llumina-based amplicon sequencing. In addition, 299 prokaryotes and 189 eukaryotes were identified. Following the fermentation process, Pichia and the family Lactobacillaceae (which includes P. acidilactici) represented more than 70% of the total microbial community. The positive interaction between the starters resulted in the formation of primary metabolites (such as ethanol and lactic acid) and important aroma-impacting compounds (ethyl acetate, isoamyl acetate, and ethyl isobutyrate). The success competitiveness of the starters towards the wild microbiota indicated that coffee farm microbiota has little influence on starter culture-added coffee fermentation. However, hygiene requirements in the fermentation process should be indicated to prevent the high microbial loads present in coffee farm soil, leaves, fruits collected on the ground, and over-ripe fruits from having access to the fermentation tank and transferring undesirable aromas to coffee beans.
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Defining the Frontiers of Synergism between Cellulolytic Enzymes for Improved Hydrolysis of Lignocellulosic Feedstocks. Catalysts 2021. [DOI: 10.3390/catal11111343] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Lignocellulose has economic potential as a bio-resource for the production of value-added products (VAPs) and biofuels. The commercialization of biofuels and VAPs requires efficient enzyme cocktail activities that can lower their costs. However, the basis of the synergism between enzymes that compose cellulolytic enzyme cocktails for depolymerizing lignocellulose is not understood. This review aims to address the degree of synergism (DS) thresholds between the cellulolytic enzymes and how this can be used in the formulation of effective cellulolytic enzyme cocktails. DS is a powerful tool that distinguishes between enzymes’ synergism and anti-synergism during the hydrolysis of biomass. It has been established that cellulases, or cellulases and lytic polysaccharide monooxygenases (LPMOs), always synergize during cellulose hydrolysis. However, recent evidence suggests that this is not always the case, as synergism depends on the specific mechanism of action of each enzyme in the combination. Additionally, expansins, nonenzymatic proteins responsible for loosening cell wall fibers, seem to also synergize with cellulases during biomass depolymerization. This review highlighted the following four key factors linked to DS: (1) a DS threshold at which the enzymes synergize and produce a higher product yield than their theoretical sum, (2) a DS threshold at which the enzymes display synergism, but not a higher product yield, (3) a DS threshold at which enzymes do not synergize, and (4) a DS threshold that displays anti-synergy. This review deconvolutes the DS concept for cellulolytic enzymes, to postulate an experimental design approach for achieving higher synergism and cellulose conversion yields.
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Midiri A, Mancuso G, Lentini G, Famà A, Galbo R, Zummo S, Giardina M, De Gaetano GV, Teti G, Beninati C, Biondo C. Characterization of an immunogenic cellulase secreted by Cryptococcus pathogens. Med Mycol 2021; 58:1138-1148. [PMID: 32246714 DOI: 10.1093/mmy/myaa012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 02/20/2020] [Accepted: 02/25/2020] [Indexed: 01/25/2023] Open
Abstract
Members of the C. neoformans/C. gattiii species complex are an important cause of serious humans infections, including meningoencephalitis. We describe here a 45 kDa extracellular cellulase purified from culture supernatants of C. neoformans var. neoformans. The N-terminal sequence obtained from the purified protein was used to isolate a clone containing the full-length coding sequence from a C. neoformans var. neoformans (strain B-3501A) cDNA library. Bioinformatics analysis indicated that this gene is present, with variable homology, in all sequenced genomes of the C. neoformans/C. gattii species complex. The cDNA clone was used to produce a recombinant 45 kDa protein in E. coli that displayed the ability to convert carboxymethyl cellulose and was therefore designated as NG-Case (standing for Neoformans Gattii Cellulase). To explore its potential use as a vaccine candidate, the recombinant protein was used to immunize mice and was found capable of inducing T helper type 1 responses and delayed-type hypersensitivity reactions, but not immune protection against a highly virulent C. neoformans var grubii strain. These data may be useful to better understand the mechanisms underlying the ability C. neoformans/C. gattii to colonize plant habitats and to interact with the human host during infection.
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Affiliation(s)
- Angelina Midiri
- Department of Human Pathology, University of Messina, Messina, Italy
| | - Giuseppe Mancuso
- Department of Human Pathology, University of Messina, Messina, Italy
| | - Germana Lentini
- Department of Human Pathology, University of Messina, Messina, Italy
| | | | - Roberta Galbo
- Department of Chemical, Biological and Pharmaceutical Sciences, University of Messina, Messina, Italy
| | - Sebastiana Zummo
- Department of Human Pathology, University of Messina, Messina, Italy
| | - Miriam Giardina
- Department of Human Pathology, University of Messina, Messina, Italy
| | | | | | - Concetta Beninati
- Department of Human Pathology, University of Messina, Messina, Italy.,Scylla Biotech Srl, Messina, Italy
| | - Carmelo Biondo
- Department of Human Pathology, University of Messina, Messina, Italy
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Hasan N, Rahman L, Kim SH, Cao J, Arjuna A, Lallo S, Jhun BH, Yoo JW. Recent advances of nanocellulose in drug delivery systems. JOURNAL OF PHARMACEUTICAL INVESTIGATION 2020. [DOI: 10.1007/s40005-020-00499-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Tokin R, Ipsen JØ, Westh P, Johansen KS. The synergy between LPMOs and cellulases in enzymatic saccharification of cellulose is both enzyme- and substrate-dependent. Biotechnol Lett 2020; 42:1975-1984. [DOI: 10.1007/s10529-020-02922-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 05/20/2020] [Indexed: 11/28/2022]
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Exploiting strain diversity and rational engineering strategies to enhance recombinant cellulase secretion by Saccharomyces cerevisiae. Appl Microbiol Biotechnol 2020; 104:5163-5184. [PMID: 32337628 DOI: 10.1007/s00253-020-10602-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 03/26/2020] [Accepted: 03/31/2020] [Indexed: 12/14/2022]
Abstract
Consolidated bioprocessing (CBP) of lignocellulosic material into bioethanol has progressed in the past decades; however, several challenges still exist which impede the industrial application of this technology. Identifying the challenges that exist in all unit operations is crucial and needs to be optimised, but only the barriers related to the secretion of recombinant cellulolytic enzymes in Saccharomyces cerevisiae will be addressed in this review. Fundamental principles surrounding CBP as a biomass conversion platform have been established through the successful expression of core cellulolytic enzymes, namely β-glucosidases, endoglucanases, and exoglucanases (cellobiohydrolases) in S. cerevisiae. This review will briefly address the challenges involved in the construction of an efficient cellulolytic yeast, with particular focus on the secretion efficiency of cellulases from this host. Additionally, strategies for studying enhanced cellulolytic enzyme secretion, which include both rational and reverse engineering approaches, will be discussed. One such technique includes bio-engineering within genetically diverse strains, combining the strengths of both natural strain diversity and rational strain development. Furthermore, with the advancement in next-generation sequencing, studies that utilise this method of exploiting intra-strain diversity for industrially relevant traits will be reviewed. Finally, future prospects are discussed for the creation of ideal CBP strains with high enzyme production levels.Key Points• Several challenges are involved in the construction of efficient cellulolytic yeast, in particular, the secretion efficiency of cellulases from the hosts.• Strategies for enhancing cellulolytic enzyme secretion, a core requirement for CBP host microorganism development, include both rational and reverse engineering approaches.• One such technique includes bio-engineering within genetically diverse strains, combining the strengths of both natural strain diversity and rational strain development.
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Bhat A, Khan I, Usmani MA, Umapathi R, Al-Kindy SM. Cellulose an ageless renewable green nanomaterial for medical applications: An overview of ionic liquids in extraction, separation and dissolution of cellulose. Int J Biol Macromol 2019; 129:750-777. [DOI: 10.1016/j.ijbiomac.2018.12.190] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Revised: 12/21/2018] [Accepted: 12/21/2018] [Indexed: 10/27/2022]
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Kucharska K, Rybarczyk P, Hołowacz I, Łukajtis R, Glinka M, Kamiński M. Pretreatment of Lignocellulosic Materials as Substrates for Fermentation Processes. Molecules 2018; 23:E2937. [PMID: 30423814 PMCID: PMC6278514 DOI: 10.3390/molecules23112937] [Citation(s) in RCA: 146] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 11/01/2018] [Accepted: 11/08/2018] [Indexed: 11/17/2022] Open
Abstract
Lignocellulosic biomass is an abundant and renewable resource that potentially contains large amounts of energy. It is an interesting alternative for fossil fuels, allowing the production of biofuels and other organic compounds. In this paper, a review devoted to the processing of lignocellulosic materials as substrates for fermentation processes is presented. The review focuses on physical, chemical, physicochemical, enzymatic, and microbiologic methods of biomass pretreatment. In addition to the evaluation of the mentioned methods, the aim of the paper is to understand the possibilities of the biomass pretreatment and their influence on the efficiency of biofuels and organic compounds production. The effects of different pretreatment methods on the lignocellulosic biomass structure are described along with a discussion of the benefits and drawbacks of each method, including the potential generation of inhibitory compounds for enzymatic hydrolysis, the effect on cellulose digestibility, the generation of compounds that are toxic for the environment, and energy and economic demand. The results of the investigations imply that only the stepwise pretreatment procedure may ensure effective fermentation of the lignocellulosic biomass. Pretreatment step is still a challenge for obtaining cost-effective and competitive technology for large-scale conversion of lignocellulosic biomass into fermentable sugars with low inhibitory concentration.
