151
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López-Mondéjar R, Algora C, Baldrian P. Lignocellulolytic systems of soil bacteria: A vast and diverse toolbox for biotechnological conversion processes. Biotechnol Adv 2019; 37:107374. [DOI: 10.1016/j.biotechadv.2019.03.013] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 03/06/2019] [Accepted: 03/21/2019] [Indexed: 12/12/2022]
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152
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Schmuck B, Gudmundsson M, Härd T, Sandgren M. Coupled chemistry kinetics demonstrate the utility of functionalized Sup35 amyloid nanofibrils in biocatalytic cascades. J Biol Chem 2019; 294:14966-14977. [PMID: 31416835 PMCID: PMC6791322 DOI: 10.1074/jbc.ra119.008455] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 08/14/2019] [Indexed: 01/06/2023] Open
Abstract
Concerns over the environment are a central driver for designing cell-free enzymatic cascade reactions that synthesize non-petrol-based commodity compounds. An often-suggested strategy that would demonstrate the economic competitiveness of this technology is recycling of valuable enzymes through their immobilization. For this purpose, amyloid nanofibrils are an ideal scaffold to realize chemistry-free covalent enzyme immobilization on a material that offers a large surface area. However, in most instances, only single enzyme-functionalized amyloid fibrils have so far been studied. To embark on the next stage, here we displayed xylanase A, β-xylosidase, and an aldose sugar dehydrogenase on Sup35(1-61) nanofibrils to convert beechwood xylan to xylonolactone. We characterized this enzymatic cascade by measuring the time-dependent accumulation of xylose, xylooligomers, and xylonolactone. Furthermore, we studied the effects of relative enzyme concentrations, pH, temperature, and agitation on product formation. Our investigations revealed that a modular cascade with a mixture of xylanase and β-xylosidase, followed by product removal and separate oxidation of xylose with the aldose sugar dehydrogenase, is more productive than an enzyme mix containing all of these enzymes together. Moreover, we found that the nanofibril-coupled enzymes do not lose activity compared with their native state. These findings provide proof of concept of the feasibility of functionalized Sup35(1-61) fibrils as a molecular scaffold for biocatalytic cascades consisting of reusable enzymes that can be used in biotechnology.
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Affiliation(s)
- Benjamin Schmuck
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Box 7015, 750 07 Uppsala, Sweden
| | - Mikael Gudmundsson
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Box 7015, 750 07 Uppsala, Sweden
| | - Torleif Härd
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Box 7015, 750 07 Uppsala, Sweden
| | - Mats Sandgren
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Box 7015, 750 07 Uppsala, Sweden
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153
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Lee FH, Wan SY, Foo HL, Loh TC, Mohamad R, Abdul Rahim R, Idrus Z. Comparative Study of Extracellular Proteolytic, Cellulolytic, and Hemicellulolytic Enzyme Activities and Biotransformation of Palm Kernel Cake Biomass by Lactic Acid Bacteria Isolated from Malaysian Foods. Int J Mol Sci 2019; 20:E4979. [PMID: 31600952 PMCID: PMC6834149 DOI: 10.3390/ijms20204979] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 08/30/2019] [Indexed: 02/07/2023] Open
Abstract
Biotransformation via solid state fermentation (SSF) mediated by microorganisms is a promising approach to produce useful products from agricultural biomass. Lactic acid bacteria (LAB) that are commonly found in fermented foods have been shown to exhibit extracellular proteolytic, β-glucosidase, β-mannosidase, and β-mannanase activities. Therefore, extracellular proteolytic, cellulolytic, and hemicellulolytic enzyme activities of seven Lactobacillus plantarum strains (a prominent species of LAB) isolated from Malaysian foods were compared in this study. The biotransformation of palm kernel cake (PKC) biomass mediated by selected L. plantarum strains was subsequently conducted. The results obtained in this study exhibited the studied L. plantarum strains produced versatile multi extracellular hydrolytic enzyme activities that were active from acidic to alkaline pH conditions. The highest total score of extracellular hydrolytic enzyme activities were recorded by L. plantarum RI11, L. plantarum RG11, and L. plantarum RG14. Therefore, they were selected for the subsequent biotransformation of PKC biomass via SSF. The hydrolytic enzyme activities of treated PKC extract were compared for each sampling interval. The scanning electron microscopy analyses revealed the formation of extracellular matrices around L. plantarum strains attached to the surface of PKC biomass during SSF, inferring that the investigated L. plantarum strains have the capability to grow on PKC biomass and perform synergistic secretions of various extracellular proteolytic, cellulolytic, and hemicellulolytic enzymes that were essential for the effective biodegradation of PKC. The substantial growth of selected L. plamtraum strains on PKC during SSF revealed the promising application of selected L. plantarum strains as a biotransformation agent for cellulosic biomass.
