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Lamote B, da Fonseca MJM, Vanderstraeten J, Meert K, Elias M, Briers Y. Current challenges in designer cellulosome engineering. Appl Microbiol Biotechnol 2023; 107:2755-2770. [PMID: 36941434 DOI: 10.1007/s00253-023-12474-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 02/28/2023] [Accepted: 03/03/2023] [Indexed: 03/23/2023]
Abstract
Designer cellulosomes (DCs) are engineered multi-enzyme complexes, comprising carbohydrate-active enzymes attached to a common backbone, the scaffoldin, via high-affinity cohesin-dockerin interactions. The use of DCs in the degradation of renewable biomass polymers is a promising approach for biorefineries. Indeed, DCs have shown significant hydrolytic activities due to the enhanced enzyme-substrate proximity and inter-enzyme synergies, but technical hurdles in DC engineering have hindered further progress towards industrial application. The challenge in DC engineering lies in the large diversity of possible building blocks and architectures, resulting in a multivariate and immense design space. Simultaneously, the precise DC composition affects many relevant parameters such as activity, stability, and manufacturability. Since protein engineers face a lack of high-throughput approaches to explore this vast design space, DC engineering may result in an unsatisfying outcome. This review provides a roadmap to guide researchers through the process of DC engineering. Each step, starting from concept to evaluation, is described and provided with its challenges, along with possible solutions, both for DCs that are assembled in vitro or are displayed on the yeast cell surface. KEY POINTS: • Construction of designer cellulosomes is a multi-step process. • Designer cellulosome research deals with multivariate construction challenges. • Boosting designer cellulosome efficiency requires exploring a vast design space.
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Affiliation(s)
- Babette Lamote
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Ghent, Belgium
- Centre for Synthetic Biology, Department of Biotechnology, Ghent University, Ghent, Belgium
| | | | - Julie Vanderstraeten
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Ghent, Belgium
| | - Kenan Meert
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Ghent, Belgium
- Laboratory of Applied Mycology and Phenomics, Department of Plants and Crops, Ghent University, Ghent, Belgium
| | - Marte Elias
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Ghent, Belgium
- Centre for Synthetic Biology, Department of Biotechnology, Ghent University, Ghent, Belgium
| | - Yves Briers
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Ghent, Belgium.
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2
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Selection of Autochthonous Yeasts Isolated from the Intestinal Tracts of Cobia Fish ( Rachycentron canadum) with Probiotic Potential. J Fungi (Basel) 2023; 9:jof9020274. [PMID: 36836388 PMCID: PMC9966584 DOI: 10.3390/jof9020274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/06/2023] [Accepted: 02/15/2023] [Indexed: 02/22/2023] Open
Abstract
Some yeast strains have been proposed as probiotics to improve the health of cultured fish. Cobia is a tropical benthopelagic fish species with potential for marine aquaculture; however, one of the main limitations to its large-scale production is the high mortality of fish larvae. In this study, we evaluated the probiotic potential of autochthonous yeasts from the intestines of cobia. Thirty-nine yeast isolates were recovered from the intestinal mucosa of 37 adult healthy cobia by culture methods. Yeasts were identified by sequencing of the ITS and D1/D2 regions of the 28S rRNA gene and typed by RAPD-PCR using the M13 primer. Yeast strains with unique RAPD patterns were characterized in terms of their cell biomass production ability; anti-Vibrio, enzymatic, and hemolytic activity; biofilm production; hydrophobicity; autoaggregation; polyamine production; safety; and protection of cobia larvae against saline stress. Candida haemuloni C27 and Debaryomyces hansenii C10 and C28 were selected as potential probiotics. They did not affect the survival of larvae and showed biomass production >1 g L-1, hydrophobicity >41.47%, hemolytic activity γ, and activity in more than 8 hydrolytic enzymes. The results suggest that the selected yeast strains could be considered as potential probiotic candidates and should be evaluated in cobia larvae.
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Tao S, Qingbin M, Zhiling L, Caiyu S, Lixin L, Lilai L. Comparative genomics reveals cellobiose hydrolysis mechanism of Ruminiclostridium thermocellum M3, a cellulosic saccharification bacterium. Front Microbiol 2023; 13:1079279. [PMID: 36687593 PMCID: PMC9852859 DOI: 10.3389/fmicb.2022.1079279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 12/07/2022] [Indexed: 01/08/2023] Open
Abstract
The cellulosome of Ruminiclostridium thermocellum was one of the most efficient cellulase systems in nature. However, the product of cellulose degradation by R. thermocellum is cellobiose, which leads to the feedback inhibition of cellulosome, and it limits the R. thermocellum application in the field of cellulosic biomass consolidated bioprocessing (CBP) industry. In a previous study, R. thermocellum M3, which can hydrolyze cellulosic feedstocks into monosaccharides, was isolated from horse manure. In this study, the complete genome of R. thermocellum M3 was sequenced and assembled. The genome of R. thermocellum M3 was compared with the other R. thermocellum to reveal the mechanism of cellulosic saccharification by R. thermocellum M3. In addition, we predicted the key genes for the elimination of feedback inhibition of cellobiose in R. thermocellum. The results indicated that the whole genome sequence of R. thermocellum M3 consisted of 3.6 Mb of chromosomes with a 38.9% of GC%. To be specific, eight gene islands and 271 carbohydrate-active enzyme-encoded proteins were detected. Moreover, the results of gene function annotation showed that 2,071, 2,120, and 1,246 genes were annotated into the Clusters of Orthologous Groups (COG), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, respectively, and most of the genes were involved in carbohydrate metabolism and enzymatic catalysis. Different from other R. thermocellum, strain M3 has three proteins related to β-glucosidase, and the cellobiose hydrolysis was enhanced by the synergy of gene BglA and BglX. Meanwhile, the GH42 family, CBM36 family, and AA8 family might participate in cellobiose degradation.
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Affiliation(s)
- Sheng Tao
- College of Environmental and Chemical Engineering, Heilongjiang University of Science and Technology, Harbin, China,*Correspondence: Sheng Tao,
| | - Meng Qingbin
- College of Environmental and Chemical Engineering, Heilongjiang University of Science and Technology, Harbin, China
| | - Li Zhiling
- State Key Lab of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, China,Li Zhiling,
| | - Sun Caiyu
- College of Environmental and Chemical Engineering, Heilongjiang University of Science and Technology, Harbin, China
| | - Li Lixin
- College of Environmental and Chemical Engineering, Heilongjiang University of Science and Technology, Harbin, China
| | - Liu Lilai
- College of Environmental and Chemical Engineering, Heilongjiang University of Science and Technology, Harbin, China
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Zhang C, Chen H, Zhu Y, Zhang Y, Li X, Wang F. Saccharomyces cerevisiae cell surface display technology: Strategies for improvement and applications. Front Bioeng Biotechnol 2022; 10:1056804. [PMID: 36568309 PMCID: PMC9767963 DOI: 10.3389/fbioe.2022.1056804] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 11/25/2022] [Indexed: 12/13/2022] Open
Abstract
Microbial cell surface display technology provides a powerful platform for engineering proteins/peptides with enhanced properties. Compared to the classical intracellular and extracellular expression (secretion) systems, this technology avoids enzyme purification, substrate transport processes, and is an effective solution to enzyme instability. Saccharomyces cerevisiae is well suited to cell surface display as a common cell factory for the production of various fuels and chemicals, with the advantages of large cell size, being a Generally Regarded As Safe (GRAS) organism, and post-translational processing of secreted proteins. In this review, we describe various strategies for constructing modified S. cerevisiae using cell surface display technology and outline various applications of this technology in industrial processes, such as biofuels and chemical products, environmental pollution treatment, and immunization processes. The approaches for enhancing the efficiency of cell surface display are also discussed.