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Affiliation(s)
- Karolina Kucharska
- Department of Process Engineering and Chemical Technology, Faculty of Chemistry, Gdańsk University of Technology, 80-233 Gdańsk, Poland.
| | - Piotr Rybarczyk
- Department of Process Engineering and Chemical Technology, Faculty of Chemistry, Gdańsk University of Technology, 80-233 Gdańsk, Poland.
| | - Iwona Hołowacz
- Department of Process Engineering and Chemical Technology, Faculty of Chemistry, Gdańsk University of Technology, 80-233 Gdańsk, Poland.
| | - Rafał Łukajtis
- Department of Process Engineering and Chemical Technology, Faculty of Chemistry, Gdańsk University of Technology, 80-233 Gdańsk, Poland.
| | - Marta Glinka
- Department of Process Engineering and Chemical Technology, Faculty of Chemistry, Gdańsk University of Technology, 80-233 Gdańsk, Poland.
- Department of Analytical Chemistry, Faculty of Chemistry, Gdańsk University of Technology, 80-233 Gdańsk, Poland.
| | - Marian Kamiński
- Department of Process Engineering and Chemical Technology, Faculty of Chemistry, Gdańsk University of Technology, 80-233 Gdańsk, Poland.
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Recent Strategies in Preparation of Cellulose Nanocrystals and Cellulose Nanofibrils Derived from Raw Cellulose Materials. INT J POLYM SCI 2018. [DOI: 10.1155/2018/7923068] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The recent strategies in preparation of cellulose nanocrystals (CNCs) and cellulose nanofibrils (CNFs) were described. CNCs and CNFs are two types of nanocelluloses (NCs), and they possess various superior properties, such as large specific surface area, high tensile strength and stiffness, low density, and low thermal expansion coefficient. Due to various applications in biomedical engineering, food, sensor, packaging, and so on, there are many studies conducted on CNCs and CNFs. In this review, various methods of preparation of CNCs and CNFs are summarized, including mechanical, chemical, and biological methods. The methods of pretreatment of cellulose are described in view of the benefits to fibrillation.
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The Role of Yeast-Surface-Display Techniques in Creating Biocatalysts for Consolidated BioProcessing. Catalysts 2018. [DOI: 10.3390/catal8030094] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Climate change is directly linked to the rapid depletion of our non-renewable fossil resources and has posed concerns on sustainability. Thus, imploring the need for us to shift from our fossil based economy to a sustainable bioeconomy centered on biomass utilization. The efficient bioconversion of lignocellulosic biomass (an ideal feedstock) to a platform chemical, such as bioethanol, can be achieved via the consolidated bioprocessing technology, termed yeast surface engineering, to produce yeasts that are capable of this feat. This approach has various strategies that involve the display of enzymes on the surface of yeast to degrade the lignocellulosic biomass, then metabolically convert the degraded sugars directly into ethanol, thus elevating the status of yeast from an immobilization material to a whole-cell biocatalyst. The performance of the engineered strains developed from these strategies are presented, visualized, and compared in this article to highlight the role of this technology in moving forward to our quest against climate change. Furthermore, the qualitative assessment synthesized in this work can serve as a reference material on addressing the areas of improvement of the field and on assessing the capability and potential of the different yeast surface display strategies on the efficient degradation, utilization, and ethanol production from lignocellulosic biomass.
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Chen R, Nie Y, Tanaka N, Niu Q, Li Q, Li YY. Enhanced methanogenic degradation of cellulose-containing sewage via fungi-methanogens syntrophic association in an anaerobic membrane bioreactor. BIORESOURCE TECHNOLOGY 2017; 245:810-818. [PMID: 28926913 DOI: 10.1016/j.biortech.2017.09.046] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 09/04/2017] [Accepted: 09/06/2017] [Indexed: 06/07/2023]
Abstract
An anaerobic membrane bioreactor was configured for methanogenic degradation of cellulose-containing sewage. The degradation performance and microbial changes were evaluated under five hydraulic retention times (HRTs). The results indicated the methane production was largely enhanced with 92.6% efficiency of chemical oxygen demand (COD) converting to methane and 80% proportion of methane in produced biogas, meanwhile the biomass yield presented the fewest at the shortest HRT 8h. Enhanced methane production with decreased biomass yield was attributed to an association between fungi and methanogens. Microbial analysis showed fungi Basidiomycota and methanogen Methanoregula apparently established the association, especially Basidiomycota reaching 93% relative abundance at HRT 8h. Specific methanogenic activity (SMA) and biochemical methane potential (BMP) tests suggested the association was derived from H2 production by fungi and H2 consumption by methanogens, during the process of cellulose degradation. The methanogenic degradation of cellulose-containing sewage was markedly promoted via the fungi-methanogens syntrophic association.
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Affiliation(s)
- Rong Chen
- International S&T Cooperation Center for Urban Alternative Water Resources Development, Key Lab of Environmental Engineering, Shaanxi Province, Xi'an University of Architecture and Technology, No.13 Yanta Road, Xi'an 710055, PR China; Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Yulun Nie
- Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, PR China
| | - Nobuyuki Tanaka
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Qigui Niu
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Qian Li
- International S&T Cooperation Center for Urban Alternative Water Resources Development, Key Lab of Environmental Engineering, Shaanxi Province, Xi'an University of Architecture and Technology, No.13 Yanta Road, Xi'an 710055, PR China
| | - Yu-You Li
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan; Graduate School of Environmental Studies, Tohoku University, 6-6-06 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan.
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Escherichia coli expressing endoglucanase gene from Thai higher termite bacteria for enzymatic and microbial hydrolysis of cellulosic materials. ELECTRON J BIOTECHN 2017. [DOI: 10.1016/j.ejbt.2017.03.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
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Scapin SMN, Souza FHM, Zanphorlin LM, de Almeida TS, Sade YB, Cardoso AM, Pinheiro GL, Murakami MT. Structure and function of a novel GH8 endoglucanase from the bacterial cellulose synthase complex of Raoultella ornithinolytica. PLoS One 2017; 12:e0176550. [PMID: 28448629 PMCID: PMC5407803 DOI: 10.1371/journal.pone.0176550] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 04/12/2017] [Indexed: 02/02/2023] Open
Abstract
Cellulose synthesis in bacteria is a complex process involving the concerted action of several enzymes whose genes are often organized in operons. This process influences many fundamental physiological aspects such as bacteria and host interaction, biofilm formation, among others. Although it might sound contradictory, the participation of cellulose-degrading enzymes is critical to this process. The presence of endoglucanases from family 8 of glycosyl hydrolases (GH8) in bacterial cellulose synthase (Bcs) complex has been described in different bacteria, including the model organism Komagataeibacter xylinus; however, their role in this process is not completely understood. In this study, we describe the biochemical characterization and three-dimensional structure of a novel GH8 member from Raoultella ornithinolytica, named AfmE1, which was previously identified by our group from the metagenomic analysis of the giant snail Achatina fulica. Our results demonstrated that AfmE1 is an endo-β-1,4-glucanase, with maximum activity in acidic to neutral pH over a wide temperature range. This enzyme cleaves cello-oligosaccharides with a degree of polymerization ≥ 5 and presents six glucosyl-binding subsites. The structural comparison of AfmE1 with other GH8 endoglucanases showed significant structural dissimilarities in the catalytic cleft, particularly in the subsite +3, which correlate with different functional mechanisms, such as the recognition of substrate molecules having different arrangements and crystallinities. Together, these findings provide new insights into molecular and structural features of evolutionarily conserved endoglucanases from the bacterial cellulose biosynthetic machinery.