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Affiliation(s)
- Fu Haw Lee
- Institute of Tropical Agriculture, Universiti Putra Malaysia, Serdang 43400 UPM, Selangor, Malaysia.
| | - Suet Ying Wan
- Department of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400 UPM, Selangor, Malaysia.
| | - Hooi Ling Foo
- Department of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400 UPM, Selangor, Malaysia.
- Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400 UPM, Selangor, Malaysia.
| | - Teck Chwen Loh
- Institute of Tropical Agriculture, Universiti Putra Malaysia, Serdang 43400 UPM, Selangor, Malaysia.
- Department of Animal Sciences, Faculty of Agriculture, Serdang 43400 UPM, Selangor, Malaysia.
| | - Rosfarizan Mohamad
- Department of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400 UPM, Selangor, Malaysia.
- Institute of Tropical Forestry and Forest Products, Universiti Putra Malaysia, Serdang 43400 UPM, Selangor, Malaysia.
| | - Raha Abdul Rahim
- Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400 UPM, Selangor, Malaysia.
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400 UPM, Selangor, Malaysia.
| | - Zulkifli Idrus
- Institute of Tropical Agriculture, Universiti Putra Malaysia, Serdang 43400 UPM, Selangor, Malaysia.
- Department of Animal Sciences, Faculty of Agriculture, Serdang 43400 UPM, Selangor, Malaysia.
- Halal Products Research Institute, Universiti Putra Malaysia, Serdang 43400 UPM, Selangor, Malaysia.
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154
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Lillington SP, Leggieri PA, Heom KA, O'Malley MA. Nature's recyclers: anaerobic microbial communities drive crude biomass deconstruction. Curr Opin Biotechnol 2019; 62:38-47. [PMID: 31593910 DOI: 10.1016/j.copbio.2019.08.015] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 08/25/2019] [Accepted: 08/29/2019] [Indexed: 12/13/2022]
Abstract
Microbial communities within anaerobic ecosystems have evolved to degrade and recycle carbon throughout the earth. A number of strains have been isolated from anaerobic microbial communities, which are rich in carbohydrate active enzymes (CAZymes) to liberate fermentable sugars from crude plant biomass (lignocellulose). However, natural anaerobic communities host a wealth of microbial diversity that has yet to be harnessed for biotechnological applications to hydrolyze crude biomass into sugars and value-added products. This review highlights recent advances in 'omics' techniques to sequence anaerobic microbial genomes, decipher microbial membership, and characterize CAZyme diversity in anaerobic microbiomes. With a focus on the herbivore rumen, we further discuss methods to discover new CAZymes, including those found within multi-enzyme fungal cellulosomes. Emerging techniques to characterize the interwoven metabolism and spatial interactions between anaerobes are also reviewed, which will prove critical to developing a predictive understanding of anaerobic communities to guide in microbiome engineering.
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Affiliation(s)
- Stephen P Lillington
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, United States
| | - Patrick A Leggieri
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, United States
| | - Kellie A Heom
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, United States
| | - Michelle A O'Malley
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, United States.
