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Bi Y, Yao Z, Zhu Z, Liu W. Enhancement of the catalytic performance of UIO-66 for the CO 2 synthesis of cyclic carbonate using natural nanomaterials as a carrier. Dalton Trans 2023; 52:18082-18089. [PMID: 37997171 DOI: 10.1039/d3dt02236f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2023]
Abstract
One of the environmentally friendly methods is the intelligent utilization of natural one-dimensional nanomaterials as carriers to improve the CO2 catalytic performance of MOF materials. This paper reports an efficient composite catalyst preparation using a cheap and readily available magnesium-aluminosilicate nanometer, attapulgite (ATP), as a carrier for MOF materials. Due to its Lewis acidic site and unique alkaline pore structure, ATP exhibits excellent catalytic activity in the coupling reaction of CO2 with epoxy compounds, and its regular one-dimensional nanorod shape has tremendous potential as a carrier compared to other natural minerals. Given the diversity of MOF material types and structures, the design of this UIO-66/ATP nanocomposite catalyst provides both a new pathway for CO2 capture and conversion and a developmental space for the synthesis of such nanocomposites.
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Affiliation(s)
- Yunshuai Bi
- College of Chemistry and Chemical Engineering, Qinghai Normal University, Xining, 810000, China
| | - Zibei Yao
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Zhen Zhu
- College of Chemistry and Chemical Engineering, Qinghai Normal University, Xining, 810000, China
| | - Weisheng Liu
- College of Chemistry and Chemical Engineering, Qinghai Normal University, Xining, 810000, China
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
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2
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Khamassi A, Dumon C. Enzyme synergy for plant cell wall polysaccharide degradation. Essays Biochem 2023; 67:521-531. [PMID: 37067158 DOI: 10.1042/ebc20220166] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 02/17/2023] [Accepted: 03/07/2023] [Indexed: 04/18/2023]
Abstract
Valorizing plant cell wall, marine and algal polysaccharides is of utmost importance for the development of the circular bioeconomy. This is because polysaccharides are by far the most abundant organic molecules found in nature with complex chemical structures that require a large set of enzymes for their degradation. Microorganisms produce polysaccharide-specific enzymes that act in synergy when performing hydrolysis. Although discovered since decades enzyme synergy is still poorly understood at the molecular level and thus it is difficult to harness and optimize. In the last few years, more attention has been given to improve and characterize enzyme synergy for polysaccharide valorization. In this review, we summarize literature to provide an overview of the different type of synergy involving carbohydrate modifying enzymes and the recent advances in the field exemplified by plant cell-wall degradation.
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Affiliation(s)
- Ahmed Khamassi
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Claire Dumon
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
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3
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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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4
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Effect of multimodularity and spatial organization of glycoside hydrolases on catalysis. Essays Biochem 2023; 67:629-638. [PMID: 36866571 DOI: 10.1042/ebc20220167] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 02/03/2023] [Accepted: 02/06/2023] [Indexed: 03/04/2023]
Abstract
The wide diversity among the carbohydrate-active enzymes (CAZymes) reflects the equally broad versatility in terms of composition and chemicals bonds found in the plant cell wall polymers on which they are active. This diversity is also expressed through the various strategies developed to circumvent the recalcitrance of these substrates to biological degradation. Glycoside hydrolases (GHs) are the most abundant of the CAZymes and are expressed as isolated catalytic modules or in association with carbohydrate-binding module (CBM), acting in synergism within complex arrays of enzymes. This multimodularity can be even more complex. The cellulosome presents a scaffold protein immobilized to the outer membrane of some microorganisms on which enzymes are grafted to prevent their dispersion and increase catalytic synergism. In polysaccharide utilization loci (PUL), GHs are also distributed across the membranes of some bacteria to co-ordinate the deconstruction of polysaccharides and the internalization of metabolizable carbohydrates. Although the study and characterization of these enzymatic activities need to take into account the entirety of this complex organization-in particular because of the dynamics involved in it-technical problems limit the present study to isolated enzymes. However, these enzymatic complexes also have a spatiotemporal organization, whose still neglected aspect must be considered. In the present review, the different levels of multimodularity that can occur in GHs will be reviewed, from its simplest forms to the most complex. In addition, attempts to characterize or study the effect on catalytic activity of the spatial organization within GHs will be addressed.
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Vanderstraeten J, da Fonseca MJM, De Groote P, Grimon D, Gerstmans H, Kahn A, Moraïs S, Bayer EA, Briers Y. Combinatorial assembly and optimisation of designer cellulosomes: a galactomannan case study. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:60. [PMID: 35637485 PMCID: PMC9153192 DOI: 10.1186/s13068-022-02158-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 05/14/2022] [Indexed: 11/10/2022]
Abstract
BACKGROUND Designer cellulosomes are self-assembled chimeric enzyme complexes that can be used to improve lignocellulosic biomass degradation. They are composed of a synthetic multimodular backbone protein, termed the scaffoldin, and a range of different chimeric docking enzymes that degrade polysaccharides. Over the years, several functional designer cellulosomes have been constructed. Since many parameters influence the efficiency of these multi-enzyme complexes, there is a need to optimise designer cellulosome architecture by testing combinatorial arrangements of docking enzyme and scaffoldin variants. However, the modular cloning procedures are tedious and cumbersome. RESULTS VersaTile is a combinatorial DNA assembly method, allowing the rapid construction and thus comparison of a range of modular proteins. Here, we present the extension of the VersaTile platform to facilitate the construction of designer cellulosomes. We have constructed a tile repository, composed of dockerins, cohesins, linkers, tags and enzymatically active modules. The developed toolbox allows us to efficiently create and optimise designer cellulosomes at an unprecedented speed. As a proof of concept, a trivalent designer cellulosome able to degrade the specific hemicellulose substrate, galactomannan, was constructed and optimised. The main factors influencing cellulosome efficiency were found to be the selected dockerins and linkers and the docking enzyme ratio on the scaffoldin. The optimised designer cellulosome was able to hydrolyse the galactomannan polysaccharide and release mannose and galactose monomers. CONCLUSION We have eliminated one of the main technical hurdles in the designer cellulosome field and anticipate the VersaTile platform to be a starting point in the development of more elaborate multi-enzyme complexes.