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Affiliation(s)
- Sandra Mara Naressi Scapin
- Division of Metrology Applied to Life Sciences, National Institute of Metrology, Quality and Technology, Duque de Caxias, Rio de Janeiro, Brazil
- * E-mail: (SMNS); (MTM)
| | - Flavio Henrique Moreira Souza
- Brazilian Bioethanol Science and Technology Laboratory, National Center for Research in Energy and Materials, Campinas, São Paulo, Brazil
| | - Leticia Maria Zanphorlin
- Brazilian Bioethanol Science and Technology Laboratory, National Center for Research in Energy and Materials, Campinas, São Paulo, Brazil
| | - Thamyres Silva de Almeida
- Division of Metrology Applied to Life Sciences, National Institute of Metrology, Quality and Technology, Duque de Caxias, Rio de Janeiro, Brazil
| | - Youssef Bacila Sade
- Division of Metrology Applied to Life Sciences, National Institute of Metrology, Quality and Technology, Duque de Caxias, Rio de Janeiro, Brazil
| | - Alexander Machado Cardoso
- Division of Metrology Applied to Life Sciences, National Institute of Metrology, Quality and Technology, Duque de Caxias, Rio de Janeiro, Brazil
| | - Guilherme Luiz Pinheiro
- Division of Metrology Applied to Life Sciences, National Institute of Metrology, Quality and Technology, Duque de Caxias, Rio de Janeiro, Brazil
| | - Mario Tyago Murakami
- Brazilian Bioethanol Science and Technology Laboratory, National Center for Research in Energy and Materials, Campinas, São Paulo, Brazil
- * E-mail: (SMNS); (MTM)
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Ibrahim E, Jones KD, Taylor KE, Hosseney EN, Mills PL, Escudero JM. Molecular and biochemical characterization of recombinant cel12B, cel8C, and peh28 overexpressed in Escherichia coli and their potential in biofuel production. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:52. [PMID: 28413443 PMCID: PMC5327597 DOI: 10.1186/s13068-017-0732-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 02/11/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND The high crystallinity of cellulosic biomass myofibrils as well as the complexity of their intermolecular structure is a significant impediment for biofuel production. Cloning of celB-, celC-encoded cellulases (cel12B and cel8C) and peh-encoded polygalacturonase (peh28) from Pectobacterium carotovorum subsp. carotovorum (Pcc) was carried out in our previous study using Escherichia coli as a host vector. The current study partially characterizes the enzymes' molecular structures as well as their catalytic performance on different substrates which can be used to improve their potential for lignocellulosic biomass conversion. RESULTS β-Jelly roll topology, (α/α)6 antiparallel helices and right-handed β-helices were the folds identified for cel12B, cel8C, and peh28, respectively, in their corresponding protein model structures. Purifications of 17.4-, 6.2-, and 6.0-fold, compared to crude extract, were achieved for cel12B and cel8C, and peh28, respectively, using specific membrane ultrafiltrations and size-exclusion chromatography. Avicel and carboxymethyl cellulose (CMC) were substrates for cel12B, whereas for cel8C catalytic activity was only shown on CMC. The enzymes displayed significant synergy on CMC but not on Avicel when tested for 3 h at 45 °C. No observed β-glucosidase activities were identified for cel8C and cel12B when tested on p-nitrophenyl-β-d-glucopyranoside. Activity stimulation of 130% was observed when a recombinant β-glucosidase from Pcc was added to cel8C and cel12B as tested for 3 h at 45 °C. Optimum temperature and pH of 45 °C and 5.4, respectively, were identified for all three enzymes using various substrates. Catalytic efficiencies (kcat/Km) were calculated for cel12B and cel8C on CMC as 0.141 and 2.45 ml/mg/s respectively, at 45 °C and pH 5.0 and for peh28 on polygalacturonic acid as 4.87 ml/mg/s, at 40 °C and pH 5.0. Glucose and cellobiose were the end-products identified for cel8C, cel12B, and β-glucosidase acting together on Avicel or CMC, while galacturonic acid and other minor co-products were identified for peh28 action on pectin. CONCLUSIONS This study provides some insight into which parameters should be optimized when application of cel8C, cel12B, and peh28 to biomass conversion is the goal.
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Affiliation(s)
- Eman Ibrahim
- Department of Environmental Engineering, Texas A&M University-Kingsville, Kingsville, TX 78363 USA
- Department of Botany and Microbiology, Al-Azhar University, Nasr City, Cairo, 11884 Egypt
| | - Kim D. Jones
- Department of Environmental Engineering, Texas A&M University-Kingsville, Kingsville, TX 78363 USA
| | - Keith E. Taylor
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON N9B 3P4 Canada
| | - Ebtesam N. Hosseney
- Department of Botany and Microbiology, Al-Azhar University, Nasr City, Cairo, 11884 Egypt
| | - Patrick L. Mills
- Department of Chemical Engineering, Texas A&M University-Kingsville, Kingsville, TX 78363 USA
| | - Jean M. Escudero
- Department of Basic Science, St. Louis College of Pharmacy, St. Louis, MO 63110-1088 USA
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Ghribi M, Meddeb-Mouelhi F, Beauregard M. Microbial diversity in various types of paper mill sludge: identification of enzyme activities with potential industrial applications. SPRINGERPLUS 2016; 5:1492. [PMID: 27652065 PMCID: PMC5013001 DOI: 10.1186/s40064-016-3147-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 08/24/2016] [Indexed: 11/11/2022]
Abstract
This study is the first comprehensive investigation of enzyme-producing bacteria isolated from four sludge samples (primary, secondary, press and machine) collected in a Kraft paper mill. Overall, 41 strains encompassing 11 different genera were identified by 16S rRNA gene analysis and biochemical testing. Both biodiversity and enzymatic activities were correlated with sludge composition. Press sludge hosted the largest variety of bacterial strains and enzymatic activities, which included hydrolytic enzymes and ligninolytic enzymes. In contrast, strains isolated from secondary sludge were devoid of several enzymatic activities. Most strains were found to metabolize Kraft liquor at its alkaline pH and to decolorize industrial lignin-mimicking dyes. Resistance to lignin or the ability to metabolize this substrate is a prerequisite to survival in any paper mill sludge type. We demonstrate here that the bacterial strains found in a typical Kraft paper mill represent a source of potential novel enzymes for both industrial applications and bioremediation.
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Affiliation(s)
- Manel Ghribi
- CRML, Centre de Recherche sur les Matériaux Lignocellulosiques, Université du Québec à Trois-Rivières, C.P. 500, Trois-Rivières, QC G9A 5H7 Canada ; PROTEO, Université Laval, Quebec, QC G1V 4G2 Canada
| | - Fatma Meddeb-Mouelhi
- CRML, Centre de Recherche sur les Matériaux Lignocellulosiques, Université du Québec à Trois-Rivières, C.P. 500, Trois-Rivières, QC G9A 5H7 Canada ; PROTEO, Université Laval, Quebec, QC G1V 4G2 Canada
| | - Marc Beauregard
- CRML, Centre de Recherche sur les Matériaux Lignocellulosiques, Université du Québec à Trois-Rivières, C.P. 500, Trois-Rivières, QC G9A 5H7 Canada ; PROTEO, Université Laval, Quebec, QC G1V 4G2 Canada
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Tayi L, Maku R, Patel HK, Sonti RV. Action of Multiple Cell Wall-Degrading Enzymes Is Required for Elicitation of Innate Immune Responses During Xanthomonas oryzae pv. oryzae Infection in Rice. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2016; 29:599-608. [PMID: 27269510 DOI: 10.1094/mpmi-02-16-0039-r] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Xanthomonas oryzae pv. oryzae secretes a number of plant cell wall-degrading enzymes (CWDEs) whose purified preparations induce defense responses in rice. These defense responses are suppressed by X. oryzae pv. oryzae using type 3 secretion system (T3SS) effectors and a type 3 secretion system mutant (T3SS(-)) of X. oryzae pv. oryzae is an inducer of rice defense responses. We assessed the role of individual CWDEs in induction of rice defense responses during infection, by mutating them in the genetic background of a T3SS(-). We mutated the genes for five different plant CWDEs secreted by X. oryzae pv. oryzae, including two cellulases (clsA and cbsA), one xylanase (xyn), one pectinase (pglA), and an esterase (lipA), singly in a T3SS(-) background. We have demonstrated that, as compared with a T3SS(-) of X. oryzae pv. oryzae, a cbsA(-)T3SS(-), a clsA(-)T3SS(-), and a xyn(-)T3SS(-) are deficient in induction of rice immune responses such as callose deposits and programmed cell death. In comparison, a lipA(-) T3SS(-) and a pglA(-)T3SS(-) is as efficient in induction of host defense responses as a T3SS(-). Overall, these results indicate that the collective action of X. oryzae pv. oryzae-secreted ClsA, CbsA, and Xyn proteins is required for induction of rice defense responses during infection.