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155
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The Cellulosome Paradigm in An Extreme Alkaline Environment. Microorganisms 2019; 7:microorganisms7090347. [PMID: 31547347 PMCID: PMC6780208 DOI: 10.3390/microorganisms7090347] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 09/01/2019] [Accepted: 09/10/2019] [Indexed: 11/19/2022] Open
Abstract
Rapid decomposition of plant biomass in soda lakes is associated with microbial activity of anaerobic cellulose-degrading communities. The alkaliphilic bacterium, Clostridium alkalicellulosi, is the single known isolate from a soda lake that demonstrates cellulolytic activity. This microorganism secretes cellulolytic enzymes that degrade cellulose under anaerobic and alkaliphilic conditions. A previous study indicated that the protein fraction of cellulose-grown cultures showed similarities in composition and size to known components of the archetypical cellulosome Clostridium thermocellum. Bioinformatic analysis of the C. alkalicellulosi draft genome sequence revealed 44 cohesins, organized into 22 different scaffoldins, and 142 dockerin-containing proteins. The modular organization of the scaffoldins shared similarities to those of C. thermocellum and Acetivibrio cellulolyticus, whereas some exhibited unconventional arrangements containing peptidases and oxidative enzymes. The binding interactions among cohesins and dockerins assessed by ELISA, revealed a complex network of cellulosome assemblies and suggested both cell-associated and cell-free systems. Based on these interactions, C. alkalicellulosi cellulosomal systems have the genetic potential to create elaborate complexes, which could integrate up to 105 enzymatic subunits. The alkalistable C. alkalicellulosi cellulosomal systems and their enzymes would be amenable to biotechnological processes, such as treatment of lignocellulosic biomass following prior alkaline pretreatment.
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156
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Zhang C, Too HP. Revalorizing Lignocellulose for the Production of Natural Pharmaceuticals and Other High Value Bioproducts. Curr Med Chem 2019; 26:2475-2484. [PMID: 28901274 DOI: 10.2174/0929867324666170912095755] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 06/02/2017] [Accepted: 08/25/2017] [Indexed: 01/27/2023]
Abstract
Lignocellulose is the most abundant renewable natural resource on earth and has been successfully used for the production of biofuels. A significant challenge is to develop cost-effective, environmentally friendly and efficient processes for the conversion of lignocellulose materials into suitable substrates for biotransformation. A number of approaches have been explored to convert lignocellulose into sugars, e.g. combining chemical pretreatment and enzymatic hydrolysis. In nature, there are organisms that can transform the complex lignocellulose efficiently, such as wood-degrading fungi (brown rot and white rot fungi), bacteria (e.g. Clostridium thermocellum), arthropods (e.g. termite) and certain animals (e.g. ruminant). Here, we highlight recent case studies of the natural degraders and the mechanisms involved, providing new utilities in biotechnology. The sugars produced from such biotransformations can be used in metabolic engineering and synthetic biology for the complete biosynthesis of natural medicine. The unique opportunities in using lignocellulose directly to produce natural drug molecules with either using mushroom and/or 'industrial workhorse' organisms (Escherichia coli and Saccharomyces cerevisiae) will be discussed.
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Affiliation(s)
- Congqiang Zhang
- Biotransformation Innovation Platform (BioTrans), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Heng-Phon Too
- Biotransformation Innovation Platform (BioTrans), Agency for Science, Technology and Research (A*STAR), Singapore.,Department of Biochemistry, National University of Singapore, Singapore
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157
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Kari J, Christensen SJ, Andersen M, Baiget SS, Borch K, Westh P. A practical approach to steady-state kinetic analysis of cellulases acting on their natural insoluble substrate. Anal Biochem 2019; 586:113411. [PMID: 31520594 DOI: 10.1016/j.ab.2019.113411] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 08/26/2019] [Accepted: 08/28/2019] [Indexed: 10/26/2022]
Abstract
Measurement of steady-state rates (vSS) is straightforward in standard enzymology with soluble substrate, and it has been instrumental for comparative biochemical analyses within this area. For insoluble substrate, however, experimental values of vss remain controversial, and this has strongly limited the amount and quality of comparative analyses for cellulases and other enzymes that act on the surface of an insoluble substrate. In the current work, we have measured progress curves over a wide range of conditions for two cellulases, TrCel6A and TrCel7A from Trichoderma reesei, acting on their natural, insoluble substrate, cellulose. Based on this, we consider practical compromises for the determination of experimental vSS values, and propose a basic protocol that provides representative reaction rates and is experimentally simple so that larger groups of enzymes and conditions can be readily assayed with standard laboratory equipment. We surmise that the suggested experimental approach can be useful in comparative biochemical studies of cellulases; an area that remains poorly developed.