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Affiliation(s)
- Julie Vanderstraeten
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Valentin Vaerwyckweg 1, 9000, Ghent, Belgium
| | - Maria João Maurício da Fonseca
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Valentin Vaerwyckweg 1, 9000, Ghent, Belgium
| | - Philippe De Groote
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Valentin Vaerwyckweg 1, 9000, Ghent, Belgium
| | - Dennis Grimon
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Valentin Vaerwyckweg 1, 9000, Ghent, Belgium
| | - Hans Gerstmans
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Valentin Vaerwyckweg 1, 9000, Ghent, Belgium.,Laboratory for Biomolecular Discovery and Engineering, Department of Biology, VIB-KU Leuven Center for Microbiology, Kasteelpark Arenberg 31, 3001, Louvain, Belgium
| | - Amaranta Kahn
- Department of Biomolecular Sciences, The Weizmann Institute of Science, 7610001, Rehovot, Israel.,Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Avenida General Norton de Matos, s/n, 4450-208, Matosinhos, Portugal
| | - Sarah Moraïs
- Department of Biomolecular Sciences, The Weizmann Institute of Science, 7610001, Rehovot, Israel.,Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, 8499000, Beer-Sheva, Israel
| | - Edward A Bayer
- Department of Biomolecular Sciences, The Weizmann Institute of Science, 7610001, Rehovot, Israel.,Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, 8499000, Beer-Sheva, Israel
| | - Yves Briers
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Valentin Vaerwyckweg 1, 9000, Ghent, Belgium.
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6
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Singh N, Mathur AS, Gupta RP, Barrow CJ, Tuli DK, Puri M. Enzyme systems of thermophilic anaerobic bacteria for lignocellulosic biomass conversion. Int J Biol Macromol 2020; 168:572-590. [PMID: 33309672 DOI: 10.1016/j.ijbiomac.2020.12.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 11/30/2020] [Accepted: 12/01/2020] [Indexed: 11/17/2022]
Abstract
Economic production of lignocellulose degrading enzymes for biofuel industries is of considerable interest to the biotechnology community. While these enzymes are widely distributed in fungi, their industrial production from other sources, particularly by thermophilic anaerobic bacteria (growth Topt ≥ 60 °C), is an emerging field. Thermophilic anaerobic bacteria produce a large number of lignocellulolytic enzymes having unique structural features and employ different schemes for biomass degradation, which can be classified into four systems namely; 'free enzyme system', 'cell anchored enzymes', 'complex cellulosome system', and 'multifunctional multimodular enzyme system'. Such enzymes exhibit high specific activity and have a natural ability to withstand harsh bioprocessing conditions. However, achieving a higher production of these thermostable enzymes at current bioprocessing targets is challenging. In this review, the research opportunities for these distinct enzyme systems in the biofuel industry and the associated technological challenges are discussed. The current status of research findings is highlighted along with a detailed description of the categorization of the different enzyme production schemes. It is anticipated that high temperature-based bioprocessing will become an integral part of sustainable bioenergy production in the near future.
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Affiliation(s)
- Nisha Singh
- Centre for Chemistry and Biotechnology, Deakin University, Waurn Ponds, Victoria 3217, Australia; DBT-IOC Centre for Advance Bioenergy Research, Research & Development Centre, Indian Oil Corporation Limited, Sector-13, Faridabad 121007, India
| | - Anshu S Mathur
- DBT-IOC Centre for Advance Bioenergy Research, Research & Development Centre, Indian Oil Corporation Limited, Sector-13, Faridabad 121007, India
| | - Ravi P Gupta
- DBT-IOC Centre for Advance Bioenergy Research, Research & Development Centre, Indian Oil Corporation Limited, Sector-13, Faridabad 121007, India
| | - Colin J Barrow
- Centre for Chemistry and Biotechnology, Deakin University, Waurn Ponds, Victoria 3217, Australia
| | - Deepak K Tuli
- DBT-IOC Centre for Advance Bioenergy Research, Research & Development Centre, Indian Oil Corporation Limited, Sector-13, Faridabad 121007, India
| | - Munish Puri
- Centre for Chemistry and Biotechnology, Deakin University, Waurn Ponds, Victoria 3217, Australia; Medical Biotechnology, Centre for Marine Bioproducts Development, College of Medicine and Public Health, Flinders University, Bedford Park, Adelaide 5042, Australia.