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Affiliation(s)
- Lavanya Tayi
- 1 CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, Telangana State, India
| | - Roshan Maku
- 1 CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, Telangana State, India
| | - Hitendra Kumar Patel
- 1 CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, Telangana State, India
| | - Ramesh V Sonti
- 1 CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, Telangana State, India
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Periplasmic Cytophaga hutchinsonii Endoglucanases Are Required for Use of Crystalline Cellulose as the Sole Source of Carbon and Energy. Appl Environ Microbiol 2016; 82:4835-4845. [PMID: 27260354 DOI: 10.1128/aem.01298-16] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 05/25/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The soil bacterium Cytophaga hutchinsonii actively digests crystalline cellulose by a poorly understood mechanism. Genome analyses identified nine genes predicted to encode endoglucanases with roles in this process. No predicted cellobiohydrolases, which are usually involved in the utilization of crystalline cellulose, were identified. Chromosomal deletions were performed in eight of the endoglucanase-encoding genes: cel5A, cel5B, cel5C, cel9A, cel9B, cel9C, cel9E, and cel9F Each mutant retained the ability to digest crystalline cellulose, although the deletion of cel9C caused a modest decrease in cellulose utilization. Strains with multiple deletions were constructed to identify the critical cellulases. Cells of a mutant lacking both cel5B and cel9C were completely deficient in growth on cellulose. Cell fractionation and biochemical analyses indicate that Cel5B and Cel9C are periplasmic nonprocessive endoglucanases. The requirement of periplasmic endoglucanases for cellulose utilization suggests that cellodextrins are transported across the outer membrane during this process. Bioinformatic analyses predict that Cel5A, Cel9A, Cel9B, Cel9D, and Cel9E are secreted across the outer membrane by the type IX secretion system, which has been linked to cellulose utilization. These secreted endoglucanases may perform the initial digestion within amorphous regions on the cellulose fibers, releasing oligomers that are transported into the periplasm for further digestion by Cel5B and Cel9C. The results suggest that both cell surface and periplasmic endoglucanases are required for the growth of C. hutchinsonii on cellulose and that novel cell surface proteins may solubilize and transport cellodextrins across the outer membrane. IMPORTANCE The bacterium Cytophaga hutchinsonii digests crystalline cellulose by an unknown mechanism. It lacks processive cellobiohydrolases that are often involved in cellulose digestion. Critical cellulolytic enzymes were identified by genetic analyses. Intracellular (periplasmic) nonprocessive endoglucanases performed an important role in cellulose utilization. The results suggest a model involving partial digestion at the cell surface, solubilization and uptake of cellodextrins across the outer membrane by an unknown mechanism, and further digestion within the periplasm. The ability to sequester cellodextrins and digest them intracellularly may limit losses of soluble cellobiose to other organisms. C. hutchinsonii uses an unusual approach to digest cellulose and is a potential source of novel proteins to increase the efficiency of conversion of cellulose into soluble sugars and biofuels.
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Pedri ZC, Lozano LMS, Hermann KL, Helm CV, Peralta RM, Tavares LBB. Influence of nitrogen sources on the enzymatic activity and grown by Lentinula edodes in biomass Eucalyptus benthamii. BRAZ J BIOL 2015; 75:940-7. [PMID: 26675911 DOI: 10.1590/1519-6984.03214] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 03/27/2014] [Indexed: 11/22/2022] Open
Abstract
Lignocellulose is the most abundant environmental component and a renewable organic resource in soil. There are some filamentous fungi which developed the ability to break down and use cellulose, hemicellulose and lignin as an energy source. The objective of this research was to analyze the effect of three nitrogen resources (ammonium sulfate, saltpetre, soybean) in the holocellulolitic activity of Lentinula edodes EF 50 using as substrate sawdust E. benthamii. An experimental design mixture was applied with repetition in the central point consisting of seven treatments (T) of equal concentrations of nitrogen in ammonium sulfate, potassium nitrate and soybean. The enzymatic activity of avicelase, carboxymetilcellulase, β-glucosidase, xylanases and manganese peroxidase was determined. The humidity, pH, water activity (aw) and qualitative analysis of mycelial growth in 8 times of cultivation were evaluated. The results showed negative effect on enzyme production in treatments with maximum concentration of ammonium sulfate and potassium nitrate. The treatments with cooked soybean flour expressed higher enzymatic activities in times of 3, 6 and 9 days of culture, except in the activity of manganese peroxidase. The highest production was observed in the treatment with ammonium sulfate, and soybean (83.86 UI.L-1) at 20 days of cultivation.
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Affiliation(s)
- Z C Pedri
- Programa de Pós-graduação, Universidade Regional de Blumenau, Blumenau, SC, Brazil
| | - L M S Lozano
- Departamento de Engenharia Química, Universidade Regional de Blumenau, Blumenau, SC, Brazil
| | - K L Hermann
- Programa de Pós-graduação em Engenharia Ambiental, Universidade Regional de Blumenau, Blumenau, SC, Brazil
| | - C V Helm
- Empresa Brasileira de Pesquisa Agropecuária, Colombo, PR, Brazil
| | - R M Peralta
- Universidade Estadual de Maringá, Maringá, PR, Brazil
| | - L B B Tavares
- Universidade Regional de Blumenau, Blumenau, SC, Brazil
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Lakhundi S, Siddiqui R, Khan NA. Cellulose degradation: a therapeutic strategy in the improved treatment of Acanthamoeba infections. Parasit Vectors 2015; 8:23. [PMID: 25586209 PMCID: PMC4300153 DOI: 10.1186/s13071-015-0642-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 01/05/2015] [Indexed: 11/10/2022] Open
Abstract
Acanthamoeba is an opportunistic free-living amoeba that can cause blinding keratitis and fatal brain infection. Early diagnosis, followed by aggressive treatment is a pre-requisite in the successful treatment but even then the prognosis remains poor. A major drawback during the course of treatment is the ability of the amoeba to enclose itself within a shell (a process known as encystment), making it resistant to chemotherapeutic agents. As the cyst wall is partly made of cellulose, thus cellulose degradation offers a potential therapeutic strategy in the effective targeting of trophozoite encased within the cyst walls. Here, we present a comprehensive report on the structure of cellulose and cellulases, as well as known cellulose degradation mechanisms with an eye to target the Acanthamoeba cyst wall. The disruption of the cyst wall will make amoeba (concealed within) susceptible to chemotherapeutic agents, and at the very least inhibition of the excystment process will impede infection recurrence, as we bring these promising drug targets into focus so that they can be explored to their fullest.
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Affiliation(s)
- Sahreena Lakhundi
- Department of Biological and Biomedical Sciences, Aga Khan University, Stadium Road, Karachi, Pakistan.
| | - Ruqaiyyah Siddiqui
- Department of Biological and Biomedical Sciences, Aga Khan University, Stadium Road, Karachi, Pakistan.
| | - Naveed Ahmed Khan
- Department of Biological and Biomedical Sciences, Aga Khan University, Stadium Road, Karachi, Pakistan.
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Abstract
AbstractPolymers have been widely used in agriculture for applications including controlled release of pesticides and other active ingredients. The ability to predict their delivery helps avoid environmental hazards. Macromolecular matrices used as carriers in controlled release of agricultural active agents, especially pesticides, are reviewed. The review focuses on the advantages and mechanisms of controlled release. It includes biodegradable polymers in agriculture, their manufacturing methods, and their degradation mechanisms and kinetics. The article also presents a critical account of recent release studies and considers upcoming challenges.
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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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Zhou XW, Cong WR, Su KQ, Zhang YM. Ligninolytic enzymes fromGanodermaspp: Current status and potential applications. Crit Rev Microbiol 2012; 39:416-26. [DOI: 10.3109/1040841x.2012.722606] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Odeniyi OA, Onilude AA, Ayodele MA. Characteristics of a β-1,4-D endoglucanase from Trichoderma virens wholly applied in a palm-fruit husk-based diet for poultry layers. Braz J Microbiol 2012; 43:1467-75. [PMID: 24031978 PMCID: PMC3769003 DOI: 10.1590/s1517-838220120004000031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2010] [Revised: 01/26/2012] [Accepted: 06/07/2012] [Indexed: 05/27/2023] Open
Abstract
The characteristics of an endoglucanase produced by a Trichoderma virens strain T9 newly isolated from a palm-fruit husk dump site, its physiological characteristics and enzyme production were studied. Whole cells of the depolymerizing-enzyme producing T. virens were applied to palm-fruit husk and bird performance characteristics when employed as poultry diet additive were considered. Endoglucanase activity in submerged fermentation was 1.6 nkat. Optimum activity was recorded at pH 6.0 and 55°C. The enzyme retained 50% residual glucanase activity at 70°C for 10 minutes. 1.0% Tween-80 and SDS yielded endoglucanase activity 2.15 times higher than the control. Activity was boosted by 20mM Ca2+ (115.0%); 10mM K+ (106.5%); and was totally inhibited by 1mM Hg2+. The addition of T. virens-fermented palm-fruit husk with other layer feed components on the bird characteristics showed that change in bird weight between the control and test birds were not significantly different (p>0.05) but differed in terms of daily feed ingested (p<0.05). The feed to weight-gain ratio was best with the unmodified palm-fruit husk based diet (8.59). There was no significant difference in the egg weights from modified palm-fruit husk based diet and control (p>0.05). The shell thickness (0.64mm) and yolk content (23.61%) were highest in the microbially-modified husk diet. The alternative to maize based diets proffered by the application of T. virens-modified palm-fruit husk in poultry nutrition in terms of bird weight and feed to weight-gain ratio affords the poultry farmer an economic advantage and allows for a greater utilization of the maize in human diets.
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Affiliation(s)
- Olubusola A Odeniyi
- Microbial Physiology and Biochemistry Research, Department of Microbiology, University of Ibadan , Ibadan , Nigeria
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Van Dyk JS, Pletschke BI. A review of lignocellulose bioconversion using enzymatic hydrolysis and synergistic cooperation between enzymes--factors affecting enzymes, conversion and synergy. Biotechnol Adv 2012; 30:1458-80. [PMID: 22445788 DOI: 10.1016/j.biotechadv.2012.03.002] [Citation(s) in RCA: 477] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Revised: 02/10/2012] [Accepted: 03/06/2012] [Indexed: 02/04/2023]
Abstract
Lignocellulose is a complex substrate which requires a variety of enzymes, acting in synergy, for its complete hydrolysis. These synergistic interactions between different enzymes have been investigated in order to design optimal combinations and ratios of enzymes for different lignocellulosic substrates that have been subjected to different pretreatments. This review examines the enzymes required to degrade various components of lignocellulose and the impact of pretreatments on the lignocellulose components and the enzymes required for degradation. Many factors affect the enzymes and the optimisation of the hydrolysis process, such as enzyme ratios, substrate loadings, enzyme loadings, inhibitors, adsorption and surfactants. Consideration is also given to the calculation of degrees of synergy and yield. A model is further proposed for the optimisation of enzyme combinations based on a selection of individual or commercial enzyme mixtures. The main area for further study is the effect of and interaction between different hemicellulases on complex substrates.