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Affiliation(s)
- Chenmeng Zhang
- Jiangsu Co Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, China,Jiangsu Provincial Key Lab for Chemistry and Utilization of Agro Forest Biomass, Jiangsu Key Lab of Biomass Based Green Fuels and Chemicals, Nanjing, China,International Innovation Center for Forest Chemicals and Materials, Nanjing Forestry University, Nanjing, China
| | - Hongyu Chen
- Jiangsu Co Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, China,Jiangsu Provincial Key Lab for Chemistry and Utilization of Agro Forest Biomass, Jiangsu Key Lab of Biomass Based Green Fuels and Chemicals, Nanjing, China,International Innovation Center for Forest Chemicals and Materials, Nanjing Forestry University, Nanjing, China
| | - Yiping Zhu
- Jiangsu Co Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, China,Jiangsu Provincial Key Lab for Chemistry and Utilization of Agro Forest Biomass, Jiangsu Key Lab of Biomass Based Green Fuels and Chemicals, Nanjing, China,International Innovation Center for Forest Chemicals and Materials, Nanjing Forestry University, Nanjing, China
| | - Yu Zhang
- Jiangsu Co Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, China,Jiangsu Provincial Key Lab for Chemistry and Utilization of Agro Forest Biomass, Jiangsu Key Lab of Biomass Based Green Fuels and Chemicals, Nanjing, China,International Innovation Center for Forest Chemicals and Materials, Nanjing Forestry University, Nanjing, China
| | - Xun Li
- Jiangsu Co Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, China,Jiangsu Provincial Key Lab for Chemistry and Utilization of Agro Forest Biomass, Jiangsu Key Lab of Biomass Based Green Fuels and Chemicals, Nanjing, China,International Innovation Center for Forest Chemicals and Materials, Nanjing Forestry University, Nanjing, China
| | - Fei Wang
- Jiangsu Co Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, China,Jiangsu Provincial Key Lab for Chemistry and Utilization of Agro Forest Biomass, Jiangsu Key Lab of Biomass Based Green Fuels and Chemicals, Nanjing, China,International Innovation Center for Forest Chemicals and Materials, Nanjing Forestry University, Nanjing, China,*Correspondence: Fei Wang,
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Hwang DH, Lee ME, Cho BH, Oh JW, You SK, Ko YJ, Hyeon JE, Han SO. Enhanced biodegradation of waste poly(ethylene terephthalate) using a reinforced plastic degrading enzyme complex. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 842:156890. [PMID: 35753492 DOI: 10.1016/j.scitotenv.2022.156890] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 05/28/2022] [Accepted: 06/18/2022] [Indexed: 06/15/2023]
Abstract
Poly(ethylene terephthalate) (PET) is synthesized via a rich ester bond between terephthalate (TPA) and ethylene glycol (EG). Because of this, PET degradation takes a long time and PET accumulates in the environment. Many studies have been conducted to improve PET degrading enzyme to increase the efficiency of PET depolymerization. However, enzymatic PET decomposition is still restricted, making upcycling and recycling difficult. Here, we report a novel PET degrading complex composed of Ideonella sakaiensis PETase and Candida antarctica lipase B (CALB) that improves degradability, binding ability and enzyme stability. The reaction mechanism of chimeric PETase (cPETase) and chimeric CALB (cCALB) was confirmed by PET and bis (2-hydroxyethyl terephthalate) (BHET). cPETase generated BHET and mono (2-hydroxyethyl terephthalate (MHET) and cCALB produced terephthalate (TPA). Carbohydrate binding module 3 (CBM3) in the scaffolding protein greatly improved PET film binding affinity. Finally, the final enzyme complex demonstrated a 6.5-fold and 8.0-fold increase in the efficiency of hydrolysis from PET with either high crystalline or waste to TPA than single enzymes, respectively. This complex could effectively break down waste PET while maintaining enzyme stability and would be applied for biological upcycling of TPA.
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Affiliation(s)
- Dong-Hyeok Hwang
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Myeong-Eun Lee
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Byeong-Hyeon Cho
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Jun Won Oh
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Seung Kyou You
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Young Jin Ko
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Jeong Eun Hyeon
- Department of Food Science and Biotechnology, College of Knowledge-Based Services Engineering, Sungshin Women's University, Seoul 01133, Republic of Korea; Department of Next Generation Applied Sciences, The Graduate School of Sungshin University, Seoul 01133, Republic of Korea
| | - Sung Ok Han
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea.
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Šuchová K, Fehér C, Ravn JL, Bedő S, Biely P, Geijer C. Cellulose- and xylan-degrading yeasts: Enzymes, applications and biotechnological potential. Biotechnol Adv 2022; 59:107981. [DOI: 10.1016/j.biotechadv.2022.107981] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 05/08/2022] [Accepted: 05/10/2022] [Indexed: 01/23/2023]
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7
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Liberato MV, Campos BM, Tomazetto G, Crouch LI, Garcia W, Zeri ACDM, Bolam DN, Squina FM. Unique properties of a Dictyostelium discoideum carbohydrate-binding module expand our understanding of CBM-ligand interactions. J Biol Chem 2022; 298:101891. [PMID: 35378128 PMCID: PMC9079177 DOI: 10.1016/j.jbc.2022.101891] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 03/23/2022] [Accepted: 03/26/2022] [Indexed: 12/04/2022] Open
Abstract
Deciphering how enzymes interact, modify, and recognize carbohydrates has long been a topic of interest in academic, pharmaceutical, and industrial research. Carbohydrate-binding modules (CBMs) are noncatalytic globular protein domains attached to carbohydrate-active enzymes that strengthen enzyme affinity to substrates and increase enzymatic efficiency via targeting and proximity effects. CBMs are considered auspicious for various biotechnological purposes in textile, food, and feed industries, representing valuable tools in basic science research and biomedicine. Here, we present the first crystallographic structure of a CBM8 family member (CBM8), DdCBM8, from the slime mold Dictyostelium discoideum, which was identified attached to an endo-β-1,4-glucanase (glycoside hydrolase family 9). We show that the planar carbohydrate-binding site of DdCBM8, composed of aromatic residues, is similar to type A CBMs that are specific for crystalline (multichain) polysaccharides. Accordingly, pull-down assays indicated that DdCBM8 was able to bind insoluble forms of cellulose. However, affinity gel electrophoresis demonstrated that DdCBM8 also bound to soluble (single chain) polysaccharides, especially glucomannan, similar to type B CBMs, although it had no apparent affinity for oligosaccharides. Therefore, the structural characteristics and broad specificity of DdCBM8 represent exceptions to the canonical CBM classification. In addition, mutational analysis identified specific amino acid residues involved in ligand recognition, which are conserved throughout the CBM8 family. This advancement in the structural and functional characterization of CBMs contributes to our understanding of carbohydrate-active enzymes and protein–carbohydrate interactions, pushing forward protein engineering strategies and enhancing the potential biotechnological applications of glycoside hydrolase accessory modules.
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Affiliation(s)
- Marcelo Vizona Liberato
- Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba (UNISO), Sorocaba, SP, Brazil
| | - Bruna Medeia Campos
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, São Paulo, Brazil
| | - Geizecler Tomazetto
- Department of Biological and Chemical Engineering (BCE), Aarhus University, Aarhus, Denmark
| | - Lucy Isobel Crouch
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Wanius Garcia
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), Santo André, São Paulo, Brazil
| | - Ana Carolina de Mattos Zeri
- Laboratório Nacional de Luz Sincrotron (LNLS), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, São Paulo, Brazil
| | - David Nichol Bolam
- Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle, United Kingdom
| | - Fabio Marcio Squina
- Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba (UNISO), Sorocaba, SP, Brazil.
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8
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Sharma J, Kumar V, Prasad R, Gaur NA. Engineering of Saccharomyces cerevisiae as a consolidated bioprocessing host to produce cellulosic ethanol: Recent advancements and current challenges. Biotechnol Adv 2022; 56:107925. [DOI: 10.1016/j.biotechadv.2022.107925] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 01/24/2022] [Accepted: 02/06/2022] [Indexed: 01/01/2023]
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10
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Lopes AMM, Martins M, Goldbeck R. Heterologous Expression of Lignocellulose-Modifying Enzymes in Microorganisms: Current Status. Mol Biotechnol 2021; 63:184-199. [PMID: 33484441 DOI: 10.1007/s12033-020-00288-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/19/2020] [Indexed: 02/06/2023]
Abstract
Heterologous expression of the carbohydrate-active enzymes in microorganisms is a promising approach to produce bio-based compounds, such as fuels, nutraceuticals and other value-added products from sustainable lignocellulosic sources. Several microorganisms, including Saccharomyces cerevisiae, Escherichia coli, and the filamentous fungi Aspergillus nidulans, have unique characteristics desirable for a biorefinery production approach like well-known genetic tools, thermotolerance, high fermentative capacity and product tolerance, and high amount of recombinant enzyme secretion. These microbial factories are already stablished in the heterologous production of the carbohydrate-active enzymes to produce, among others, ethanol, xylooligosaccharides and the valuable coniferol. A complete biocatalyst able to heterologous express the CAZymes of glycoside hydrolases, carbohydrate esterases and auxiliary activities families could release these compounds faster, with higher yield and specificity. Recent advances in the synthetic biology tools could expand the number and diversity of enzymes integrated in these microorganisms, and also modify those already integrated. This review outlines the heterologous expression of carbohydrate-active enzymes in microorganisms, as well as recent updates in synthetic biology.
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Affiliation(s)
- Alberto Moura Mendes Lopes
- Bioprocess and Metabolic Engineering Laboratory, School of Food Engineering, University of Campinas (UNICAMP), Rua Monteiro Lobato no 80, Cidade Universitária, Campinas, São Paulo, 13083-862, Brazil
| | - Manoela Martins
- Bioprocess and Metabolic Engineering Laboratory, School of Food Engineering, University of Campinas (UNICAMP), Rua Monteiro Lobato no 80, Cidade Universitária, Campinas, São Paulo, 13083-862, Brazil
| | - Rosana Goldbeck
- Bioprocess and Metabolic Engineering Laboratory, School of Food Engineering, University of Campinas (UNICAMP), Rua Monteiro Lobato no 80, Cidade Universitária, Campinas, São Paulo, 13083-862, Brazil.