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7
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Vanderstraeten J, Briers Y. Synthetic protein scaffolds for the colocalisation of co-acting enzymes. Biotechnol Adv 2020; 44:107627. [DOI: 10.1016/j.biotechadv.2020.107627] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 08/17/2020] [Accepted: 08/25/2020] [Indexed: 02/06/2023]
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8
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Zhan M, Wang L, Xie C, Fu X, Zhang S, Wang A, Zhou Y, Xu C, Zhang H. Succession of Gut Microbial Structure in Twin Giant Pandas During the Dietary Change Stage and Its Role in Polysaccharide Metabolism. Front Microbiol 2020; 11:551038. [PMID: 33072012 PMCID: PMC7537565 DOI: 10.3389/fmicb.2020.551038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Accepted: 08/27/2020] [Indexed: 12/23/2022] Open
Abstract
Adaptation to a bamboo diet is an essential process for giant panda growth, and gut microbes play an important role in the digestion of the polysaccharides in bamboo. The dietary transition in giant panda cubs is particularly complex, but it is an ideal period in which to study the effects of gut microbes on polysaccharide use because their main food changes from milk to bamboo (together with some bamboo shoot and coarse pastry). Here, we used 16S rDNA and internal transcribed spacer 1 (ITS1) DNA sequencing and metagenomic sequencing analysis to investigate the succession of the gut microbial structure in feces sampled from twin giant panda cubs during the completely dietary transition and determine the abundances of polysaccharide-metabolizing genes and their corresponding microbes to better understand the degradation of bamboo polysaccharides. Successive changes in the gut microbial diversity and structure were apparent in the growth of pandas during dietary shift process. Microbial diversity increased after the introduction of supplementary foods and then varied in a complex way for 1.5–2 years as bamboo and complex food components were introduced. They then stabilized after 2 years, when the cubs consumed a specialized bamboo diet. The microbes had more potential to metabolize the cellulose in bamboo than the hemicellulose, providing genes encoding cellulase systems corresponding to glycoside hydrolases (GHs; such as GH1, GH3, GH5, GH8, GH9, GH74, and GH94). The cellulose-metabolizing species (or genes) of gut bacteria was more abundant than that of gut fungi. Although cellulose-metabolizing species did not predominate in the gut bacterial community, microbial interactions allowed the giant pandas to achieve the necessary dietary shift and ultimately adapt to a bamboo diet.
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Affiliation(s)
- Mingye Zhan
- College of Environmental Science and Engineering, Institute of Pollution Control and Ecological Safety, Tongji University, Shanghai, China
| | - Lei Wang
- College of Environmental Science and Engineering, Institute of Pollution Control and Ecological Safety, Tongji University, Shanghai, China
| | - Chunyu Xie
- Shanghai Wild Animal Park Development Co., Ltd., Shanghai, China
| | - Xiaohua Fu
- College of Environmental Science and Engineering, Institute of Pollution Control and Ecological Safety, Tongji University, Shanghai, China
| | | | | | - Yingmin Zhou
- China Conservation and Research Centre for the Giant Panda, Dujiangyan, China
| | - Chunzhong Xu
- Shanghai Wild Animal Park Development Co., Ltd., Shanghai, China
| | - Hemin Zhang
- China Conservation and Research Centre for the Giant Panda, Dujiangyan, China
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Kim HG, Seo B, Lim CS. Metal- and halide-free catalysts supported on silica and their applications to CO2 cycloaddition reactions. J IND ENG CHEM 2019. [DOI: 10.1016/j.jiec.2019.03.025] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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10
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Changing surface grafting density has an effect on the activity of immobilized xylanase towards natural polysaccharides. Sci Rep 2019; 9:5763. [PMID: 30962508 PMCID: PMC6453946 DOI: 10.1038/s41598-019-42206-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 03/25/2019] [Indexed: 12/22/2022] Open
Abstract
Enzymes are involved in various types of biological processes. In many cases, they are part of multi-component machineries where enzymes are localized in close proximity to each-other. In such situations, it is still not clear whether inter-enzyme spacing actually plays a role or if the colocalization of complementary activities is sufficient to explain the efficiency of the system. Here, we focus on the effect of spatial proximity when identical enzymes are immobilized onto a surface. By using an innovative grafting procedure based on the use of two engineered protein fragments, Jo and In, we produce model systems in which enzymes are immobilized at surface densities that can be controlled precisely. The enzyme used is a xylanase that participates to the hydrolysis of plant cell wall polymers. By using a small chromogenic substrate, we first show that the intrinsic activity of the enzymes is fully preserved upon immobilization and does not depend on surface density. However, when using beechwood xylan, a naturally occurring polysaccharide, as substrate, we find that the enzymatic efficiency decreases by 10–60% with the density of grafting. This unexpected result is probably explained through steric hindrance effects at the nanoscale that hinder proper interaction between the enzymes and the polymer. A second effect of enzyme immobilization at high densities is the clear tendency for the system to release preferentially shorter oligosaccharides from beechwood xylan as compared to enzymes in solution.
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11
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Liang X, Whitham JM, Holwerda EK, Shao X, Tian L, Wu YW, Lombard V, Henrissat B, Klingeman DM, Yang ZK, Podar M, Richard TL, Elkins JG, Brown SD, Lynd LR. Development and characterization of stable anaerobic thermophilic methanogenic microbiomes fermenting switchgrass at decreasing residence times. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:243. [PMID: 30202438 PMCID: PMC6126044 DOI: 10.1186/s13068-018-1238-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 08/27/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Anaerobic fermentation of lignocellulose occurs in both natural and managed environments, and is an essential part of the carbon cycle as well as a promising route to sustainable production of fuels and chemicals. Lignocellulose solubilization by mixed microbiomes is important in these contexts. RESULTS Here, we report the development of stable switchgrass-fermenting enrichment cultures maintained at various residence times and moderately high (55 °C) temperatures. Anaerobic microbiomes derived from a digester inoculum were incubated at 55 °C and fed semi-continuously with medium containing 30 g/L mid-season harvested switchgrass to achieve residence times (RT) of 20, 10, 5, and 3.3 days. Stable, time-invariant cellulolytic methanogenic cultures with minimal accumulation of organic acids were achieved for all RTs. Fractional carbohydrate solubilization was 0.711, 0.654, 0.581 and 0.538 at RT = 20, 10, 5 and 3.3 days, respectively, and glucan solubilization was proportional to xylan solubilization at all RTs. The rate of solubilization was described well by the equation r = k(C - C0fr), where C represents the concentration of unutilized carbohydrate, C0 is the concentration of carbohydrate (cellulose and hemicellulose) entering the bioreactor and fr is the extrapolated fraction of entering carbohydrate that is recalcitrant at infinite residence time. The 3.3 day RT is among the shortest RT reported for stable thermophilic, methanogenic digestion of a lignocellulosic feedstock. 16S rDNA phylotyping and metagenomic analyses were conducted to characterize the effect of RT on community dynamics and to infer functional roles in the switchgrass to biogas conversion to the various microbial taxa. Firmicutes were the dominant phylum, increasing in relative abundance from 54 to 96% as RT decreased. A Clostridium clariflavum strain with genetic markers for xylose metabolism was the most abundant lignocellulose-solubilizing bacterium. A Thermotogae (Defluviitoga tunisiensis) was the most abundant bacterium in switchgrass digesters at RT = 20 days but decreased in abundance at lower RTs as did multiple Chloroflexi. Synergistetes and Euryarchaeota were present at roughly constant levels over the range of RTs examined. CONCLUSIONS A system was developed in which stable methanogenic steady-states were readily obtained with a particulate biomass feedstock, mid-season switchgrass, at laboratory (1 L) scale. Characterization of the extent and rate of carbohydrate solubilization in combination with 16S rDNA and metagenomic sequencing provides a multi-dimensional view of performance, species composition, glycoside hydrolases, and metabolic function with varying residence time. These results provide a point of reference and guidance for future studies and organism development efforts involving defined cultures.