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Affiliation(s)
- J S Van Dyk
- Department of Biochemistry, Microbiology and Biotechnology, Rhodes University, PO Box 94, Grahamstown, 6140, South Africa
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Warden AC, Little BA, Haritos VS. A cellular automaton model of crystalline cellulose hydrolysis by cellulases. BIOTECHNOLOGY FOR BIOFUELS 2011; 4:39. [PMID: 22005054 PMCID: PMC3214134 DOI: 10.1186/1754-6834-4-39] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Accepted: 10/17/2011] [Indexed: 05/07/2023]
Abstract
BACKGROUND Cellulose from plant biomass is an abundant, renewable material which could be a major feedstock for low emissions transport fuels such as cellulosic ethanol. Cellulase enzymes that break down cellulose into fermentable sugars are composed of different types - cellobiohydrolases I and II, endoglucanase and β-glucosidase - with separate functions. They form a complex interacting network between themselves, soluble hydrolysis product molecules, solution and solid phase substrates and inhibitors. There have been many models proposed for enzymatic saccharification however none have yet employed a cellular automaton approach, which allows important phenomena, such as enzyme crowding on the surface of solid substrates, denaturation and substrate inhibition, to be considered in the model. RESULTS The Cellulase 4D model was developed de novo taking into account the size and composition of the substrate and surface-acting enzymes were ascribed behaviors based on their movements, catalytic activities and rates, affinity for, and potential for crowding of, the cellulose surface, substrates and inhibitors, and denaturation rates. A basic case modeled on literature-derived parameters obtained from Trichoderma reesei cellulases resulted in cellulose hydrolysis curves that closely matched curves obtained from published experimental data. Scenarios were tested in the model, which included variation of enzyme loadings, adsorption strengths of surface acting enzymes and reaction periods, and the effect on saccharide production over time was assessed. The model simulations indicated an optimal enzyme loading of between 0.5 and 2 of the base case concentrations where a balance was obtained between enzyme crowding on the cellulose crystal, and that the affinities of enzymes for the cellulose surface had a large effect on cellulose hydrolysis. In addition, improvements to the cellobiohydrolase I activity period substantially improved overall glucose production. CONCLUSIONS Cellulase 4D simulates the enzymatic hydrolysis of cellulose to glucose by surface and solution phase-acting enzymes and accounts for complex phenomena that have previously not been included in cellulose hydrolysis models. The model is intended as a tool for industry, researchers and educators alike to explore options for enzyme engineering and process development and to test hypotheses regarding cellulase mechanisms.
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Affiliation(s)
- Andrew C Warden
- CSIRO Energy Transformed Flagship and CSIRO Ecosystems Sciences, PO Box 1700, Canberra, Australian Capital Territory 2601, Australia
| | - Bryce A Little
- CSIRO Livestock Industries, FD McMaster Laboratory, Armidale, New South Wales 2350, Australia
- CSIRO Livestock Industries, Queensland Biosciences Precinct, 306 Carmody Road, St Lucia, Queensland 4067, Australia
| | - Victoria S Haritos
- CSIRO Energy Transformed Flagship and CSIRO Ecosystems Sciences, PO Box 1700, Canberra, Australian Capital Territory 2601, Australia
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la Grange DC, den Haan R, van Zyl WH. Engineering cellulolytic ability into bioprocessing organisms. Appl Microbiol Biotechnol 2010; 87:1195-208. [DOI: 10.1007/s00253-010-2660-x] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2010] [Revised: 05/02/2010] [Accepted: 05/02/2010] [Indexed: 10/19/2022]
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Dashtban M, Schraft H, Syed TA, Qin W. Fungal biodegradation and enzymatic modification of lignin. INTERNATIONAL JOURNAL OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2010; 1:36-50. [PMID: 21968746 PMCID: PMC3180040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/25/2010] [Accepted: 05/21/2010] [Indexed: 05/31/2023]
Abstract
Lignin, the most abundant aromatic biopolymer on Earth, is extremely recalcitrant to degradation. By linking to both hemicellulose and cellulose, it creates a barrier to any solutions or enzymes and prevents the penetration of lignocellulolytic enzymes into the interior lignocellulosic structure. Some basidiomycetes white-rot fungi are able to degrade lignin efficiently using a combination of extracellular ligninolytic enzymes, organic acids, mediators and accessory enzymes. This review describes ligninolytic enzyme families produced by these fungi that are involved in wood decay processes, their molecular structures, biochemical properties and the mechanisms of action which render them attractive candidates in biotechnological applications. These enzymes include phenol oxidase (laccase) and heme peroxidases [lignin peroxidase (LiP), manganese peroxidase (MnP) and versatile peroxidase (VP)]. Accessory enzymes such as H(2)O(2)-generating oxidases and degradation mechanisms of plant cell-wall components in a non-enzymatic manner by production of free hydroxyl radicals (·OH) are also discussed.
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Verma D, Kanagaraj A, Jin S, Singh ND, Kolattukudy PE, Daniell H. Chloroplast-derived enzyme cocktails hydrolyse lignocellulosic biomass and release fermentable sugars. PLANT BIOTECHNOLOGY JOURNAL 2010; 8:332-50. [PMID: 20070870 PMCID: PMC2854225 DOI: 10.1111/j.1467-7652.2009.00486.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
It is widely recognized that biofuel production from lignocellulosic materials is limited by inadequate technology to efficiently and economically release fermentable sugars from the complex multi-polymeric raw materials. Therefore, endoglucanases, exoglucanase, pectate lyases, cutinase, swollenin, xylanase, acetyl xylan esterase, beta glucosidase and lipase genes from bacteria or fungi were expressed in Escherichia coli or tobacco chloroplasts. A PCR-based method was used to clone genes without introns from Trichoderma reesei genomic DNA. Homoplasmic transplastomic lines showed normal phenotype and were fertile. Based on observed expression levels, up to 49, 64 and 10, 751 million units of pectate lyases or endoglucanase can be produced annually, per acre of tobacco. Plant production cost of endoglucanase is 3100-fold, and pectate lyase is 1057 or 1480-fold lower than the same recombinant enzymes sold commercially, produced via fermentation. Chloroplast-derived enzymes had higher temperature stability and wider pH optima than enzymes expressed in E. coli. Plant crude-extracts showed higher enzyme activity than E. coli with increasing protein concentration, demonstrating their direct utility without purification. Addition of E. coli extracts to the chloroplast-derived enzymes significantly decreased their activity. Chloroplast-derived crude-extract enzyme cocktails yielded more (up to 3625%) glucose from filter paper, pine wood or citrus peel than commercial cocktails. Furthermore, pectate lyase transplastomic plants showed enhanced resistance to Erwina soft rot. This is the first report of using plant-derived enzyme cocktails for production of fermentable sugars from lignocellulosic biomass. Limitations of higher cost and lower production capacity of fermentation systems are addressed by chloroplast-derived enzyme cocktails.
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Affiliation(s)
- Dheeraj Verma
- Department of Molecular Biology and Microbiology, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Biomolecular Science Building, 4000 Central Florida Blvd, Orlando, FL 32816-2364, USA
| | - Anderson Kanagaraj
- Department of Molecular Biology and Microbiology, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Biomolecular Science Building, 4000 Central Florida Blvd, Orlando, FL 32816-2364, USA
| | - Shuangxia Jin
- Department of Molecular Biology and Microbiology, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Biomolecular Science Building, 4000 Central Florida Blvd, Orlando, FL 32816-2364, USA
| | - Nameirakpam D. Singh
- Department of Molecular Biology and Microbiology, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Biomolecular Science Building, 4000 Central Florida Blvd, Orlando, FL 32816-2364, USA
| | - Pappachan E Kolattukudy
- Department of Molecular Biology and Microbiology, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Biomolecular Science Building, 4000 Central Florida Blvd, Orlando, FL 32816-2364, USA
| | - Henry Daniell
- Department of Molecular Biology and Microbiology, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Biomolecular Science Building, 4000 Central Florida Blvd, Orlando, FL 32816-2364, USA
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Baptista JC, Machado MA, Homem RA, Torres PS, Vojnov AA, do Amaral AM. Mutation in the xpsD gene of Xanthomonas axonopodis pv. citri affects cellulose degradation and virulence. Genet Mol Biol 2010; 33:146-53. [PMID: 21637619 PMCID: PMC3036071 DOI: 10.1590/s1415-47572009005000110] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2008] [Accepted: 07/06/2009] [Indexed: 02/05/2023] Open
Abstract
The Gram-negative bacterium Xanthomonas axonopodis pv. citri, the causal agent of citrus canker, is a major threat to the citrus industry worldwide. Although this is a leaf spot pathogen, it bears genes highly related to degradation of plant cell walls, which are typically found in plant pathogens that cause symptoms of tissue maceration. Little is known on Xac capacity to cause disease and hydrolyze cellulose. We investigated the contribution of various open reading frames on degradation of a cellulose compound by means of a global mutational assay to selectively screen for a defect in carboxymethyl cellulase (CMCase) secretion in X. axonopodis pv. citri. Screening on CMC agar revealed one mutant clone defective in extracellular glycanase activity, out of nearly 3,000 clones. The insertion was located in the xpsD gene, a component of the type II secretion system (T2SS) showing an influence in the ability of Xac to colonize tissues and hydrolyze cellulose. In summary, these data show for the first time, that X. axonopodis pv. citri is capable of hydrolyzing cellulose in a T2SS-dependent process. Furthermore, it was demonstrated that the ability to degrade cellulose contributes to the infection process as a whole.