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Adegboye MF, Ojuederie OB, Talia PM, Babalola OO. Bioprospecting of microbial strains for biofuel production: metabolic engineering, applications, and challenges. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:5. [PMID: 33407786 PMCID: PMC7788794 DOI: 10.1186/s13068-020-01853-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 12/09/2020] [Indexed: 05/17/2023]
Abstract
The issues of global warming, coupled with fossil fuel depletion, have undoubtedly led to renewed interest in other sources of commercial fuels. The search for renewable fuels has motivated research into the biological degradation of lignocellulosic biomass feedstock to produce biofuels such as bioethanol, biodiesel, and biohydrogen. The model strain for biofuel production needs the capability to utilize a high amount of substrate, transportation of sugar through fast and deregulated pathways, ability to tolerate inhibitory compounds and end products, and increased metabolic fluxes to produce an improved fermentation product. Engineering microbes might be a great approach to produce biofuel from lignocellulosic biomass by exploiting metabolic pathways economically. Metabolic engineering is an advanced technology for the construction of highly effective microbial cell factories and a key component for the next-generation bioeconomy. It has been extensively used to redirect the biosynthetic pathway to produce desired products in several native or engineered hosts. A wide range of novel compounds has been manufactured through engineering metabolic pathways or endogenous metabolism optimizations by metabolic engineers. This review is focused on the potential utilization of engineered strains to produce biofuel and gives prospects for improvement in metabolic engineering for new strain development using advanced technologies.
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Affiliation(s)
- Mobolaji Felicia Adegboye
- Food Security and Safety Niche Area, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, Private Bag X2046, 2735, South Africa
| | - Omena Bernard Ojuederie
- Food Security and Safety Niche Area, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, Private Bag X2046, 2735, South Africa
- Department of Biological Sciences, Faculty of Science, Kings University, Ode-Omu, PMB 555, Osun State, Nigeria
| | - Paola M Talia
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA CICVyA, CNIA, INTA Castelar, Dr. N. Repetto y Los Reseros s/n, (1686) Hurlingham, 1686) Hurlingham, Provincia de Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas Y Tecnológicas (CONICET), Buenos Aires, Provincia de Buenos Aires, Argentina
| | - Olubukola Oluranti Babalola
- Food Security and Safety Niche Area, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, Private Bag X2046, 2735, South Africa.
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Ye M, Ye Y, Du Z, Chen G. Cell-surface engineering of yeasts for whole-cell biocatalysts. Bioprocess Biosyst Eng 2021; 44:1003-1019. [PMID: 33389168 DOI: 10.1007/s00449-020-02484-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 11/16/2020] [Indexed: 01/23/2023]
Abstract
Due to the unique advantages comparing with traditional free enzymes and chemical catalysis, whole-cell biocatalysts have been widely used to catalyze reactions effectively, simply and environment friendly. Cell-surface display technology provides a novel and effective approach for improved whole-cell biocatalysts expressing heterologous enzymes on the cell surface. They can overcome the substrate transport limitation of the intracellular expression and provide the enzymes with enhanced properties. Among all the host surface-displaying microorganisms, yeast is ideally suitable for constructing whole cell-surface-displaying biocatalyst, because of the large cell size, the generally regarded as safe (GRAS) status, and the perfect post-translational processing of secreted proteins. Yeast cell-surface display system has been a promising and powerful method for development of novel and improved engineered biocatalysts. In this review, the characterization and principles of yeast cell-surface display and the applications of yeast cell-surface display in engineered whole-cell biocatalysts as well as the improvement of the enzyme efficiency are summarized and discussed.
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Affiliation(s)
- Mengqi Ye
- Marine College, Shandong University, Weihai, 264209, China
| | - Yuqi Ye
- Marine College, Shandong University, Weihai, 264209, China
| | - Zongjun Du
- Marine College, Shandong University, Weihai, 264209, China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Guanjun Chen
- Marine College, Shandong University, Weihai, 264209, China.
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China.
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13
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Mechanism by which β-glucanase improves the quality of fermented barley flour-based food products. Food Chem 2020; 311:126026. [DOI: 10.1016/j.foodchem.2019.126026] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 11/15/2019] [Accepted: 12/04/2019] [Indexed: 11/19/2022]
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14
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Cell surface display of proteins on filamentous fungi. Appl Microbiol Biotechnol 2019; 103:6949-6972. [PMID: 31359105 DOI: 10.1007/s00253-019-10026-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 07/11/2019] [Accepted: 07/15/2019] [Indexed: 12/14/2022]
Abstract
Protein display approaches have been useful to endow the cell surface of yeasts with new catalytic activities so that they can act as enhanced whole-cell biocatalysts. Despite their biotechnological potential, protein display technologies remain poorly developed for filamentous fungi. The lignocellulolytic character of some of them coupled to the cell surface biosynthesis of valuable molecules by a single or a cascade of several displayed enzymes is an appealing prospect. Cell surface protein display consists in the co-translational fusion of a functional protein (passenger) to an anchor one, usually a cell-wall-resident protein. The abundance, spacing, and local environment of the displayed enzymes-determined by the relationship of the anchor protein with the structure and dynamics of the engineered cell wall-are factors that influence the performance of display-based biocatalysts. The development of protein display strategies in filamentous fungi could be based on the field advances in yeasts; however, the unique composition, structure, and biology of filamentous fungi cell walls require the customization of the approach to those microorganisms. In this prospective review, the cellular bases, the design principles, and the available tools to foster the development of cell surface protein display technologies in filamentous fungi are discussed.
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Xin F, Dong W, Zhang W, Ma J, Jiang M. Biobutanol Production from Crystalline Cellulose through Consolidated Bioprocessing. Trends Biotechnol 2019; 37:167-180. [DOI: 10.1016/j.tibtech.2018.08.007] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 08/22/2018] [Accepted: 08/24/2018] [Indexed: 01/08/2023]
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16
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Ben-David Y, Morais S, Stern J, Mizrahi I, Bayer EA. Cell-surface display of designer cellulosomes by Lactobacillus plantarum. Methods Enzymol 2019; 617:241-263. [PMID: 30784404 DOI: 10.1016/bs.mie.2018.12.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Cell-surface display of designer cellulosomes complexes has attracted increased interest in recent years. These engineered microorganisms can efficiently degrade lignocellulosic biomass that represents an abundant resource for conversion into fermentable sugars, suitable for production of biofuels. The designer cellulosome is an artificial enzymatic complex that mimics the architecture of the natural cellulosome and allows the control of the positions, type, and copy number of the cellulosomal enzymes within the complex. Lactobacillus plantarum is an attractive candidate for metabolic engineering of lignocellulosic biomass to biofuels, as its natural characteristics include high ethanol and acid tolerance and the ability to metabolize hexose sugars. In recent years, successful expression of a variety of designer cellulosomes on the cell surface of this bacterium has been demonstrated using the cell-consortium approach. This strategy minimized genomic interference on each strain upon genetic engineering, thereby maximizing the ability of each strain to grow, express, and secrete each enzyme. In addition, this strategy allows stoichiometric control of the cellulosome elements and facile exchange of the secreted proteins. A detailed procedure for display of designer cellulosomes on the cell surface of L. plantarum is described in this chapter.
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Affiliation(s)
- Yonit Ben-David
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Sarah Morais
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel; Faculty of Natural Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Johanna Stern
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Itzhak Mizrahi
- Faculty of Natural Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Edward A Bayer
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel.
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Tang H, Wang J, Wang S, Shen Y, Petranovic D, Hou J, Bao X. Efficient yeast surface-display of novel complex synthetic cellulosomes. Microb Cell Fact 2018; 17:122. [PMID: 30086751 PMCID: PMC6081942 DOI: 10.1186/s12934-018-0971-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 08/01/2018] [Indexed: 11/12/2022] Open
Abstract
Background The self-assembly of cellulosomes on the surface of yeast is a promising strategy for consolidated bioprocessing to convert cellulose into ethanol in one step. Results In this study, we developed a novel synthetic cellulosome that anchors to the endogenous yeast cell wall protein a-agglutinin through disulfide bonds. A synthetic scaffoldin ScafAGA3 was constructed using the repeated N-terminus of Aga1p and displayed on the yeast cell surface. Secreted cellulases were then fused with Aga2p to assemble the cellulosome. The display efficiency of the synthetic scaffoldin and the assembly efficiency of each enzyme were much higher than those of the most frequently constructed cellulosome using scaffoldin ScafCipA3 from Clostridium thermocellum. A complex cellulosome with two scaffoldins was also constructed using interactions between the displayed anchoring scaffoldin ScafAGA3 and scaffoldin I ScafCipA3 through disulfide bonds, and the assembly of secreted cellulases to ScafCipA3. The newly designed cellulosomes enabled yeast to directly ferment cellulose into ethanol. Conclusions This is the first report on the development of complex multiple-component assembly system through disulfide bonds. This strategy could facilitate the construction of yeast cell factories to express synergistic enzymes for use in biotechnology. Electronic supplementary material The online version of this article (10.1186/s12934-018-0971-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hongting Tang
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Jimo, Qingdao, 266237, People's Republic of China
| | - Jiajing Wang
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Jimo, Qingdao, 266237, People's Republic of China
| | - Shenghuan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Jimo, Qingdao, 266237, People's Republic of China
| | - Yu Shen
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Jimo, Qingdao, 266237, People's Republic of China
| | - Dina Petranovic
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivagen 10, 41296, Gothenburg, Sweden
| | - Jin Hou
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Jimo, Qingdao, 266237, People's Republic of China.
| | - Xiaoming Bao
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Jimo, Qingdao, 266237, People's Republic of China. .,Shandong Provincial Key Laboratory of Microbial Engineering, Qi Lu University of Technology, Jinan, 250353, People's Republic of China.