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Affiliation(s)
- Xiaoyu Liang
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755 USA
- BioEnergy Sciences Center, Oak Ridge, TN 37830 USA
| | - Jason M. Whitham
- BioEnergy Sciences Center, Oak Ridge, TN 37830 USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
| | - Evert K. Holwerda
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755 USA
- BioEnergy Sciences Center, Oak Ridge, TN 37830 USA
| | - Xiongjun Shao
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755 USA
- BioEnergy Sciences Center, Oak Ridge, TN 37830 USA
| | - Liang Tian
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755 USA
- BioEnergy Sciences Center, Oak Ridge, TN 37830 USA
| | - Yu-Wei Wu
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, 106 Taiwan
| | - Vincent Lombard
- CNRS, UMR 7257, Aix-Marseille University, 13288 Marseille, France
- INRA, USC 1408 AFMB, 13288 Marseille, France
| | - Bernard Henrissat
- CNRS, UMR 7257, Aix-Marseille University, 13288 Marseille, France
- INRA, USC 1408 AFMB, 13288 Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Dawn M. Klingeman
- BioEnergy Sciences Center, Oak Ridge, TN 37830 USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
| | - Zamin K. Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
| | - Mircea Podar
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
| | - Tom L. Richard
- Department of Agricultural and Biological Engineering, The Pennsylvania State University, University Park, State College, PA 16802 USA
| | - James G. Elkins
- BioEnergy Sciences Center, Oak Ridge, TN 37830 USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
| | - Steven D. Brown
- BioEnergy Sciences Center, Oak Ridge, TN 37830 USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
- Present Address: LanzaTech, Inc., Skokie, IL 60077 USA
| | - Lee R. Lynd
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755 USA
- BioEnergy Sciences Center, Oak Ridge, TN 37830 USA
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12
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Chen L, Ge X. Correlation Between Size and Activity Enhancement of Recombinantly Assembled Cellulosomes. Appl Biochem Biotechnol 2018; 186:937-948. [PMID: 29797297 DOI: 10.1007/s12010-018-2786-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 05/15/2018] [Indexed: 11/25/2022]
Abstract
As multienzyme complexes, cellulosomes hydrolyze cellulosic biomass with high efficiency, which is believed to be attributed to either one or both factors: (1) synergy among the catalytic and substrate-binding entities and (2) the large size of cellulosome complexes. Although the former factor has been extensively documented, the correlation between size and specific activity of cellulosomes is still elusive to date. In this study, primary and secondary scaffoldins with 1, 3, or 5 copies of type I/II cohesin domains were recombinantly synthesized and various cellulosomes carrying 1, 3, 5, 9, 15, or 25 molecules of cellulase mixtures of family 5, 9, and 48 glycoside hydrolases were assembled. In addition, the assembled complex was annexed to cellulose with the aid of a family 3a carbohydrate-binding module (CBM3a). Measuring cellulolytic hydrolysis activities of assembled cellulosomes on crystalline Avicel revealed that higher degree of cellulosome complexity resulted in more efficient cellulose hydrolysis with plateaued synergic effects after the cellulosome size reaches certain degree.
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Affiliation(s)
- Long Chen
- Department of Chemical and Environmental Engineering, University of California Riverside, 900 University Ave, Riverside, CA, 92512, USA
| | - Xin Ge
- Department of Chemical and Environmental Engineering, University of California Riverside, 900 University Ave, Riverside, CA, 92512, USA.
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13
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14
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Nguyen STC, Freund HL, Kasanjian J, Berlemont R. Function, distribution, and annotation of characterized cellulases, xylanases, and chitinases from CAZy. Appl Microbiol Biotechnol 2018; 102:1629-1637. [PMID: 29359269 DOI: 10.1007/s00253-018-8778-y] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 01/06/2018] [Accepted: 01/09/2018] [Indexed: 11/30/2022]
Abstract
The enzymatic deconstruction of structural polysaccharides, which relies on the production of specific glycoside hydrolases (GHs), is an essential process across environments. Over the past few decades, researchers studying the diversity and evolution of these enzymes have isolated and biochemically characterized thousands of these proteins. The carbohydrate-active enzymes database (CAZy) lists these proteins and provides some metadata. Here, the sequences and metadata of characterized sequences derived from GH families associated with the deconstruction of cellulose, xylan, and chitin were collected and discussed. First, although few polyspecific enzymes are identified, characterized GH families are mostly monospecific. Next, the taxonomic distribution of characterized GH mirrors the distribution of identified sequences in sequenced genomes. This provides a rationale for connecting the identification of GH sequences to specific reactions or lineages. Finally, we tested the annotation of the characterized GHs using HMM scan and the protein families database (Pfam). The vast majority of GHs targeting cellulose, xylan, and chitin can be identified using this publicly accessible approach.