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Nazir A, Soni R, Saini HS, Kaur A, Chadha BS. Profiling differential expression of cellulases and metabolite footprints in Aspergillus terreus. Appl Biochem Biotechnol 2009; 162:538-47. [PMID: 19779865 DOI: 10.1007/s12010-009-8775-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2009] [Accepted: 09/09/2009] [Indexed: 11/30/2022]
Abstract
This study reports differential expression of endoglucanase (EG) and beta-glucosidase (betaG) isoforms of Aspergillus terreus. Expression of multiple isoforms was observed, in presence of different carbon sources and culture conditions, by activity staining of poly acrylamide gel electrophoresis gels. Maximal expression of four EG isoforms was observed in presence of rice straw (28 U/g DW substrate) and corn cobs (1.147 U/ml) under solid substrate and shake flask culture, respectively. Furthermore, the sequential induction of EG isoforms was found to be associated with the presence of distinct metabolites (monosaccharides/oligosaccharides) i.e., xylose (X), G(1), G(3) and G(4) as well as putative positional isomers (G(1)/G(2), G(2)/G(3)) in the culture extracts sampled at different time intervals, indicating specific role of these metabolites in the sequential expression of multiple EGs. Addition of fructose and cellobiose to corn cobs containing medium during shake flask culture resulted in up-regulation of EG activity, whereas addition of mannitol, ethanol and glycerol selectively repressed the expression of three EG isoforms (Ia, Ic and Id). The observed regulation profile of betaG isoforms was distinct when compared to EG isoforms, and addition of glucose, fructose, sucrose, cellobiose, mannitol and glycerol resulted in down-regulation of one or more of the four betaG isoforms.
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Affiliation(s)
- Asiya Nazir
- Department of Microbiology, Guru Nanak Dev University, Amritsar 143 005, India
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Dashtban M, Schraft H, Qin W. Fungal bioconversion of lignocellulosic residues; opportunities & perspectives. Int J Biol Sci 2009; 5:578-95. [PMID: 19774110 PMCID: PMC2748470 DOI: 10.7150/ijbs.5.578] [Citation(s) in RCA: 324] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2009] [Accepted: 08/02/2009] [Indexed: 11/28/2022] Open
Abstract
The development of alternative energy technology is critically important because of the rising prices of crude oil, security issues regarding the oil supply, and environmental issues such as global warming and air pollution. Bioconversion of biomass has significant advantages over other alternative energy strategies because biomass is the most abundant and also the most renewable biomaterial on our planet. Bioconversion of lignocellulosic residues is initiated primarily by microorganisms such as fungi and bacteria which are capable of degrading lignocellulolytic materials. Fungi such as Trichoderma reesei and Aspergillus niger produce large amounts of extracellular cellulolytic enzymes, whereas bacterial and a few anaerobic fungal strains mostly produce cellulolytic enzymes in a complex called cellulosome, which is associated with the cell wall. In filamentous fungi, cellulolytic enzymes including endoglucanases, cellobiohydrolases (exoglucanases) and beta-glucosidases work efficiently on cellulolytic residues in a synergistic manner. In addition to cellulolytic/hemicellulolytic activities, higher fungi such as basidiomycetes (e.g. Phanerochaete chrysosporium) have unique oxidative systems which together with ligninolytic enzymes are responsible for lignocellulose degradation. This review gives an overview of different fungal lignocellulolytic enzymatic systems including extracellular and cellulosome-associated in aerobic and anaerobic fungi, respectively. In addition, oxidative lignocellulose-degradation mechanisms of higher fungi are discussed. Moreover, this paper reviews the current status of the technology for bioconversion of biomass by fungi, with focus on mutagenesis, co-culturing and heterologous gene expression attempts to improve fungal lignocellulolytic activities to create robust fungal strains.
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Affiliation(s)
- Mehdi Dashtban
- 1. Biorefining Research Initiative, Lakehead University, 955 Oliver Rd, Thunder Bay, Ontario, Canada, P7B 5E1
- 2. Department of Biology, Lakehead University, 955 Oliver Rd, Thunder Bay, Ontario, Canada, P7B 5E1
| | - Heidi Schraft
- 2. Department of Biology, Lakehead University, 955 Oliver Rd, Thunder Bay, Ontario, Canada, P7B 5E1
| | - Wensheng Qin
- 1. Biorefining Research Initiative, Lakehead University, 955 Oliver Rd, Thunder Bay, Ontario, Canada, P7B 5E1
- 2. Department of Biology, Lakehead University, 955 Oliver Rd, Thunder Bay, Ontario, Canada, P7B 5E1
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35
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Abstract
To move our economy onto a sustainable basis, it is essential that we find a replacement for fossil carbon as a source of liquid fuels and chemical industry feedstocks. Lignocellulosic biomass, available in enormous quantities, is the only feasible replacement. Many micro-organisms are capable of rapid and efficient degradation of biomass, employing a battery of specialized enzymes, but do not produce useful products. Attempts to transfer biomass-degrading capability to industrially useful organisms by heterologous expression of one or a few biomass-degrading enzymes have met with limited success. It seems probable that an effective biomass-degradation system requires the synergistic action of a large number of enzymes, the individual and collective actions of which are poorly understood. By offering the ability to combine any number of transgenes in a modular, combinatorial way, synthetic biology offers a new approach to elucidating the synergistic action of combinations of biomass-degrading enzymes in vivo and may ultimately lead to a transferable biomass-degradation system. Also, synthetic biology offers the potential for assembly of novel product-formation pathways, as well as mechanisms for increased solvent tolerance. Thus, synthetic biology may finally lead to cheap and effective processes for conversion of biomass to useful products.
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Peterson JD, Ingram LO. Anaerobic respiration in engineered Escherichia coli with an internal electron acceptor to produce fuel ethanol. Ann N Y Acad Sci 2008; 1125:363-72. [PMID: 18378606 DOI: 10.1196/annals.1419.020] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Environmental concerns and unease with U.S. dependence on foreign oil have renewed interest in converting biomass into fuel ethanol. The volume of plant matter available makes lignocellulose conversion to ethanol desirable, although no one isolated organism has been shown to break bonds in lignocellulose and efficiently metabolize resulting sugars into one product. This work reviews directed engineering coupled with metabolic evolution resulting in microbial biocatalysts that produce up to 45 g L(-1) ethanol in 48 hours in a simple mineral salts medium and that convert various compounds of lignocellulosic materials to ethanol. Mutations contributing to ethanologenesis are discussed along with adding enzymatic capabilities to existing biocatalysts in order to decrease the commercial enzymes required to reduce plant matter into fermentable sugars.
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Selig MJ, Knoshaug EP, Adney WS, Himmel ME, Decker SR. Synergistic enhancement of cellobiohydrolase performance on pretreated corn stover by addition of xylanase and esterase activities. BIORESOURCE TECHNOLOGY 2008; 99:4997-5005. [PMID: 18006303 DOI: 10.1016/j.biortech.2007.09.064] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2007] [Revised: 09/06/2007] [Accepted: 09/06/2007] [Indexed: 05/05/2023]
Abstract
Significant increases in the depolymerization of corn stover cellulose by cellobiohydrolase I (Cel7A) from Trichoderma reesei were observed using small quantities of non-cellulolytic cell wall-degrading enzymes. Purified endoxylanase (XynA), ferulic acid esterase (FaeA), and acetyl xylan esterase (Axe1) all enhanced Cel7A performance on corn stover subjected to hot water pretreatment. In all cases, the addition of these activities improved the effectiveness of the enzymatic hydrolysis in terms of the quantity of cellulose converted per milligram of total protein. Improvement in cellobiose release by the addition of the non-cellulolytic enzymes ranged from a 13-84% increase over Cel7A alone. The most effective combinations included the addition of both XynA and Axe1, which synergistically enhance xylan conversions resulting in additional synergistic improvements in glucan conversion. Additionally, we note a direct relationship between enzymatic xylan removal in the presence of XynA and the enhancement of cellulose hydrolysis by Cel7A.