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18
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Tabañag IDF, Chu IM, Wei YH, Tsai SL. Ethanol production from hemicellulose by a consortium of different genetically-modified sacharomyces cerevisiae. J Taiwan Inst Chem Eng 2018. [DOI: 10.1016/j.jtice.2018.04.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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19
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Chang JJ, Anandharaj M, Ho CY, Tsuge K, Tsai TY, Ke HM, Lin YJ, Ha Tran MD, Li WH, Huang CC. Biomimetic strategy for constructing Clostridium thermocellum cellulosomal operons in Bacillus subtilis. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:157. [PMID: 29930703 PMCID: PMC5991470 DOI: 10.1186/s13068-018-1151-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 05/23/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Enzymatic conversion of lignocellulosic biomass into soluble sugars is a major bottleneck in the plant biomass utilization. Several anaerobic organisms cope these issues via multiple-enzyme complex system so called 'cellulosome'. Hence, we proposed a "biomimic operon" concept for making an artificial cellulosome which can be used as a promising tool for the expression of cellulosomal enzymes in Bacillus subtilis. RESULTS According to the proteomic analysis of Clostridium thermocellum ATCC27405 induced by Avicel or cellobiose, we selected eight highly expressed cellulosomal genes including a scaffoldin protein gene (cipA), a cell-surface anchor gene (sdbA), two exoglucanase genes (celK and celS), two endoglucanase genes (celA and celR), and two xylanase genes (xynC and xynZ). Arranging these eight genes in two different orders, we constructed two different polycistronic operons using the ordered gene assembly in Bacillus method. This is the first study to express the whole CipA along with cellulolytic enzymes in B. subtilis. Each operon was successfully expressed in B. subtilis RM125, and the protein complex assembly, cellulose-binding ability, thermostability, and cellulolytic activity were demonstrated. The operon with a higher xylanase activity showed greater saccharification on complex cellulosic substrates such as Napier grass than the other operon. CONCLUSIONS In this study, a strategy for constructing an efficient cellulosome system was developed and two different artificial cellulosomal operons were constructed. Both operons could efficiently express the cellulosomal enzymes and exhibited cellulose saccharification. This strategy can be applied to different industries with cellulose-containing materials, such as papermaking, biofuel, agricultural compost, mushroom cultivation, and waste processing industries.
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Affiliation(s)
- Jui-Jen Chang
- Department of Medical Research, China Medical University Hospital, China Medical University, Taichung, 402 Taiwan
| | - Marimuthu Anandharaj
- Biodiversity Research Center, Academia Sinica, Taipei, 11529 Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, Taipei, 11529 Taiwan
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, 40227 Taiwan
| | - Cheng-Yu Ho
- Department of Life Sciences, National Chung Hsing University, Taichung, 40227 Taiwan
| | - Kenji Tsuge
- Institute for Advanced Biosciences, Keio University, 403-1 Nipponkoku, Daihoji, Tsuruoka, Yamagata 997-0017 Japan
| | - Tsung-Yu Tsai
- Biodiversity Research Center, Academia Sinica, Taipei, 11529 Taiwan
| | - Huei-Mien Ke
- Biodiversity Research Center, Academia Sinica, Taipei, 11529 Taiwan
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, 40227 Taiwan
| | - Yu-Ju Lin
- Biodiversity Research Center, Academia Sinica, Taipei, 11529 Taiwan
| | - Minh Dung Ha Tran
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, Taipei, 11529 Taiwan
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, 40227 Taiwan
- Department of Life Sciences, National Chung Hsing University, Taichung, 40227 Taiwan
| | - Wen-Hsiung Li
- Biodiversity Research Center, Academia Sinica, Taipei, 11529 Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, Taipei, 11529 Taiwan
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, 40227 Taiwan
- Biotechnology Center, National Chung Hsing University, Taichung, 40227 Taiwan
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637 USA
| | - Chieh-Chen Huang
- Department of Life Sciences, National Chung Hsing University, Taichung, 40227 Taiwan
- Innovation and Development Center of Sustainable Agriculture, National Chung Hsing University, Taichung, 40227 Taiwan
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20
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Liu H, Sun J, Chang JS, Shukla P. Engineering microbes for direct fermentation of cellulose to bioethanol. Crit Rev Biotechnol 2018; 38:1089-1105. [DOI: 10.1080/07388551.2018.1452891] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Hao Liu
- State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou, China
| | - Jianliang Sun
- State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou, China
| | - Jo-Shu Chang
- Department of Chemical Engineering, National Cheng Kung University, Tainan, Taiwan, China
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
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21
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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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22
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Scholz SA, Graves I, Minty JJ, Lin XN. Production of cellulosic organic acids via synthetic fungal consortia. Biotechnol Bioeng 2017; 115:1096-1100. [PMID: 29205274 DOI: 10.1002/bit.26509] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 11/16/2017] [Accepted: 11/27/2017] [Indexed: 11/10/2022]
Abstract
Consolidated bioprocessing (CBP) is a potential breakthrough technology for reducing costs of biochemical production from lignocellulosic biomass. Production of cellulase enzymes, saccharification of lignocellulose, and conversion of the resulting sugars into a chemical of interest occur simultaneously within a single bioreactor. In this study, synthetic fungal consortia composed of the cellulolytic fungus Trichoderma reesei and the production specialist Rhizopus delemar demonstrated conversion of microcrystalline cellulose (MCC) and alkaline pre-treated corn stover (CS) to fumaric acid in a fully consolidated manner without addition of cellulase enzymes or expensive supplements such as yeast extract. A titer of 6.87 g/L of fumaric acid, representing 0.17 w/w yield, were produced from 40 g/L MCC with a productivity of 31.8 mg/L/hr. In addition, lactic acid was produced from MCC using a fungal consortium with Rhizopus oryzae as the production specialist. These results are proof-of-concept demonstration of engineering synthetic microbial consortia for CBP production of naturally occurring biomolecules.
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Affiliation(s)
- Scott A Scholz
- Graduate Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, Michigan
| | - Ian Graves
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan
| | - Jeremy J Minty
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan
| | - Xiaoxia N Lin
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan.,Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan
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23
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Selwal KK, Li YF, Yu Z. Functional display of amylase on yeast surface from Rhizopus oryzae as a novel enzyme delivery method. FOOD BIOTECHNOL 2017. [DOI: 10.1080/08905436.2017.1369098] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Krishan K. Selwal
- Department of Biotechnology, DCR University of Science & Technology, Murthal (Sonepat), Haryana, India
- Department of Animal Sciences, The Ohio State University, Columbus, Ohio, USA
| | - Yueh-Fen Li
- Department of Animal Sciences, The Ohio State University, Columbus, Ohio, USA
| | - Zhongtang Yu
- Department of Animal Sciences, The Ohio State University, Columbus, Ohio, USA
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24
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Dvořák P, Nikel PI, Damborský J, de Lorenzo V. Bioremediation 3 . 0 : Engineering pollutant-removing bacteria in the times of systemic biology. Biotechnol Adv 2017; 35:845-866. [DOI: 10.1016/j.biotechadv.2017.08.001] [Citation(s) in RCA: 126] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Revised: 08/01/2017] [Accepted: 08/04/2017] [Indexed: 01/07/2023]
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25
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Hu BB, Zhu MJ. Enhanced hydrogen production and biological saccharification from spent mushroom compost by Clostridium thermocellum 27405 supplemented with recombinant β-glucosidases. INTERNATIONAL JOURNAL OF HYDROGEN ENERGY 2017; 42:7866-7874. [DOI: 10.1016/j.ijhydene.2017.01.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
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26
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Ábrego U, Chen Z, Wan C. Consolidated Bioprocessing Systems for Cellulosic Biofuel Production. ADVANCES IN BIOENERGY 2017. [DOI: 10.1016/bs.aibe.2017.01.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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27
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Inokuma K, Bamba T, Ishii J, Ito Y, Hasunuma T, Kondo A. Enhanced cell-surface display and secretory production of cellulolytic enzymes withSaccharomyces cerevisiaeSed1 signal peptide. Biotechnol Bioeng 2016; 113:2358-66. [DOI: 10.1002/bit.26008] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2015] [Revised: 05/11/2016] [Accepted: 05/12/2016] [Indexed: 12/17/2022]
Affiliation(s)
- Kentaro Inokuma
- Organization of Advanced Science and Technology; Kobe University; Kobe Japan
| | - Takahiro Bamba
- Department of Chemical Science and Engineering; Graduate School of Engineering; Kobe University; 1-1 Rokkodai, Nada Kobe 657-8501 Japan
| | - Jun Ishii
- Organization of Advanced Science and Technology; Kobe University; Kobe Japan
| | - Yoichiro Ito
- Department of Chemical Science and Engineering; Graduate School of Engineering; Kobe University; 1-1 Rokkodai, Nada Kobe 657-8501 Japan
| | - Tomohisa Hasunuma
- Organization of Advanced Science and Technology; Kobe University; Kobe Japan
| | - Akihiko Kondo
- Department of Chemical Science and Engineering; Graduate School of Engineering; Kobe University; 1-1 Rokkodai, Nada Kobe 657-8501 Japan
- Biomass Engineering Program; RIKEN; 1-7-22 Suehiro-cho Tsurumi-ku, Yokohama Kanagawa 230-0045 Japan
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28
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Singh G, Verma AK, Kumar V. Catalytic properties, functional attributes and industrial applications of β-glucosidases. 3 Biotech 2016; 6:3. [PMID: 28330074 PMCID: PMC4697909 DOI: 10.1007/s13205-015-0328-z] [Citation(s) in RCA: 124] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 06/19/2015] [Indexed: 12/18/2022] Open
Abstract
β-Glucosidases are diverse group of enzymes with great functional importance to biological systems. These are grouped in multiple glycoside hydrolase families based on their catalytic and sequence characteristics. Most studies carried out on β-glucosidases are focused on their industrial applications rather than their endogenous function in the target organisms. β-Glucosidases performed many functions in bacteria as they are components of large complexes called cellulosomes and are responsible for the hydrolysis of short chain oligosaccharides and cellobiose. In plants, β-glucosidases are involved in processes like formation of required intermediates for cell wall lignification, degradation of endosperm’s cell wall during germination and in plant defense against biotic stresses. Mammalian β-glucosidases are thought to play roles in metabolism of glycolipids and dietary glucosides, and signaling functions. These enzymes have diverse biotechnological applications in food, surfactant, biofuel, and agricultural industries. The search for novel and improved β-glucosidase is still continued to fulfills demand of an industrially suitable enzyme. In this review, a comprehensive overview on detailed functional roles of β-glucosidases in different organisms, their industrial applications, and recent cloning and expression studies with biochemical characterization of such enzymes is presented for the better understanding and efficient use of diverse β-glucosidases.