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Affiliation(s)
- Stanley T C Nguyen
- Department of Biological Sciences, California State University-Long Beach, 1250 Bellflower Blvd., Long Beach, CA, 90840-9502, USA
| | - Hannah L Freund
- Department of Biological Sciences, California State University-Long Beach, 1250 Bellflower Blvd., Long Beach, CA, 90840-9502, USA
| | - Joshua Kasanjian
- Department of Biological Sciences, California State University-Long Beach, 1250 Bellflower Blvd., Long Beach, CA, 90840-9502, USA
| | - Renaud Berlemont
- Department of Biological Sciences, California State University-Long Beach, 1250 Bellflower Blvd., Long Beach, CA, 90840-9502, USA.
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Verdorfer T, Bernardi RC, Meinhold A, Ott W, Luthey-Schulten Z, Nash MA, Gaub HE. Combining in Vitro and in Silico Single-Molecule Force Spectroscopy to Characterize and Tune Cellulosomal Scaffoldin Mechanics. J Am Chem Soc 2017; 139:17841-17852. [PMID: 29058444 PMCID: PMC5737924 DOI: 10.1021/jacs.7b07574] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Cellulosomes are polyprotein machineries that efficiently degrade cellulosic material. Crucial to their function are scaffolds consisting of highly homologous cohesin domains, which serve a dual role by coordinating a multiplicity of enzymes as well as anchoring the microbe to its substrate. Here we combined two approaches to elucidate the mechanical properties of the main scaffold ScaA of Acetivibrio cellulolyticus. A newly developed parallelized one-pot in vitro transcription-translation and protein pull-down protocol enabled high-throughput atomic force microscopy (AFM)-based single-molecule force spectroscopy (SMFS) measurements of all cohesins from ScaA with a single cantilever, thus promising improved relative force comparability. Albeit very similar in sequence, the hanging cohesins showed considerably lower unfolding forces than the bridging cohesins, which are subjected to force when the microbe is anchored to its substrate. Additionally, all-atom steered molecular dynamics (SMD) simulations on homology models offered insight into the process of cohesin unfolding under force. Based on the differences among the individual force propagation pathways and their associated correlation communities, we designed mutants to tune the mechanical stability of the weakest hanging cohesin. The proposed mutants were tested in a second high-throughput AFM SMFS experiment revealing that in one case a single alanine to glycine point mutation suffices to more than double the mechanical stability. In summary, we have successfully characterized the force induced unfolding behavior of all cohesins from the scaffoldin ScaA, as well as revealed how small changes in sequence can have large effects on force resilience in cohesin domains. Our strategy provides an efficient way to test and improve the mechanical integrity of protein domains in general.
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Affiliation(s)
- Tobias Verdorfer
- Lehrstuhl für Angewandte Physik and Center for Nanoscience, Ludwig-Maximilians-Universität, 80799 Munich, Germany
| | - Rafael C Bernardi
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Aylin Meinhold
- Lehrstuhl für Angewandte Physik and Center for Nanoscience, Ludwig-Maximilians-Universität, 80799 Munich, Germany
| | - Wolfgang Ott
- Lehrstuhl für Angewandte Physik and Center for Nanoscience, Ludwig-Maximilians-Universität, 80799 Munich, Germany
| | - Zaida Luthey-Schulten
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Michael A Nash
- Department of Chemistry, University of Basel, 4056 Basel, Switzerland
- Department of Biosystems Science and Engineering, Swiss Federal Institute of Technology (ETH Zurich), 4058 Basel, Switzerland
| | - Hermann E Gaub
- Lehrstuhl für Angewandte Physik and Center for Nanoscience, Ludwig-Maximilians-Universität, 80799 Munich, Germany
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Setter-Lamed E, Moraïs S, Stern J, Lamed R, Bayer EA. Modular Organization of the Thermobifida fusca Exoglucanase Cel6B Impacts Cellulose Hydrolysis and Designer Cellulosome Efficiency. Biotechnol J 2017; 12. [PMID: 28901714 DOI: 10.1002/biot.201700205] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 09/06/2017] [Indexed: 11/09/2022]
Abstract
Cellulose deconstruction can be achieved by three distinct enzymatic paradigms: free enzymes, multifunctional enzymes, and self-assembled, multi-enzyme complexes (cellulosomes). To study their comparative efficiency, the simple and efficient cellulolytic system of the aerobic bacterium, Thermobifida fusca, is developed as an enzymatic model. In previous studies, most of its cellulases are successfully converted to the cellulosomal mode and exhibited high cellulolytic activities, except for Cel6B, a key exoglucanase of the T. fusca enzymatic system. Here, the impact of the modular organization of Cel6B on enzymatic activity is investigated. The position of the cellulose-binding module (CBM), its family and linker segment are shown to affect activity. Surprisingly, exchange of the native family-2 CBM to family-3 generates an increase in Cel6B activity on cellulosic substrates. Conversion of Cel6B to the cellulosomal mode by fusing a cohesin to the catalytic module enables formation of divalent enzyme complexes with dockerin-bearing enzymes. The resultant pseudo-cellulosomes, containing Cel6B combined with endoglucanase Cel5A, exhibits enhanced enzymatic activity, compared to mixtures of wild-type enzymes or bifunctional enzymes, unlike similar pseudo-cellulosomes containing endoglucanase Cel6A or proccessive endoglucanase Cel9A. Insight into the different enzymatic paradigms benefits ongoing development of efficient cellulolytic systems for conversion of plant-derived biomass into valuable sugars. NOVELTY STATEMENT The protein engineering of the modular arrangement of a key exoglucanase from a highly cellulolytic bacterium, Thermobifida fusca, served to explore and compare three major enzymatic paradigms for cellulose degradation. This approach revealed highly active chimaeric forms of the exoglucanase that act in synergy together with a potent endoglucanase in bifunctional enzymes or divalent pseudo-cellulosome-like complexes. Such engineered enzymes could be further integrated into larger enzymatic complexes, thereby providing a significant step forward towards conversion of the entire T. fusca free cellulolytic system into the cellulosomal modex and the enhanced conversion of cellulosic biomass into soluble sugars.