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Affiliation(s)
- Jeppe Kari
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800, Kgs. Lyngby, Denmark
| | - Stefan Jarl Christensen
- Department of Science and Environment, Roskilde University, Universitetsvej, Build. 28.C, DK-4000, Roskilde, Denmark
| | - Morten Andersen
- Department of Science and Environment, Roskilde University, Universitetsvej, Build. 28.C, DK-4000, Roskilde, Denmark
| | | | - Kim Borch
- Novozymes A/S, Krogshøjvej 36, DK-2880, Bagsværd, Denmark
| | - Peter Westh
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800, Kgs. Lyngby, Denmark.
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158
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Bernardi RC, Durner E, Schoeler C, Malinowska KH, Carvalho BG, Bayer EA, Luthey-Schulten Z, Gaub HE, Nash MA. Mechanisms of Nanonewton Mechanostability in a Protein Complex Revealed by Molecular Dynamics Simulations and Single-Molecule Force Spectroscopy. J Am Chem Soc 2019; 141:14752-14763. [PMID: 31464132 PMCID: PMC6939381 DOI: 10.1021/jacs.9b06776] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
![]()
Can molecular dynamics
simulations predict the mechanical behavior of protein complexes?
Can simulations decipher the role of protein domains of unknown function
in large macromolecular complexes? Here, we employ a wide-sampling
computational approach to demonstrate that molecular dynamics simulations,
when carefully performed and combined with single-molecule atomic
force spectroscopy experiments, can predict and explain the behavior
of highly mechanostable protein complexes. As a test case, we studied
a previously unreported homologue from Ruminococcus flavefaciens called X-module-Dockerin (XDoc) bound to its partner Cohesin (Coh).
By performing dozens of short simulation replicas near the rupture
event, and analyzing dynamic network fluctuations, we were able to
generate large simulation statistics and directly compare them with
experiments to uncover the mechanisms involved in mechanical stabilization.
Our single-molecule force spectroscopy experiments show that the XDoc-Coh
homologue complex withstands forces up to 1 nN at loading rates of
105 pN/s. Our simulation results reveal that this remarkable
mechanical stability is achieved by a protein architecture that directs
molecular deformation along paths that run perpendicular to the pulling
axis. The X-module was found to play a crucial role in shielding the
adjacent protein complex from mechanical rupture. These mechanisms
of protein mechanical stabilization have potential applications in
biotechnology for the development of systems exhibiting shear enhanced
adhesion or tunable mechanics.
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Affiliation(s)
- Rafael C Bernardi
- Beckman Institute for Advanced Science and Technology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Ellis Durner
- Lehrstuhl für Angewandte Physik and Center for Nanoscience , Ludwig-Maximilians-Universität , 80799 Munich , Germany
| | - Constantin Schoeler
- Lehrstuhl für Angewandte Physik and Center for Nanoscience , Ludwig-Maximilians-Universität , 80799 Munich , Germany
| | - Klara H Malinowska
- Lehrstuhl für Angewandte Physik and Center for Nanoscience , Ludwig-Maximilians-Universität , 80799 Munich , Germany
| | - Bruna G Carvalho
- School of Chemical Engineering , University of Campinas , 13083-852 Campinas , Brazil
| | - Edward A Bayer
- Department of Biomolecular Sciences , Weizmann Institute of Science , 76100 Rehovot , Israel
| | - 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
| | - Hermann E Gaub
- Lehrstuhl für Angewandte Physik and Center for Nanoscience , Ludwig-Maximilians-Universität , 80799 Munich , Germany
| | - Michael A Nash
- Department of Chemistry , University of Basel , 4058 Basel , Switzerland.,Department of Biosystems Science and Engineering , ETH Zurich , 4058 Basel , Switzerland
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159