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Affiliation(s)
- Gopal Singh
- Institute of Himalayan Bioresource Technology, Palampur, 176062, India
| | - A K Verma
- Department of Biochemistry, College of Basic Sciences and Humanities, G. B. Pant University of Agriculture and Technology, Pantnagar, 263145, India
| | - Vinod Kumar
- Department of Biotechnology, Akal College of Agriculture, Eternal University, Baru Sahib, Sirmour, 173101, India.
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29
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Kim S, Bae SJ, Hahn JS. Redirection of pyruvate flux toward desired metabolic pathways through substrate channeling between pyruvate kinase and pyruvate-converting enzymes in Saccharomyces cerevisiae. Sci Rep 2016; 6:24145. [PMID: 27052099 PMCID: PMC4823786 DOI: 10.1038/srep24145] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 03/21/2016] [Indexed: 11/08/2022] Open
Abstract
Spatial organization of metabolic enzymes allows substrate channeling, which accelerates processing of intermediates. Here, we investigated the effect of substrate channeling on the flux partitioning at a metabolic branch point, focusing on pyruvate metabolism in Saccharomyces cerevisiae. As a platform strain for the channeling of pyruvate flux, PYK1-Coh-Myc strain was constructed in which PYK1 gene encoding pyruvate kinase is tagged with cohesin domain. By using high-affinity cohesin-dockerin interaction, the pyruvate-forming enzyme Pyk1 was tethered to heterologous pyruvate-converting enzymes, lactate dehydrogenase and α-acetolactate synthase, to produce lactic acid and 2,3-butanediol, respectively. Pyruvate flux was successfully redirected toward desired pathways, with a concomitant decrease in ethanol production even without genetic attenuation of the ethanol-producing pathway. This pyruvate channeling strategy led to an improvement of 2,3-butanediol production by 38%, while showing a limitation in improving lactic acid production due to a reduced activity of lactate dehydrogenase by dockerin tagging.
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Affiliation(s)
- Sujin Kim
- School of Chemical and Biological Engineering, Seoul National University, Institute of Chemical Processes, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Sang-Jeong Bae
- School of Chemical and Biological Engineering, Seoul National University, Institute of Chemical Processes, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Ji-Sook Hahn
- School of Chemical and Biological Engineering, Seoul National University, Institute of Chemical Processes, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
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30
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Fan LH, Zhang ZJ, Mei S, Lu YY, Li M, Wang ZY, Yang JG, Yang ST, Tan TW. Engineering yeast with bifunctional minicellulosome and cellodextrin pathway for co-utilization of cellulose-mixed sugars. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:137. [PMID: 27382414 PMCID: PMC4932713 DOI: 10.1186/s13068-016-0554-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 06/23/2016] [Indexed: 05/13/2023]
Abstract
BACKGROUND Consolidated bioprocessing (CBP), integrating cellulase production, cellulose saccharification, and fermentation into one step has been widely considered as the ultimate low-cost configuration for producing second-generation fuel ethanol. However, the requirement of a microbial strain able to hydrolyze cellulosic biomass and convert the resulting sugars into high-titer ethanol limits CBP application. RESULTS In this work, cellulolytic yeasts were developed by engineering Saccharomyces cerevisiae with a heterologous cellodextrin utilization pathway and bifunctional minicellulosomes. The cell-displayed minicellulosome was two-scaffoldin derived, and contained an endoglucanase and an exoglucanase, while the intracellular cellodextrin pathway consisted of a cellodextrin transporter and a β-glucosidase, which mimicked the unique cellulose-utilization system in Clostridium thermocellum and allowed S. cerevisiae to degrade and use cellulose without glucose inhibition/repression on cellulases and mixed-sugar uptake. Consequently, only a small inoculation of the non-induced yeast cells was required to efficiently co-convert both cellulose and galactose to ethanol in a single-step co-fermentation process, achieving a high specific productivity of ~62.61 mg cellulosic ethanol/g cell·h from carboxymethyl cellulose and ~56.37 mg cellulosic ethanol/g cell·h from phosphoric acid-swollen cellulose. CONCLUSIONS Our work provides a versatile engineering strategy for co-conversion of cellulose-mixed sugars to ethanol by S. cerevisiae, and the achievements in this work may further promote cellulosic biofuel production.
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Affiliation(s)
- Li-Hai Fan
- />College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, People’s Republic of China
- />Beijing Key Laboratory of Bioprocess, Beijing, People’s Republic of China
| | - Zi-Jian Zhang
- />College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, People’s Republic of China
- />Beijing Key Laboratory of Bioprocess, Beijing, People’s Republic of China
| | - Sen Mei
- />College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, People’s Republic of China
- />Beijing Key Laboratory of Bioprocess, Beijing, People’s Republic of China
| | - Yang-Yang Lu
- />College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, People’s Republic of China
- />Beijing Key Laboratory of Bioprocess, Beijing, People’s Republic of China
| | - Mei Li
- />College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, People’s Republic of China
- />Beijing Key Laboratory of Bioprocess, Beijing, People’s Republic of China
| | - Zai-Yu Wang
- />College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, People’s Republic of China
- />Beijing Key Laboratory of Bioprocess, Beijing, People’s Republic of China
| | - Jian-Guo Yang
- />College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, People’s Republic of China
- />Beijing Key Laboratory of Bioprocess, Beijing, People’s Republic of China
| | - Shang-Tian Yang
- />Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH USA
| | - Tian-Wei Tan
- />College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, People’s Republic of China
- />Beijing Key Laboratory of Bioprocess, Beijing, People’s Republic of China
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31
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Better together: engineering and application of microbial symbioses. Curr Opin Biotechnol 2015; 36:40-9. [DOI: 10.1016/j.copbio.2015.08.008] [Citation(s) in RCA: 187] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 07/28/2015] [Accepted: 08/09/2015] [Indexed: 12/26/2022]
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32
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Yeast with surface displayed xylanase as a new dual purpose delivery vehicle of xylanase and yeast. Anim Feed Sci Technol 2015. [DOI: 10.1016/j.anifeedsci.2015.07.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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33
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Arora R, Behera S, Sharma NK, Kumar S. Bioprospecting thermostable cellulosomes for efficient biofuel production from lignocellulosic biomass. BIORESOUR BIOPROCESS 2015. [DOI: 10.1186/s40643-015-0066-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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34
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Kavšček M, Stražar M, Curk T, Natter K, Petrovič U. Yeast as a cell factory: current state and perspectives. Microb Cell Fact 2015; 14:94. [PMID: 26122609 PMCID: PMC4486425 DOI: 10.1186/s12934-015-0281-x] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 06/11/2015] [Indexed: 02/06/2023] Open
Abstract
The yeast Saccharomyces cerevisiae is one of the oldest and most frequently used microorganisms in biotechnology with successful applications in the production of both bulk and fine chemicals. Yet, yeast researchers are faced with the challenge to further its transition from the old workhorse to a modern cell factory, fulfilling the requirements for next generation bioprocesses. Many of the principles and tools that are applied for this development originate from the field of synthetic biology and the engineered strains will indeed be synthetic organisms. We provide an overview of the most important aspects of this transition and highlight achievements in recent years as well as trends in which yeast currently lags behind. These aspects include: the enhancement of the substrate spectrum of yeast, with the focus on the efficient utilization of renewable feedstocks, the enhancement of the product spectrum through generation of independent circuits for the maintenance of redox balances and biosynthesis of common carbon building blocks, the requirement for accurate pathway control with improved genome editing and through orthogonal promoters, and improvement of the tolerance of yeast for specific stress conditions. The causative genetic elements for the required traits of the future yeast cell factories will be assembled into genetic modules for fast transfer between strains. These developments will benefit from progress in bio-computational methods, which allow for the integration of different kinds of data sets and algorithms, and from rapid advancement in genome editing, which will enable multiplexed targeted integration of whole heterologous pathways. The overall goal will be to provide a collection of modules and circuits that work independently and can be combined at will, depending on the individual conditions, and will result in an optimal synthetic host for a given production process.