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Affiliation(s)
- Eva Setter-Lamed
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Sarah Moraïs
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Johanna Stern
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Raphael Lamed
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, Israel
| | - Edward A Bayer
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
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Malgas S, Thoresen M, van Dyk JS, Pletschke BI. Time dependence of enzyme synergism during the degradation of model and natural lignocellulosic substrates. Enzyme Microb Technol 2017; 103:1-11. [DOI: 10.1016/j.enzmictec.2017.04.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 04/18/2017] [Accepted: 04/21/2017] [Indexed: 10/19/2022]
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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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Abstract
Designer cellulosomes consist of chimeric cohesin-bearing scaffoldins for the controlled incorporation of recombinant dockerin-containing enzymes. The largest designer cellulosome reported to date is a chimeric scaffoldin that contains 6 cohesins. This scaffoldin represented a technical limit of sorts, since adding another cohesin proved problematic, owing to resultant low expression levels, instability (cleavage) of the scaffoldin polypeptide, and limited numbers of available cohesin-dockerin specificities—the hallmark of designer cellulosomes. Nevertheless, increasing the number of enzymes integrated into designer cellulosomes is critical, in order to further enhance degradation of plant cell wall material. Adaptor scaffoldins comprise an intermediate type of scaffoldin that can both incorporate various enzymes and attach to an additional scaffoldin. Using this strategy, we constructed an efficient form of adaptor scaffoldin that possesses three type I cohesins for enzyme integration, a single type II dockerin for interaction with an additional scaffoldin, and a carbohydrate-binding module for targeting to the cellulosic substrate. In parallel, we designed a hexavalent scaffoldin capable of connecting to the adaptor scaffoldin by the incorporation of an appropriate type II cohesin. The resultant extended designer cellulosome comprised 8 recombinant enzymes—4 xylanases and 4 cellulases—thereby representing a potent enzymatic cocktail for solubilization of natural lignocellulosic substrates. The contribution of the adaptor scaffoldin clearly demonstrated that proximity between the two scaffoldins and their composite set of enzymes is crucial for optimized degradation. After 72 h of incubation, the performance of the extended designer cellulosome was determined to be approximately 70% compared to that of native cellulosomes. Plant cell wall residues represent a major source of renewable biomass for the production of biofuels such as ethanol via breakdown to soluble sugars. The natural microbial degradation process, however, is inefficient for achieving cost-effective processes in the conversion of plant-derived biomass to biofuels, either from dedicated crops or human-generated cellulosic wastes. The accumulation of the latter is considered a major environmental pollutant. The development of designer cellulosome nanodevices for enhanced plant cell wall degradation thus has major impacts in the fields of environmental pollution, bioenergy production, and biotechnology in general. The findings reported in this article comprise a true breakthrough in our capacity to produce extended designer cellulosomes via synthetic biology means, thus enabling the assembly of higher-order complexes that can supersede the number of enzymes included in a single multienzyme complex.
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Xu Q, Resch MG, Podkaminer K, Yang S, Baker JO, Donohoe BS, Wilson C, Klingeman DM, Olson DG, Decker SR, Giannone RJ, Hettich RL, Brown SD, Lynd LR, Bayer EA, Himmel ME, Bomble YJ. Dramatic performance of Clostridium thermocellum explained by its wide range of cellulase modalities. SCIENCE ADVANCES 2016; 2:e1501254. [PMID: 26989779 PMCID: PMC4788478 DOI: 10.1126/sciadv.1501254] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 11/30/2015] [Indexed: 05/18/2023]
Abstract
Clostridium thermocellum is the most efficient microorganism for solubilizing lignocellulosic biomass known to date. Its high cellulose digestion capability is attributed to efficient cellulases consisting of both a free-enzyme system and a tethered cellulosomal system wherein carbohydrate active enzymes (CAZymes) are organized by primary and secondary scaffoldin proteins to generate large protein complexes attached to the bacterial cell wall. This study demonstrates that C. thermocellum also uses a type of cellulosomal system not bound to the bacterial cell wall, called the "cell-free" cellulosomal system. The cell-free cellulosome complex can be seen as a "long range cellulosome" because it can diffuse away from the cell and degrade polysaccharide substrates remotely from the bacterial cell. The contribution of these two types of cellulosomal systems in C. thermocellum was elucidated by characterization of mutants with different combinations of scaffoldin gene deletions. The primary scaffoldin, CipA, was found to play the most important role in cellulose degradation by C. thermocellum, whereas the secondary scaffoldins have less important roles. Additionally, the distinct and efficient mode of action of the C. thermocellum exoproteome, wherein the cellulosomes splay or divide biomass particles, changes when either the primary or secondary scaffolds are removed, showing that the intact wild-type cellulosomal system is necessary for this essential mode of action. This new transcriptional and proteomic evidence shows that a functional primary scaffoldin plays a more important role compared to secondary scaffoldins in the proper regulation of CAZyme genes, cellodextrin transport, and other cellular functions.