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Hu B, Zhu M. Reconstitution of cellulosome: Research progress and its application in biorefinery. Biotechnol Appl Biochem 2019; 66:720-730. [DOI: 10.1002/bab.1804] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Accepted: 08/03/2019] [Indexed: 09/01/2023]
Affiliation(s)
- Bin‐Bin Hu
- Guangdong Provincial Engineering and Technology Research Center of Biopharmaceuticals School of Biology and Biological Engineering South China University of Technology, Guangzhou Higher Education Mega Center Panyu Guangzhou People's Republic of China
- Yunnan Academy of Tobacco Agricultural Sciences Kunming People's Republic of China
- State Key Laboratory of Pulp and Paper Engineering South China University of Technology Guangzhou People's Republic of China
| | - Ming‐Jun Zhu
- Guangdong Provincial Engineering and Technology Research Center of Biopharmaceuticals School of Biology and Biological Engineering South China University of Technology, Guangzhou Higher Education Mega Center Panyu Guangzhou People's Republic of China
- State Key Laboratory of Pulp and Paper Engineering South China University of Technology Guangzhou People's Republic of China
- College of Life and Geographic Sciences Kashi University Kashi People's Republic of China
- The Key Laboratory of Ecology and Biological Resources in Yarkand Oasis at Colleges & Universities under the Department of Education of Xinjiang Uygur Autonomous Region Kashi University Kashi People's Republic of China
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160
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Ribeiro LF, Amarelle V, Alves LDF, Viana de Siqueira GM, Lovate GL, Borelli TC, Guazzaroni ME. Genetically Engineered Proteins to Improve Biomass Conversion: New Advances and Challenges for Tailoring Biocatalysts. Molecules 2019; 24:molecules24162879. [PMID: 31398877 PMCID: PMC6719137 DOI: 10.3390/molecules24162879] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 07/30/2019] [Accepted: 08/06/2019] [Indexed: 01/02/2023] Open
Abstract
Protein engineering emerged as a powerful approach to generate more robust and efficient biocatalysts for bio-based economy applications, an alternative to ecologically toxic chemistries that rely on petroleum. On the quest for environmentally friendly technologies, sustainable and low-cost resources such as lignocellulosic plant-derived biomass are being used for the production of biofuels and fine chemicals. Since most of the enzymes used in the biorefinery industry act in suboptimal conditions, modification of their catalytic properties through protein rational design and in vitro evolution techniques allows the improvement of enzymatic parameters such as specificity, activity, efficiency, secretability, and stability, leading to better yields in the production lines. This review focuses on the current application of protein engineering techniques for improving the catalytic performance of enzymes used to break down lignocellulosic polymers. We discuss the use of both classical and modern methods reported in the literature in the last five years that allowed the boosting of biocatalysts for biomass degradation.
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Affiliation(s)
- Lucas Ferreira Ribeiro
- Department of Biology, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, University of São Paulo, Ribeirão Preto 14040-901, Brazil.
| | - Vanesa Amarelle
- Department of Microbial Biochemistry and Genomics, Biological Research Institute Clemente Estable, Montevideo, PC 11600, Uruguay
| | - Luana de Fátima Alves
- Department of Biochemistry and Immunology, Faculdade de Medicina de Ribeirão Preto, University of São Paulo, Ribeirão Preto 14049-900, Brazil
| | | | - Gabriel Lencioni Lovate
- Department of Biochemistry and Immunology, Faculdade de Medicina de Ribeirão Preto, University of São Paulo, Ribeirão Preto 14049-900, Brazil
| | - Tiago Cabral Borelli
- Department of Biology, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, University of São Paulo, Ribeirão Preto 14040-901, Brazil
| | - María-Eugenia Guazzaroni
- Department of Biology, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, University of São Paulo, Ribeirão Preto 14040-901, Brazil.