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Affiliation(s)
- Michael J Selig
- National Renewable Energy Laboratory, Chemical and BioSciences Center, 1617 Cole Boulevard, Golden, CO 80401, United States.
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38
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Kumar R, Singh S, Singh OV. Bioconversion of lignocellulosic biomass: biochemical and molecular perspectives. J Ind Microbiol Biotechnol 2008; 35:377-391. [PMID: 18338189 DOI: 10.1007/s10295-008-0327-8] [Citation(s) in RCA: 821] [Impact Index Per Article: 51.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2007] [Accepted: 01/28/2008] [Indexed: 11/28/2022]
Abstract
In view of rising prices of crude oil due to increasing fuel demands, the need for alternative sources of bioenergy is expected to increase sharply in the coming years. Among potential alternative bioenergy resources, lignocellulosics have been identified as the prime source of biofuels and other value-added products. Lignocelluloses as agricultural, industrial and forest residuals account for the majority of the total biomass present in the world. To initiate the production of industrially important products from cellulosic biomass, bioconversion of the cellulosic components into fermentable sugars is necessary. A variety of microorganisms including bacteria and fungi may have the ability to degrade the cellulosic biomass to glucose monomers. Bacterial cellulases exist as discrete multi-enzyme complexes, called cellulosomes that consist of multiple subunits. Cellulolytic enzyme systems from the filamentous fungi, especially Trichoderma reesei, contain two exoglucanases or cellobiohydrolases (CBH1 and CBH2), at least four endoglucanases (EG1, EG2, EG3, EG5), and one beta-glucosidase. These enzymes act synergistically to catalyse the hydrolysis of cellulose. Different physical parameters such as pH, temperature, adsorption, chemical factors like nitrogen, phosphorus, presence of phenolic compounds and other inhibitors can critically influence the bioconversion of lignocellulose. The production of cellulases by microbial cells is governed by genetic and biochemical controls including induction, catabolite repression, or end product inhibition. Several efforts have been made to increase the production of cellulases through strain improvement by mutagenesis. Various physical and chemical methods have been used to develop bacterial and fungal strains producing higher amounts of cellulase, all with limited success. Cellulosic bioconversion is a complex process and requires the synergistic action of the three enzymatic components consisting of endoglucanases, exoglucanases and beta-glucosidases. The co-cultivation of microbes in fermentation can increase the quantity of the desirable components of the cellulase complex. An understanding of the molecular mechanism leading to biodegradation of lignocelluloses and the development of the bioprocessing potential of cellulolytic microorganisms might effectively be accomplished with recombinant DNA technology. For instance, cloning and sequencing of the various cellulolytic genes could economize the cellulase production process. Apart from that, metabolic engineering and genomics approaches have great potential for enhancing our understanding of the molecular mechanism of bioconversion of lignocelluloses to value added economically significant products in the future.
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Affiliation(s)
- Raj Kumar
- Radiation Biotechnology Unit, Division of Radiation Biology and Radiation Protection, Institute of Nuclear Medicine and Allied Sciences, New Delhi, 110054, India.
| | - Sompal Singh
- Radiation Biotechnology Unit, Division of Radiation Biology and Radiation Protection, Institute of Nuclear Medicine and Allied Sciences, New Delhi, 110054, India
| | - Om V Singh
- Department of Pediatrics, The Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
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39
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Cho KM, Math RK, Hong SY, Asraful Islam SM, Kim JO, Hong SJ, Kim H, Yun HD. Changes in the activity of the multifunctional β-glycosyl hydrolase (Cel44C-Man26A) from Paenibacillus polymyxa by removal of the C-terminal region to minimum size. Biotechnol Lett 2008; 30:1061-8. [DOI: 10.1007/s10529-008-9640-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2007] [Revised: 01/07/2008] [Accepted: 01/07/2008] [Indexed: 11/27/2022]
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40
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Haichar FEZ, Achouak W, Christen R, Heulin T, Marol C, Marais MF, Mougel C, Ranjard L, Balesdent J, Berge O. Identification of cellulolytic bacteria in soil by stable isotope probing. Environ Microbiol 2007; 9:625-34. [PMID: 17298363 DOI: 10.1111/j.1462-2920.2006.01182.x] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Plant residues, mainly made up of cellulose, are the largest fraction of organic carbon material in terrestrial ecosystems. Soil microorganisms are mainly responsible for the transfer of this carbon to the atmosphere, but their contribution is not accurately known. The aim of the present study was to identify bacterial populations that are actively involved in cellulose degradation, using the DNA-stable isotope probing (DNA-SIP) technique. (13)C-cellulose was produced by Acetobacter xylinus and incubated in soil for 7, 14, 30 and 90 days. Total DNA was extracted from the soil, the (13)C-labelled (heavy) and unlabelled (light) DNA fractions were separated by ultracentrifugation, and the structure of active bacterial communities was analysed by bacterial-automated ribosomal intergenic spacer analysis (B-ARISA) and characterized with denaturing gradient gel electrophoresis (DGGE). Cellulose degradation was associated with significant changes in bacterial community structure issued from heavy DNA, leading to the appearance of new bands and increase in relative intensities of other bands until day 30. The majority of bands decreased in relative intensity at day 90. Sequencing and phylogenetic analysis of 10 of these bands in DGGE profiles indicated that most sequences were closely related to sequences from organisms known for their ability to degrade cellulose or to uncultured soil bacteria.
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Affiliation(s)
- Feth El Zahar Haichar
- CEA, DSV, DEVM, Laboratoire d'Ecologie Microbienne de la Rhizosphère et des Environnements extrêmes (LEMiRE), UMR 6191 CNRS, CEA, Aix Marseille-Univ, IFR-E 112, Saint-Paul-Lez-Durance F-13108, France
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41
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Jarboe LR, Grabar TB, Yomano LP, Shanmugan KT, Ingram LO. Development of ethanologenic bacteria. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2007; 108:237-61. [PMID: 17665158 DOI: 10.1007/10_2007_068] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The utilization of lignocellulosic biomass as a petroleum alternative faces many challenges. This work reviews recent progress in the engineering of Escherichia coli and Klebsiella oxytoca to produce ethanol from biomass with minimal nutritional supplementation. A combination of directed engineering and metabolic evolution has resulted in microbial biocatalysts that produce up to 45 g L(-1) ethanol in 48 h in a simple mineral salts medium, and convert various lignocellulosic materials to ethanol. Mutations contributing to ethanologenesis are discussed. The ethanologenic biocatalyst design approach was applied to other commodity chemicals, including optically pure D: (-)- and L: (+)-lactic acid, succinate and L: -alanine with similar success. This review also describes recent progress in growth medium development, the reduction of hemicellulose hydrolysate toxicity and reduction of the demand for fungal cellulases.
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Affiliation(s)
- L R Jarboe
- Department of Microbiology and Cell Science, University of Florida, 32611, Gainesville, FL 32611, USA.
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42
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Liu H, Zhang S, Schell MA, Denny TP. Pyramiding unmarked deletions in Ralstonia solanacearum shows that secreted proteins in addition to plant cell-wall-degrading enzymes contribute to virulence. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2005; 18:1296-305. [PMID: 16478049 DOI: 10.1094/mpmi-18-1296] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Ralstonia solanacearum, like many phytopathogenic bacteria, makes multiple extracellular plant cell-wall-degrading enzymes (CWDE), some of which contribute to its ability to cause wilt disease. CWDE and many other proteins are secreted to the milieu via the highly conserved type II protein secretion system (T2SS). R. solanacearum with a defective T2SS is weakly virulent, but it is not known whether this is due to absence of all the CWDE or the loss of other secreted proteins that contribute to disease. These alternatives were investigated by creating mutants of wild-type strain GMI1000 lacking either the T2SS or up to six CWDE and comparing them for virulence on tomato plants. To create unmarked deletions, genomic regions flanking the target gene were polymerase chain reaction (PCR)-amplified, were fused using splice overlap extension PCR, were cloned into a suicide plasmid harboring the sacB counter-selectable marker, and then, were site-specifically introduced into the genome. Various combinations of five deletions (delta pehA, delta pehB, delta B, PehC, and Pme) was not statistically different from GMI1000, but all the mutants lacking one or both cellulolytic enzymes (Egl or CbhA) wilted plants significantly more slowly than did the wild type. The GMI-6 mutant that lacks all six CWDE was more virulent than the mutant lacking only its two cellulolytic enzymes, and both were significantly more virulent than the T2SS mutant (GMI-D). Very similar results were observed in wounded-petiole inoculation assays, so GMI-6 and GMI-D appear to be less capable of colonizing tomato tissues after invasion. Because the T2SS mutant was much less virulent than the sixfold CWDE mutant, we conclude that other secreted proteins contribute substantially to the ability of R. solanacearum GMI1000 to systemically colonize tomato plants.