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Affiliation(s)
- Qi Xu
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
- BioEnergy Science Center, Oak Ridge, TN 37831, USA
| | - Michael G. Resch
- BioEnergy Science Center, Oak Ridge, TN 37831, USA
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Kara Podkaminer
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
- BioEnergy Science Center, Oak Ridge, TN 37831, USA
| | - Shihui Yang
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - John O. Baker
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
- BioEnergy Science Center, Oak Ridge, TN 37831, USA
| | - Bryon S. Donohoe
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
- BioEnergy Science Center, Oak Ridge, TN 37831, USA
| | - Charlotte Wilson
- BioEnergy Science Center, Oak Ridge, TN 37831, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Dawn M. Klingeman
- BioEnergy Science Center, Oak Ridge, TN 37831, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Daniel G. Olson
- BioEnergy Science Center, Oak Ridge, TN 37831, USA
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA
| | - Stephen R. Decker
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
- BioEnergy Science Center, Oak Ridge, TN 37831, USA
| | - Richard J. Giannone
- BioEnergy Science Center, Oak Ridge, TN 37831, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Robert L. Hettich
- BioEnergy Science Center, Oak Ridge, TN 37831, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Steven D. Brown
- BioEnergy Science Center, Oak Ridge, TN 37831, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Lee R. Lynd
- BioEnergy Science Center, Oak Ridge, TN 37831, USA
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA
| | | | - Michael E. Himmel
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
- BioEnergy Science Center, Oak Ridge, TN 37831, USA
| | - Yannick J. Bomble
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
- BioEnergy Science Center, Oak Ridge, TN 37831, USA
- Corresponding author. E-mail:
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21
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Talamantes D, Biabini N, Dang H, Abdoun K, Berlemont R. Natural diversity of cellulases, xylanases, and chitinases in bacteria. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:133. [PMID: 27366206 PMCID: PMC4928363 DOI: 10.1186/s13068-016-0538-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Accepted: 05/31/2016] [Indexed: 05/16/2023]
Abstract
BACKGROUND Glycoside hydrolases (GH) targeting cellulose, xylan, and chitin are common in the bacterial genomes that have been sequenced. Little is known, however, about the architecture of multi-domain and multi-activity glycoside hydrolases. In these enzymes, combined catalytic domains act synergistically and thus display overall improved catalytic efficiency, making these proteins of high interest for the biofuel technology industry. RESULTS Here, we identify the domain organization in 40,946 proteins targeting cellulose, xylan, and chitin derived from 11,953 sequenced bacterial genomes. These bacteria are known to be capable, or to have the potential, to degrade polysaccharides, or are newly identified potential degraders (e.g., Actinospica, Hamadaea, Cystobacter, and Microbispora). Most of the proteins we identified contain a single catalytic domain that is frequently associated with an accessory non-catalytic domain. Regarding multi-domain proteins, we found that many bacterial strains have unique GH protein architectures and that the overall protein organization is not conserved across most genera. We identified 217 multi-activity proteins with at least two GH domains for cellulose, xylan, and chitin. Of these proteins, 211 have GH domains targeting similar or associated substrates (i.e., cellulose and xylan), whereas only six proteins target both cellulose and chitin. Fifty-two percent of multi-activity GHs are hetero-GHs. Finally, GH6, -10, -44 and -48 domains were mostly C-terminal; GH9, -11, -12, and -18 were mostly N-terminal; and GH5 domains were either N- or C-terminal. CONCLUSION We identified 40,946 multi-domain/multi-activity proteins targeting cellulase, chitinase, and xylanase in bacterial genomes and proposed new candidate lineages and protein architectures for carbohydrate processing that may play a role in biofuel production.
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Affiliation(s)
- Darrian Talamantes
- Department of Biological Sciences, California State University, Long Beach, 1250 Bellflower Blvd., Long Beach, 90840-9502 USA
| | - Nazmehr Biabini
- Department of Biological Sciences, California State University, Long Beach, 1250 Bellflower Blvd., Long Beach, 90840-9502 USA
| | - Hoang Dang
- Department of Biological Sciences, California State University, Long Beach, 1250 Bellflower Blvd., Long Beach, 90840-9502 USA
| | - Kenza Abdoun
- Department of Biological Sciences, California State University, Long Beach, 1250 Bellflower Blvd., Long Beach, 90840-9502 USA
| | - Renaud Berlemont
- Department of Biological Sciences, California State University, Long Beach, 1250 Bellflower Blvd., Long Beach, 90840-9502 USA
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22
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Sun Q, Chen W. HaloTag mediated artificial cellulosome assembly on a rolling circle amplification DNA template for efficient cellulose hydrolysis. Chem Commun (Camb) 2016; 52:6701-4. [DOI: 10.1039/c6cc02035f] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
We report here the generation of artificial cellulosomes onto a DNA scaffold using the self-labeling HaloTag for DNA conjugation. Rolling circle amplification multiplexing templates were used to increase the complexity of this system with higher efficiency observed.