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161
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Genomic and physiological analyses reveal that extremely thermophilic Caldicellulosiruptor changbaiensis deploys uncommon cellulose attachment mechanisms. J Ind Microbiol Biotechnol 2019; 46:1251-1263. [PMID: 31392469 DOI: 10.1007/s10295-019-02222-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 08/01/2019] [Indexed: 10/26/2022]
Abstract
The genus Caldicellulosiruptor is comprised of extremely thermophilic, heterotrophic anaerobes that degrade plant biomass using modular, multifunctional enzymes. Prior pangenome analyses determined that this genus is genetically diverse, with the current pangenome remaining open, meaning that new genes are expected with each additional genome sequence added. Given the high biodiversity observed among the genus Caldicellulosiruptor, we have sequenced and added a 14th species, Caldicellulosiruptor changbaiensis, to the pangenome. The pangenome now includes 3791 ortholog clusters, 120 of which are unique to C. changbaiensis and may be involved in plant biomass degradation. Comparisons between C. changbaiensis and Caldicellulosiruptor bescii on the basis of growth kinetics, cellulose solubilization and cell attachment to polysaccharides highlighted physiological differences between the two species which are supported by their respective gene inventories. Most significantly, these comparisons indicated that C. changbaiensis possesses uncommon cellulose attachment mechanisms not observed among the other strongly cellulolytic members of the genus Caldicellulosiruptor.
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162
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Moraïs S, Mizrahi I. Islands in the stream: from individual to communal fiber degradation in the rumen ecosystem. FEMS Microbiol Rev 2019; 43:362-379. [PMID: 31050730 PMCID: PMC6606855 DOI: 10.1093/femsre/fuz007] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Accepted: 04/05/2019] [Indexed: 12/20/2022] Open
Abstract
The herbivore rumen ecosystem constitutes an extremely efficient degradation machinery for the intricate chemical structure of fiber biomass, thus, enabling the hosting animal to digest its feed. The challenging task of deconstructing and metabolizing fiber is performed by microorganisms inhabiting the rumen. Since most of the ingested feed is comprised of plant fiber, these fiber-degrading microorganisms are of cardinal importance to the ecology of the rumen microbial community and to the hosting animal, and have a great impact on our environment and food sustainability. We summarize herein the enzymological fundamentals of fiber degradation, how the genes encoding these enzymes are spread across fiber-degrading microbes, and these microbes' interactions with other members of the rumen microbial community and potential effect on community structure. An understanding of these concepts has applied value for agriculture and our environment, and will also contribute to a better understanding of microbial ecology and evolution in anaerobic ecosystems.
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Affiliation(s)
- Sarah Moraïs
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Sderot Ben Gurion 1, Beer-Sheva 8499000, Israel
| | - Itzhak Mizrahi
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Sderot Ben Gurion 1, Beer-Sheva 8499000, Israel
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163
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Pratama R, Schneider D, Böer T, Daniel R. First Insights Into Bacterial Gastrointestinal Tract Communities of the Eurasian Beaver ( Castor fiber). Front Microbiol 2019; 10:1646. [PMID: 31428060 PMCID: PMC6690062 DOI: 10.3389/fmicb.2019.01646] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 07/03/2019] [Indexed: 01/08/2023] Open
Abstract
The Eurasian or European beaver (Castor fiber) is the second-largest living rodent after the capybara. It is a semi-aquatic animal known for building dams and lodges. They strictly feed on lignocellulose-rich plants and correspondingly harbor cellulolytic microbial communities in their digestive tract. In this study, the bacterial community composition, diversity, and functional profile of different gut compartments ranging from stomach to colon have been explored. A total of 277 bacterial operational taxonomic units (OTUs) at species level were obtained from the gut systems of two males (juvenile and subadult) and one subadult female beaver. In general, cecum and colon are dominated by Firmicutes and Actinobacteria. High abundance of Bacteroidetes was observed only in male juvenile beaver cecum and colon, suggesting that the bacterial composition changes with age. Within the cecum and colon, members of known cellulase-producing bacterial taxa including the families Ruminococcaceae, Lachnospiraceae, and Clostridiaceae 1 were detected. The presence of putative genes encoding cellulolytic and carbohydrate-degrading enzymes indicated also the degradation of recalcitrant plant material in both gut compartments. The bacterial community in the gut systems of the Eurasian beaver differed from that of the North American beaver. Higher abundance of Actinobacteria and lower abundances of Bacteroidetes were recorded in the Eurasian beaver. Similar differences were obtained to bacterial communities of termites and herbivorous animals such as bovine. The data presented in this study provides the first insight into bacterial communities in the gut system of the Eurasian beaver.