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Affiliation(s)
- Huanli Liu
- Department of Plant Pathology, The University of Georgia, Athens, Georgia 30602, USA
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43
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Lim WJ, Hong SY, An CL, Cho KM, Choi BR, Kim YK, An JM, Kang JM, Lee SM, Cho SJ, Kim H, Yun HD. Construction of minimum size cellulase (Cel5Z) from Pectobacterium chrysanthemi PY35 by removal of the C-terminal region. Appl Microbiol Biotechnol 2005; 68:46-52. [PMID: 15666145 DOI: 10.1007/s00253-004-1880-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2004] [Revised: 12/06/2004] [Accepted: 12/13/2004] [Indexed: 10/25/2022]
Abstract
Pectobacterium chrysanthemi PY35 secretes the endoglucanase Cel5Z, an enzyme of the glycoside hydrolase family 5. Cel5Z is a 426 amino acid, signal peptide (SP)-containing protein composed of two domains: a large N-terminal catalytic domain (CD; 291 amino acids) and a small C-terminal cellulose binding domain (CBD; 62 amino acids). These two domains are separated by a 30 amino acid linker region (LR). A truncated cel5Z gene was constructed with the addition of a nonsense mutation that removes the C-terminal region of the protein. A truncated Cel5Z protein, consisting of 280 amino acid residues, functioned as a mature enzyme despite the absence of the SP, 11 amino acid CD, LR, and CBD region. In fact, this truncated Cel5Z protein showed an enzymatic activity 80% higher than that of full-length Cel5Z. However, cellulase activity was undetectable in mature Cel5Z proteins truncated to less than 280 amino acids.
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Affiliation(s)
- Woo Jin Lim
- Division of Applied Life Science, Gyeongsang National University, Chinju, 660-701, Korea
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44
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Lynd LR, Weimer PJ, van Zyl WH, Pretorius IS. Microbial cellulose utilization: fundamentals and biotechnology. Microbiol Mol Biol Rev 2002. [PMID: 12209002 DOI: 10.1128/mmbr.66.3.506] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/24/2023] Open
Abstract
Fundamental features of microbial cellulose utilization are examined at successively higher levels of aggregation encompassing the structure and composition of cellulosic biomass, taxonomic diversity, cellulase enzyme systems, molecular biology of cellulase enzymes, physiology of cellulolytic microorganisms, ecological aspects of cellulase-degrading communities, and rate-limiting factors in nature. The methodological basis for studying microbial cellulose utilization is considered relative to quantification of cells and enzymes in the presence of solid substrates as well as apparatus and analysis for cellulose-grown continuous cultures. Quantitative description of cellulose hydrolysis is addressed with respect to adsorption of cellulase enzymes, rates of enzymatic hydrolysis, bioenergetics of microbial cellulose utilization, kinetics of microbial cellulose utilization, and contrasting features compared to soluble substrate kinetics. A biological perspective on processing cellulosic biomass is presented, including features of pretreated substrates and alternative process configurations. Organism development is considered for "consolidated bioprocessing" (CBP), in which the production of cellulolytic enzymes, hydrolysis of biomass, and fermentation of resulting sugars to desired products occur in one step. Two organism development strategies for CBP are examined: (i) improve product yield and tolerance in microorganisms able to utilize cellulose, or (ii) express a heterologous system for cellulose hydrolysis and utilization in microorganisms that exhibit high product yield and tolerance. A concluding discussion identifies unresolved issues pertaining to microbial cellulose utilization, suggests approaches by which such issues might be resolved, and contrasts a microbially oriented cellulose hydrolysis paradigm to the more conventional enzymatically oriented paradigm in both fundamental and applied contexts.
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Affiliation(s)
- Lee R Lynd
- Chemical and Biochemical Engineering, Thayer School of Engineering and Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755, USA.
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45
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Lynd LR, Weimer PJ, van Zyl WH, Pretorius IS. Microbial cellulose utilization: fundamentals and biotechnology. Microbiol Mol Biol Rev 2002; 66:506-77, table of contents. [PMID: 12209002 PMCID: PMC120791 DOI: 10.1128/mmbr.66.3.506-577.2002] [Citation(s) in RCA: 2319] [Impact Index Per Article: 105.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Fundamental features of microbial cellulose utilization are examined at successively higher levels of aggregation encompassing the structure and composition of cellulosic biomass, taxonomic diversity, cellulase enzyme systems, molecular biology of cellulase enzymes, physiology of cellulolytic microorganisms, ecological aspects of cellulase-degrading communities, and rate-limiting factors in nature. The methodological basis for studying microbial cellulose utilization is considered relative to quantification of cells and enzymes in the presence of solid substrates as well as apparatus and analysis for cellulose-grown continuous cultures. Quantitative description of cellulose hydrolysis is addressed with respect to adsorption of cellulase enzymes, rates of enzymatic hydrolysis, bioenergetics of microbial cellulose utilization, kinetics of microbial cellulose utilization, and contrasting features compared to soluble substrate kinetics. A biological perspective on processing cellulosic biomass is presented, including features of pretreated substrates and alternative process configurations. Organism development is considered for "consolidated bioprocessing" (CBP), in which the production of cellulolytic enzymes, hydrolysis of biomass, and fermentation of resulting sugars to desired products occur in one step. Two organism development strategies for CBP are examined: (i) improve product yield and tolerance in microorganisms able to utilize cellulose, or (ii) express a heterologous system for cellulose hydrolysis and utilization in microorganisms that exhibit high product yield and tolerance. A concluding discussion identifies unresolved issues pertaining to microbial cellulose utilization, suggests approaches by which such issues might be resolved, and contrasts a microbially oriented cellulose hydrolysis paradigm to the more conventional enzymatically oriented paradigm in both fundamental and applied contexts.
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Affiliation(s)
- Lee R Lynd
- Chemical and Biochemical Engineering, Thayer School of Engineering and Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755, USA.
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46
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Park SR, Cho SJ, Kim MK, Ryu SK, Lim WJ, An CL, Hong SY, Kim JH, Kim H, Yun HD. Activity enhancement of Cel5Z from Pectobacterium chrysanthemi PY35 by removing C-terminal region. Biochem Biophys Res Commun 2002; 291:425-30. [PMID: 11846423 DOI: 10.1006/bbrc.2002.6437] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The phytopathogenic bacterium Pectobacteium chrysanthemi PY35 secretes Cel5Z endoglucanase belonging to the glycoside hydrolase family 5 of EC 3.2.1.4. The mutation of cel5Z::Omega gene was constructed by cloning the 2.0-kb SmaI fragment containing the streptomycin/spectinomycin-resistance gene of pHP45(Omega) into the BalI site of pPY100. The insertion of Omega fragment generated a new stop codon, removing the Ser/Thr-rich linker region and the cellulose binding domain (CBD) in the C-terminal region of cel5Z gene. By subsequent subcloning from this 4.9-kb fragment (pPY1001), a 1.0-kb (pPY1002) fragment was obtained and designated as cel5Z::Omega. The cel5Z::Omega gene had an open reading frame (ORF) of 1011 bp, encoding 336 amino acids, starting with an ATG codon and ending with a new TGA stop codon. The molecular mass of the Cel5Z::Omega protein in E. coli transformant appeared to be 32 kDa by SDS-PAGE analysis in the presence of carboxymethyl-cellulose (CMC). The Cel5Z::Omega protein hydrolyzed CMC with 1.7-fold higher activity than the intact Cel5Z cellulase.
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Affiliation(s)
- Sang Ryeol Park
- Research Institute of Life Science, Gyeongsang National University, Chinju 660-701, Korea
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47
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Zhou S, Davis FC, Ingram LO. Gene integration and expression and extracellular secretion of Erwinia chrysanthemi endoglucanase CelY (celY) and CelZ (celZ) in ethanologenic Klebsiella oxytoca P2. Appl Environ Microbiol 2001; 67:6-14. [PMID: 11133422 PMCID: PMC92505 DOI: 10.1128/aem.67.1.6-14.2001] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The development of methods to reduce costs associated with the solubilization of cellulose is essential for the utilization of lignocellulose as a renewable feedstock for fuels and chemicals. One promising approach is the genetic engineering of ethanol-producing microorganisms that also produce cellulase enzymes during fermentation. By starting with an ethanologenic derivative (strain P2) of Klebsiella oxytoca M5A1 with the native ability to metabolize cellobiose, the need for supplemental beta-glucosidase was previously eliminated. In the current study, this approach has been extended by adding genes encoding endoglucanase activities. Genes celY and celZ from Erwinia chrysanthemi have been functionally integrated into the chromosome of P2 using surrogate promoters from Zymomonas mobilis for expression. Both were secreted into the extracellular milieu, producing more than 20,000 endoglucanase units (carboxymethyl cellulase activity) per liter of fermentation broth. During the fermentation of crystalline cellulose with low levels of commercial cellulases of fungal origin, these new strains produced up to 22% more ethanol than unmodified P2. Most of the beneficial contribution was attributed to CelY rather than to CelZ. These results suggest that fungal enzymes with substrate profiles resembling CelY (preference for long-chain polymers and lack of activity on soluble cello-oligosaccharides of two to five glucosyl residues) may be limiting in commercial cellulase preparations.
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Affiliation(s)
- S Zhou
- Institute of Food and Agricultural Sciences, Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611, USA
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