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Affiliation(s)
- Qing Sun
- Department of Chemical and Biomolecular Engineering
- University of Delaware
- Newark
- USA
| | - Wilfred Chen
- Department of Chemical and Biomolecular Engineering
- University of Delaware
- Newark
- USA
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23
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Hong W, Zhang J, Feng Y, Mohr G, Lambowitz AM, Cui GZ, Liu YJ, Cui Q. The contribution of cellulosomal scaffoldins to cellulose hydrolysis by Clostridium thermocellum analyzed by using thermotargetrons. BIOTECHNOLOGY FOR BIOFUELS 2014; 7:80. [PMID: 24955112 PMCID: PMC4045903 DOI: 10.1186/1754-6834-7-80] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2013] [Accepted: 05/13/2014] [Indexed: 05/23/2023]
Abstract
BACKGROUND Clostridium thermocellum is a thermophilic anaerobic bacterium that degrades cellulose by using a highly effective cellulosome, a macromolecular complex consisting of multiple cellulose degrading enzymes organized and attached to the cell surface by non-catalytic scaffoldins. However, due largely to lack of efficient methods for genetic manipulation of C. thermocellum, it is still unclear how the different scaffoldins and their functional modules contribute to cellulose hydrolysis. RESULTS We constructed C. thermocellum mutants with the primary scaffoldin CipA (cellulosome-integrating protein A) truncated at different positions or lacking four different secondary scaffoldins by using a newly developed thermotargetron system, and we analyzed cellulose hydrolysis, cellulosome formation, and cellulose binding of the mutants. A CipA truncation that deletes six type I cohesin modules, which bind cellulolytic enzymes, decreased cellulose hydrolysis rates by 46%, and slightly longer truncations that also delete the carbohydrate binding module decreased rates by 89 to 92%, indicating strong cellulosome-substrate synergy. By contrast, a small CipA truncation that deletes only the C-terminal type II dockerin (XDocII) module detached cellulosomes from the cells, but decreased cellulose hydrolysis rates by only 9%, suggesting a relatively small contribution of cellulosome-cell synergy. Disruptants lacking any of four different secondary scaffoldins (OlpB, 7CohII, Orf2p, or SdbA) showed moderately decreased cellulose hydrolysis rates, suggesting additive contributions. Surprisingly, the CipA-ΔXDocII mutant, which lacks cell-associated polycellulosomes, adheres to cellulose almost as strongly as wild-type cells, revealing an alternate, previously unknown cellulose-binding mechanism. CONCLUSIONS Our results emphasize the important role of cellulosome-substrate synergy in cellulose degradation, demonstrate a contribution of secondary scaffoldins, and suggest a previously unknown, non-cellulosomal system for binding insoluble cellulose. Our findings provide new insights into cellulosome function and impact genetic engineering of microorganisms to enhance bioconversions of cellulose substrates.
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Affiliation(s)
- Wei Hong
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, P R China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100049, P R China
| | - Jie Zhang
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, P R China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100049, P R China
| | - Yingang Feng
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, P R China
| | - Georg Mohr
- Departments of Molecular Biosciences and Chemistry, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Alan M Lambowitz
- Departments of Molecular Biosciences and Chemistry, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Gu-Zhen Cui
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, P R China
| | - Ya-Jun Liu
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, P R China
| | - Qiu Cui
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, P R China
- Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, P R China
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Harris PV, Xu F, Kreel NE, Kang C, Fukuyama S. New enzyme insights drive advances in commercial ethanol production. Curr Opin Chem Biol 2014; 19:162-70. [DOI: 10.1016/j.cbpa.2014.02.015] [Citation(s) in RCA: 142] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Revised: 02/08/2014] [Accepted: 02/12/2014] [Indexed: 01/19/2023]
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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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Vazana Y, Barak Y, Unger T, Peleg Y, Shamshoum M, Ben-Yehezkel T, Mazor Y, Shapiro E, Lamed R, Bayer EA. A synthetic biology approach for evaluating the functional contribution of designer cellulosome components to deconstruction of cellulosic substrates. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:182. [PMID: 24341331 PMCID: PMC3878649 DOI: 10.1186/1754-6834-6-182] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Accepted: 11/27/2013] [Indexed: 05/04/2023]
Abstract
BACKGROUND Select cellulolytic bacteria produce multi-enzymatic cellulosome complexes that bind to the plant cell wall and catalyze its efficient degradation. The multi-modular interconnecting cellulosomal subunits comprise dockerin-containing enzymes that bind cohesively to cohesin-containing scaffoldins. The organization of the modules into functional polypeptides is achieved by intermodular linkers of different lengths and composition, which provide flexibility to the complex and determine its overall architecture. RESULTS Using a synthetic biology approach, we systematically investigated the spatial organization of the scaffoldin subunit and its effect on cellulose hydrolysis by designing a combinatorial library of recombinant trivalent designer scaffoldins, which contain a carbohydrate-binding module (CBM) and 3 divergent cohesin modules. The positions of the individual modules were shuffled into 24 different arrangements of chimaeric scaffoldins. This basic set was further extended into three sub-sets for each arrangement with intermodular linkers ranging from zero (no linkers), 5 (short linkers) and native linkers of 27-35 amino acids (long linkers). Of the 72 possible scaffoldins, 56 were successfully cloned and 45 of them expressed, representing 14 full sets of chimaeric scaffoldins. The resultant 42-component scaffoldin library was used to assemble designer cellulosomes, comprising three model C. thermocellum cellulases. Activities were examined using Avicel as a pure microcrystalline cellulose substrate and pretreated cellulose-enriched wheat straw as a model substrate derived from a native source. All scaffoldin combinations yielded active trivalent designer cellulosome assemblies on both substrates that exceeded the levels of the free enzyme systems. A preferred modular arrangement for the trivalent designer scaffoldin was not observed for the three enzymes used in this study, indicating that they could be integrated at any position in the designer cellulosome without significant effect on cellulose-degrading activity. Designer cellulosomes assembled with the long-linker scaffoldins achieved higher levels of activity, compared to those assembled with short-and no-linker scaffoldins. CONCLUSIONS The results demonstrate the robustness of the cellulosome system. Long intermodular scaffoldin linkers are preferable, thus leading to enhanced degradation of cellulosic substrates, presumably due to the increased flexibility and spatial positioning of the attached enzymes in the complex. These findings provide a general basis for improved designer cellulosome systems as a platform for bioethanol production.
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Affiliation(s)
- Yael Vazana
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yoav Barak
- Chemical Research Support, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Tamar Unger
- Structural Proteomics, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yoav Peleg
- Structural Proteomics, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Melina Shamshoum
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Tuval Ben-Yehezkel
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
- Department of Computer Science and Applied Mathematics, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yair Mazor
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
- Department of Computer Science and Applied Mathematics, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ehud Shapiro
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
- Department of Computer Science and Applied Mathematics, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Raphael Lamed
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Edward A Bayer
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
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