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Affiliation(s)
- Martin Kavšček
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50/II, 8010, Graz, Austria.
| | - Martin Stražar
- Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia.
| | - Tomaž Curk
- Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia.
| | - Klaus Natter
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50/II, 8010, Graz, Austria.
| | - Uroš Petrovič
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Jamova 39, 1000, Ljubljana, Slovenia.
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Tanaka T, Kondo A. Cell surface engineering of industrial microorganisms for biorefining applications. Biotechnol Adv 2015; 33:1403-11. [PMID: 26070720 DOI: 10.1016/j.biotechadv.2015.06.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2014] [Revised: 06/04/2015] [Accepted: 06/06/2015] [Indexed: 11/19/2022]
Abstract
In order to decrease carbon emissions and negative environmental impacts of various pollutants, biofuel/biochemical production should be promoted for replacing fossil-based industrial processes. Utilization of abundant lignocellulosic biomass as a feedstock has recently become an attractive option. In this review, we focus on recent efforts of cell surface display using industrial microorganisms such as Escherichia coli and yeast. Cell surface display is used primarily for endowing cellulolytic activity on the host cells, and enables direct fermentation to generate useful fuels and chemicals from lignocellulosic biomass. Cell surface display systems are systematically summarized, and the drawbacks/perspectives as well as successful application of surface display for industrial biotechnology are discussed.
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Affiliation(s)
- Tsutomu Tanaka
- Department of Chemical Science and Technology, Graduate School of Engineering, Kobe University, 1-1, Rokkodaicho, Nada, Kobe 657-8501 Japan
| | - Akihiko Kondo
- Department of Chemical Science and Technology, Graduate School of Engineering, Kobe University, 1-1, Rokkodaicho, Nada, Kobe 657-8501 Japan.
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Engineering Saccharomyces pastorianus for the co-utilisation of xylose and cellulose from biomass. Microb Cell Fact 2015; 14:61. [PMID: 25928878 PMCID: PMC4417197 DOI: 10.1186/s12934-015-0242-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 04/08/2015] [Indexed: 01/24/2023] Open
Abstract
Background Lignocellulosic biomass is a viable source of renewable energy for bioethanol production. For the efficient conversion of biomass into bioethanol, it is essential that sugars from both the cellulose and hemicellulose fractions of lignocellulose be utilised. Results We describe the development of a recombinant yeast system for the fermentation of cellulose and xylose, the most abundant pentose sugar in the hemicellulose fraction of biomass. The brewer’s yeast Saccharomyces pastorianus was chosen as a host as significantly higher recombinant enzyme activities are achieved, when compared to the more commonly used S. cerevisiae. When expressed in S. pastorianus, the Trichoderma reesei xylose oxidoreductase pathway was more efficient at alcohol production from xylose than the xylose isomerase pathway. The alcohol yield was influenced by the concentration of xylose in the medium and was significantly improved by the additional expression of a gene encoding for xylulose kinase. The xylose reductase, xylitol dehydrogenase and xylulose kinase genes were co-expressed with genes encoding for the three classes of T. reesei cellulases, namely endoglucanase (EG2), cellobiohydrolysase (CBH2) and β-glucosidase (BGL1). The initial metabolism of xylose by the engineered strains facilitated production of cellulases at fermentation temperatures. The sequential metabolism of xylose and cellulose generated an alcohol yield of 82% from the available sugars. Several different types of biomass, such as the energy crop Miscanthus sinensis and the industrial waste, brewer’s spent grains, were examined as biomass sources for fermentation using the developed yeast strains. Xylose metabolism and cell growth were inhibited in fermentations carried out with acid-treated spent grain liquor, resulting in a 30% reduction in alcohol yield compared to fermentations carried out with mixed sugar substrates. Conclusions Reconstitution of complete enzymatic pathways for cellulose hydrolysis and xylose utilisation in S. pastorianus facilitates the co-fermentation of cellulose and xylose without the need for added exogenous cellulases and provides a basis for the development of a consolidated process for co-utilisation of hemicellulose and cellulose sugars. Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0242-4) contains supplementary material, which is available to authorized users.
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Bartsch M, Gassmeyer SK, Köninger K, Igarashi K, Liauw P, Dyczmons-Nowaczyk N, Miyamoto K, Nowaczyk MM, Kourist R. Photosynthetic production of enantioselective biocatalysts. Microb Cell Fact 2015; 14:53. [PMID: 25889799 PMCID: PMC4412116 DOI: 10.1186/s12934-015-0233-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 03/25/2015] [Indexed: 12/30/2022] Open
Abstract
Background Global resource depletion poses a dramatic threat to our society and creates a strong demand for alternative resources that do not compete with the production of food. Meeting this challenge requires a thorough rethinking of all steps of the value chain regarding their sustainability resource demand and the possibility to substitute current, petrol-based supply-chains with renewable resources. This regards also the production of catalysts for chemical synthesis. Phototrophic microorganisms have attracted considerable attention as a biomanufacturing platform for the sustainable production of chemicals and biofuels. They allow the direct utilization of carbon dioxide and do not compete with food production. Photosynthetic enzyme production of catalysts would be a sustainable supply of these important components of the biotechnological and chemical industries. This paper focuses on the usefulness of recombinant cyanobacteria for the photosynthetic expression of enantioselective catalysts. As a proof of concept, we used the cyanobacterium Synechocystis sp. PCC 6803 for the heterologous expression of two highly enantioselective enzymes. Results We investigated the expression yield and the usefulness of cyanobacterial cell extracts for conducting stereoselective reactions. The cyanobacterial enzyme expression achieved protein yields of 3% of total soluble protein (%TSP) while the expression in E. coli yielded 6-8% TSP. Cell-free extracts from a recombinant strain expressing the recombinant esterase ST0071 from the thermophilic organism Sulfolobus tokodai ST0071 and arylmalonate decarboxylase from Bordetella bronchiseptica showed excellent enantioselectivity (>99% ee) and yield (>91%) in the desymmetrisation of prochiral malonates. Conclusions We were able to present the proof-of-concept of photoautotrophic enzyme expression as a viable alternative to heterotrophic expression hosts. Our results show that the introduction of foreign genes is straightforward. Cell components from Synechocystis did not interfere with the stereoselective transformations, underlining the usability of photoautotrophic organisms for the production of enzymes. Given the considerable commercial value of recombinant biocatalysts, cyanobacterial enzyme expression has thus the potential to complement existing approaches to use phototrophic organisms for the production of chemicals and biofuels.
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Affiliation(s)
- Maik Bartsch
- Junior Research Group for Microbial Biotechnology, Ruhr-Universität Bochum, Universitätsstr. 150, 44780, Bochum, Germany.
| | - Sarah K Gassmeyer
- Junior Research Group for Microbial Biotechnology, Ruhr-Universität Bochum, Universitätsstr. 150, 44780, Bochum, Germany.
| | - Katharina Köninger
- Junior Research Group for Microbial Biotechnology, Ruhr-Universität Bochum, Universitätsstr. 150, 44780, Bochum, Germany.
| | - Kosuke Igarashi
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Yokohama, 223-8522, Japan.
| | - Pasqual Liauw
- Chair for Plant Biochemistry, Ruhr-Universität Bochum, Universitätsstr. 150, 44780, Bochum, Germany.
| | - Nina Dyczmons-Nowaczyk
- Chair for Plant Biochemistry, Ruhr-Universität Bochum, Universitätsstr. 150, 44780, Bochum, Germany.
| | - Kenji Miyamoto
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Yokohama, 223-8522, Japan.
| | - Marc M Nowaczyk
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Yokohama, 223-8522, Japan.
| | - Robert Kourist
- Junior Research Group for Microbial Biotechnology, Ruhr-Universität Bochum, Universitätsstr. 150, 44780, Bochum, Germany.
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Challenges for the production of bioethanol from biomass using recombinant yeasts. ADVANCES IN APPLIED MICROBIOLOGY 2015; 92:89-125. [PMID: 26003934 DOI: 10.1016/bs.aambs.2015.02.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Lignocellulose biomass, one of the most abundant renewable resources on the planet, is an alternative sustainable energy source for the production of second-generation biofuels. Energy in the form of simple or complex carbohydrates can be extracted from lignocellulose biomass and fermented by microorganisms to produce bioethanol. Despite 40 years of active and cutting-edge research invested into the development of technologies to produce bioethanol from lignocellulosic biomass, the process remains commercially unviable. This review describes the achievements that have been made in generating microorganisms capable of utilizing both simple and complex sugars from lignocellulose biomass and the fermentation of these sugars into ethanol. We also provide a discussion on the current "roadblocks" standing in the way of making second-generation bioethanol a commercially viable alternative to fossil fuels.
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Noda S, Kawai Y, Tanaka T, Kondo A. 4-Vinylphenol biosynthesis from cellulose as the sole carbon source using phenolic acid decarboxylase- and tyrosine ammonia lyase-expressing Streptomyces lividans. BIORESOURCE TECHNOLOGY 2015; 180:59-65. [PMID: 25585255 DOI: 10.1016/j.biortech.2014.12.064] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 12/19/2014] [Accepted: 12/20/2014] [Indexed: 06/04/2023]
Abstract
Streptomyces lividans was adopted as a host strain for 4-vinylphenol (4VPh) production directly from cellulose. In order to obtain novel phenolic acid decarboxylase (PAD) expressed in S. lividans, PADs distributed among Streptomyces species were screened. Three novel PADs, derived from Streptomycessviceus, Streptomyceshygroscopicus, and Streptomycescattleya, were successfully obtained and expressed in S. lividans. S. sviceus PAD (SsPAD) could convert p-hydroxycinnamic acid (pHCA) to 4VPh more efficiently than the others both in vitro and in vivo. For 4VPh production directly from cellulose, l-tyrosine ammonia lyase derived from Rhodobacter sphaeroides and SsPAD were introduced into endoglucanase-secreting S. lividans, and the 4VPh biosynthetic pathway was constructed therein. The created transformants successfully produced 4VPh directly from cellulose.
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Affiliation(s)
- Shuhei Noda
- Biomass Engineering Program, RIKEN, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Yoshifumi Kawai
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Tsutomu Tanaka
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Akihiko Kondo
- Biomass Engineering Program, RIKEN, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan.
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Recombinant CBM-fusion technology - Applications overview. Biotechnol Adv 2015; 33:358-69. [PMID: 25689072 DOI: 10.1016/j.biotechadv.2015.02.006] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 02/06/2015] [Accepted: 02/09/2015] [Indexed: 02/04/2023]
Abstract
Carbohydrate-binding modules (CBMs) are small components of several enzymes, which present an independent fold and function, and specific carbohydrate-binding activity. Their major function is to bind the enzyme to the substrate enhancing its catalytic activity, especially in the case of insoluble substrates. The immense diversity of CBMs, together with their unique properties, has long raised their attention for many biotechnological applications. Recombinant DNA technology has been used for cloning and characterizing new CBMs. In addition, it has been employed to improve the purity and availability of many CBMs, but mainly, to construct bi-functional CBM-fused proteins for specific applications. This review presents a comprehensive summary of the uses of CBMs recombinantly produced from heterologous organisms, or by the original host, along with the latest advances. Emphasis is given particularly to the applications of recombinant CBM-fusions in: (a) modification of fibers, (b) production, purification and immobilization of recombinant proteins, (c) functionalization of biomaterials and (d) development of microarrays and probes.
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Tanaka T, Kondo A. Cell-surface display of enzymes by the yeast Saccharomyces cerevisiae for synthetic biology. FEMS Yeast Res 2015; 15:1-9. [PMID: 25243459 DOI: 10.1111/1567-1364.12212] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 05/09/2014] [Accepted: 09/15/2014] [Indexed: 01/26/2023] Open
Abstract
In yeast cell-surface displays, functional proteins, such as cellulases, are genetically fused to an anchor protein and expressed on the cell surface. Saccharomyces cerevisiae, which is often utilized as a cell factory for the production of fuels, chemicals, and proteins, is the most commonly used yeast for cell-surface display. To construct yeast cells with a desired function, such as the ability to utilize cellulose as a substrate for bioethanol production, cell-surface display techniques for the efficient expression of enzymes on the cell membrane need to be combined with metabolic engineering approaches for manipulating target pathways within cells. In this Minireview, we summarize the recent progress of biorefinery fields in the development and application of yeast cell-surface displays from a synthetic biology perspective and discuss approaches for further enhancing cell-surface display efficiency.
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Affiliation(s)
- Tsutomu Tanaka
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Nada, Kobe, Japan
| | - Akihiko Kondo
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Nada, Kobe, Japan
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Abstract
The method of displaying recombinant proteins on the surface of Saccharomyces cerevisiae via genetic fusion to an abundant cell wall protein, a technology known as yeast surface display, or simply, yeast display, has become a valuable protein engineering tool for a broad spectrum of biotechnology and biomedical applications. This review focuses on the use of yeast display for engineering protein affinity, stability, and enzymatic activity. Strategies and examples for each protein engineering goal are discussed. Additional applications of yeast display are also briefly presented, including protein epitope mapping, identification of protein-protein interactions, and uses of displayed proteins in industry and medicine.
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Kim S, Hahn JS. Synthetic scaffold based on a cohesin–dockerin interaction for improved production of 2,3-butanediol in Saccharomyces cerevisiae. J Biotechnol 2014; 192 Pt A:192-6. [PMID: 25456062 DOI: 10.1016/j.jbiotec.2014.10.015] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Revised: 09/22/2014] [Accepted: 10/13/2014] [Indexed: 11/20/2022]
Abstract
Substrate channeling is a process of transferring an intermediate from one enzyme to the next enzyme without diffusion into the bulk phase, thereby leading to an enhanced reaction rate. Here, we newly designed substrate channeling modules in Saccharomyces cerevisiae based on a high affinity interaction between dockerin and cohesin domains, which is a key process in the formation of cellulosome structure. Synthetic scaffolds containing two, three, or seven cohesin domains were constructed, and the assembly of dockerin-tagged proteins onto the scaffolds was confirmed by pull-down assay and bimolecular fluorescent complementation (BiFC) assay in vivo. This system was applied to produce 2,3-butanediol in S. cerevisiae by using dockerin-tagged AlsS, AlsD, and Bdh1 enzymes, resulting in a gradual increase in 2,3-butanediol production depending on the number of cohesin domains in the scaffold.
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Moraïs S, Shterzer N, Lamed R, Bayer EA, Mizrahi I. A combined cell-consortium approach for lignocellulose degradation by specialized Lactobacillus plantarum cells. BIOTECHNOLOGY FOR BIOFUELS 2014; 7:112. [PMID: 25788977 PMCID: PMC4364503 DOI: 10.1186/1754-6834-7-112] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2014] [Accepted: 07/09/2014] [Indexed: 05/28/2023]
Abstract
BACKGROUND Lactobacillus plantarum is an attractive candidate for metabolic engineering towards bioprocessing of lignocellulosic biomass to ethanol or polylactic acid, as its natural characteristics include high ethanol and acid tolerance and the ability to metabolize the two major polysaccharide constituents of lignocellulolytic biomass (pentoses and hexoses). We recently engineered L. plantarum via separate introduction of a potent cellulase and xylanase, thereby creating two different L. plantarum strains. We used these strains as a combined cell-consortium for synergistic degradation of cellulosic biomass. RESULTS To optimize enzymatic degradation, we applied the cell-consortium approach to assess the significance of enzyme localization by comparing three enzymatic paradigms prevalent in nature: (i) a secreted enzymes system, (ii) enzymes anchored to the bacterial cell surface and (iii) enzymes integrated into cellulosome complexes. The construction of the three paradigmatic systems involved the division of the production and organization of the enzymes and scaffold proteins into different strains of L. plantarum. The spatial differentiation of the components of the enzymatic systems alleviated the load on the cell machinery of the different bacterial strains. Active designer cellulosomes containing a xylanase and a cellulase were thus assembled on L. plantarum cells by co-culturing three distinct engineered strains of the bacterium: two helper strains for enzyme secretion and one producing only the anchored scaffoldin. Alternatively, the two enzymes were anchored separately to the cell wall. The secreted enzyme consortium appeared to have a slight advantage over the designer cellulosome system in degrading the hypochlorite pretreated wheat straw substrate, and both exhibited significantly higher levels of activity compared to the anchored enzyme consortium. However, the secreted enzymes appeared to be less stable than the enzymes integrated into designer cellulosomes, suggesting an advantage of the latter over longer time periods. CONCLUSIONS By developing the potential of L. plantarum to express lignocellulolytic enzymes and to control their functional combination and stoichiometry on the cell wall, this study provides a step forward towards optimal biomass bioprocessing and soluble fermentable sugar production. Future expansion of the preferred secreted-enzyme and designer-cellulosome systems to include additional types of enzymes will promote enhanced deconstruction of cellulosic feedstocks.
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Affiliation(s)
- Sarah Moraïs
- />Department of Biological Chemistry, The Weizmann Institute of Science, 234 Herzl St, Rehovot, 7610001 Israel
| | - Naama Shterzer
- />Department of Ruminant Science, Institute of Animal Sciences, Agricultural Research Organization, P.O.B. 6, Bet-Dagan, 50250 Israel
| | - Raphael Lamed
- />Department of Molecular Microbiology and Biotechnology, Tel Aviv University, P.O. Box 39040, Ramat Aviv, 69978 Israel
| | - Edward A Bayer
- />Department of Biological Chemistry, The Weizmann Institute of Science, 234 Herzl St, Rehovot, 7610001 Israel
| | - Itzhak Mizrahi
- />Department of Ruminant Science, Institute of Animal Sciences, Agricultural Research Organization, P.O.B. 6, Bet-Dagan, 50250 Israel
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Integration of bacterial lytic polysaccharide monooxygenases into designer cellulosomes promotes enhanced cellulose degradation. Proc Natl Acad Sci U S A 2014; 111:9109-14. [PMID: 24927597 DOI: 10.1073/pnas.1404148111] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Efficient conversion of cellulose into soluble sugars is a key technological bottleneck limiting efficient production of plant-derived biofuels and chemicals. In nature, the process is achieved by the action of a wide range of cellulases and associated enzymes. In aerobic microrganisms, cellulases are secreted as free enzymes. Alternatively, in certain anaerobic microbes, cellulases are assembled into large multienzymes complexes, termed "cellulosomes," which allow for efficient hydrolysis of cellulose. Recently, it has been shown that enzymes classified as lytic polysaccharide monooxygenases (LPMOs) were able to strongly enhance the activity of cellulases. However, LPMOs are exclusively found in aerobic organisms and, thus, cannot benefit from the advantages offered by the cellulosomal system. In this study, we designed several dockerin-fused LPMOs based on enzymes from the bacterium Thermobifida fusca. The resulting chimeras exhibited activity levels on microcrystalline cellulose similar to that of the wild-type enzymes. The dockerin moieties of the chimeras were demonstrated to be functional and to specifically bind to their corresponding cohesin partner. The chimeric LPMOs were able to self-assemble in designer cellulosomes alongside an endo- and an exo-cellulase also converted to the cellulosomal mode. The resulting complexes showed a 1.7-fold increase in the release of soluble sugars from cellulose, compared with the free enzymes, and a 2.6-fold enhancement compared with free cellulases without LPMO enhancement. These results highlight the feasibility of the conversion of LPMOs to the cellulosomal mode, and that these enzymes can benefit from the proximity effects generated by the cellulosome architecture.
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Haitjema CH, Solomon KV, Henske JK, Theodorou MK, O'Malley MA. Anaerobic gut fungi: Advances in isolation, culture, and cellulolytic enzyme discovery for biofuel production. Biotechnol Bioeng 2014; 111:1471-82. [PMID: 24788404 DOI: 10.1002/bit.25264] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Revised: 04/09/2014] [Accepted: 04/10/2014] [Indexed: 12/12/2022]
Abstract
Anaerobic gut fungi are an early branching family of fungi that are commonly found in the digestive tract of ruminants and monogastric herbivores. It is becoming increasingly clear that they are the primary colonizers of ingested plant biomass, and that they significantly contribute to the decomposition of plant biomass into fermentable sugars. As such, anaerobic fungi harbor a rich reservoir of undiscovered cellulolytic enzymes and enzyme complexes that can potentially transform the conversion of lignocellulose into bioenergy products. Despite their unique evolutionary history and cellulolytic activity, few species have been isolated and studied in great detail. As a result, their life cycle, cellular physiology, genetics, and cellulolytic metabolism remain poorly understood compared to aerobic fungi. To help address this limitation, this review briefly summarizes the current body of knowledge pertaining to anaerobic fungal biology, and describes progress made in the isolation, cultivation, molecular characterization, and long-term preservation of these microbes. We also discuss recent cellulase- and cellulosome-discovery efforts from gut fungi, and how these interesting, non-model microbes could be further adapted for biotechnology applications.
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Affiliation(s)
- Charles H Haitjema
- Department of Chemical Engineering, University of California, Santa Barbara, California, 93106
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Bhutto AW, Qureshi K, Harijan K, Zahedi G, Bahadori A. Strategies for the consolidation of biologically mediated events in the conversion of pre-treated lignocellulose into ethanol. RSC Adv 2014. [DOI: 10.1039/c3ra44020f] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Lambertz C, Garvey M, Klinger J, Heesel D, Klose H, Fischer R, Commandeur U. Challenges and advances in the heterologous expression of cellulolytic enzymes: a review. BIOTECHNOLOGY FOR BIOFUELS 2014; 7:135. [PMID: 25356086 PMCID: PMC4212100 DOI: 10.1186/s13068-014-0135-5] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Accepted: 09/03/2014] [Indexed: 05/03/2023]
Abstract
Second generation biofuel development is increasingly reliant on the recombinant expression of cellulases. Designing or identifying successful expression systems is thus of preeminent importance to industrial progress in the field. Recombinant production of cellulases has been performed using a wide range of expression systems in bacteria, yeasts and plants. In a number of these systems, particularly when using bacteria and plants, significant challenges have been experienced in expressing full-length proteins or proteins at high yield. Further difficulties have been encountered in designing recombinant systems for surface-display of cellulases and for use in consolidated bioprocessing in bacteria and yeast. For establishing cellulase expression in plants, various strategies are utilized to overcome problems, such as the auto-hydrolysis of developing plant cell walls. In this review, we investigate the major challenges, as well as the major advances made to date in the recombinant expression of cellulases across the commonly used bacterial, plant and yeast systems. We review some of the critical aspects to be considered for industrial-scale cellulase production.
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Affiliation(s)
- Camilla Lambertz
- />Institute for Molecular Biotechnology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Megan Garvey
- />Institute for Molecular Biotechnology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
- />Present address: School of Medicine, Deakin University, CSIRO Australian Animal Health Laboratory, 5 Portarlington Rd, Newcomb, VIC 3219 Australia
| | - Johannes Klinger
- />Institute for Molecular Biotechnology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Dirk Heesel
- />Institute for Molecular Biotechnology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Holger Klose
- />Institute for Molecular Biotechnology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
- />Present address: Institute for Botany and Molecular Genetics, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Rainer Fischer
- />Institute for Molecular Biotechnology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
- />Fraunhofer Institute for Molecular Biology and Applied Ecology, Forckenbeckstrasse 6, 52074 Aachen, Germany
| | - Ulrich Commandeur
- />Institute for Molecular Biotechnology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
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Huang GL, Anderson TD, Clubb RT. Engineering microbial surfaces to degrade lignocellulosic biomass. Bioengineered 2013; 5:96-106. [PMID: 24430239 PMCID: PMC4049913 DOI: 10.4161/bioe.27461] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Renewable lignocellulosic plant biomass is a promising feedstock from which to produce biofuels, chemicals, and materials. One approach to cost-effectively exploit this resource is to use consolidating bioprocessing (CBP) microbes that directly convert lignocellulose into valuable end products. Because many promising CBP-enabling microbes are non-cellulolytic, recent work has sought to engineer them to display multi-cellulase containing minicellulosomes that hydrolyze biomass more efficiently than isolated enzymes. In this review, we discuss progress in engineering the surfaces of the model microorganisms: Bacillus subtilis, Escherichia coli, and Saccharomyces cerevisiae. We compare the distinct approaches used to display cellulases and minicellulosomes, as well as their surface enzyme densities and cellulolytic activities. Thus far, minicellulosomes have only been grafted onto the surfaces of B. subtilis and S. cerevisiae, suggesting that the absence of an outer membrane in fungi and Gram-positive bacteria may make their surfaces better suited for displaying the elaborate multi-enzyme complexes needed to efficiently degrade lignocellulose.
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Affiliation(s)
- Grace L Huang
- Department of Chemistry and Biochemistry; University of California-Los Angeles; Los Angeles, CA USA; UCLA-DOE Institute of Genomics and Proteomics; University of California-Los Angeles; Los Angeles, CA USA
| | - Timothy D Anderson
- Department of Chemistry and Biochemistry; University of California-Los Angeles; Los Angeles, CA USA; UCLA-DOE Institute of Genomics and Proteomics; University of California-Los Angeles; Los Angeles, CA USA
| | - Robert T Clubb
- Department of Chemistry and Biochemistry; University of California-Los Angeles; Los Angeles, CA USA; UCLA-DOE Institute of Genomics and Proteomics; University of California-Los Angeles; Los Angeles, CA USA; Molecular Biology Institute; University of California-Los Angeles; Los Angeles, CA USA
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Garvey M, Klose H, Fischer R, Lambertz C, Commandeur U. Cellulases for biomass degradation: comparing recombinant cellulase expression platforms. Trends Biotechnol 2013; 31:581-93. [DOI: 10.1016/j.tibtech.2013.06.006] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Revised: 06/21/2013] [Accepted: 06/24/2013] [Indexed: 10/26/2022]
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