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Affiliation(s)
- Rahadian Pratama
- Göttingen Genomics Laboratory, Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
- Department of Biochemistry, Faculty of Mathematics and Natural Sciences, Bogor Agricultural University (IPB University), Bogor, Indonesia
| | - Dominik Schneider
- Göttingen Genomics Laboratory, Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Tim Böer
- Göttingen Genomics Laboratory, Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Rolf Daniel
- Göttingen Genomics Laboratory, Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
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164
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Abstract
Proteins are a class of nanoscale building block with remarkable chemical complexity and sophistication: their diverse functions, shapes, and symmetry as well as atomically monodisperse structures far surpass the range of conventional nanoparticles that can be accessed synthetically. The chemical topologies of proteins that drive their assembly into materials are central to their functions in nature. However, despite the importance of protein materials in biology, efforts to harness these building blocks synthetically to engineer new materials have been impeded by the chemical complexity of protein surfaces, making it difficult to reliably design protein building blocks that can be robustly transformed into targeted materials. Here we describe our work aimed at exploiting a simple but important concept: if one could exchange complex protein-protein interactions with well-defined and programmable DNA-DNA interactions, one could control the assembly of proteins into structurally well-defined oligomeric and polymeric materials and three-dimensional crystals. As a class of nanoscale building block, proteins with surface DNA modifications have a vast design space that exceeds what is practically and conceptually possible with their inorganic counterparts: the sequences of the DNA and protein and the chemical nature and position of DNA attachment all play roles in dictating the assembly behavior of protein-DNA conjugates. We summarize how each of these design parameters can influence structural outcome, beginning with proteins with a single surface DNA modification, where energy barriers between protein monomers can be tuned through the sequence and secondary structure of the oligonucleotide. We then explore challenges and progress in designing directional interactions and valency on protein surfaces. The directional binding properties of protein-DNA conjugates are ultimately imposed by the amino acid sequence of the protein, which defines the spatial distribution of DNA modification sites on the protein. Through careful design and mutagenesis, bivalent building blocks that bind directionally to form one-dimensional assemblies can be realized. Finally, we discuss the assembly of proteins densely modified with DNA into crystalline superlattices. At first glance, these protein building blocks display crystallization behavior remarkably similar to that of their DNA-functionalized inorganic nanoparticle counterparts, which allows design principles elucidated for DNA-guided nanoparticle crystallization to be used as predictive tools in determining structural outcomes in protein systems. Proteins additionally offer design handles that nanoparticles do not: unlike nanoparticles, the number and spatial distribution of DNA can be controlled through the protein sequence and DNA modification chemistry. Changing the spatial distributions of DNA can drive otherwise identical proteins down distinct crystallization pathways and yield building blocks with exotic distributions of DNA that crystallize into structures that are not yet attainable using isotropically functionalized particles. We highlight challenges in accessing other classes of architectures and establishing general design rules for DNA-mediated protein assembly. Harnessing surface DNA modifications to build protein materials creates many opportunities to realize new architectures and answer fundamental questions about DNA-modified nanostructures in both materials and biological contexts. Proteins with surface DNA modifications are a powerful class of nanomaterial building blocks for which the DNA and protein sequences and the nature of their conjugation dictate the material structure.
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165
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Wang Y, Leng L, Islam MK, Liu F, Lin CSK, Leu SY. Substrate-Related Factors Affecting Cellulosome-Induced Hydrolysis for Lignocellulose Valorization. Int J Mol Sci 2019; 20:ijms20133354. [PMID: 31288425 PMCID: PMC6651384 DOI: 10.3390/ijms20133354] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 06/30/2019] [Accepted: 07/03/2019] [Indexed: 11/22/2022] Open
Abstract
Cellulosomes are an extracellular supramolecular multienzyme complex that can efficiently degrade cellulose and hemicelluloses in plant cell walls. The structural and unique subunit arrangement of cellulosomes can promote its adhesion to the insoluble substrates, thus providing individual microbial cells with a direct competence in the utilization of cellulosic biomass. Significant progress has been achieved in revealing the structures and functions of cellulosomes, but a knowledge gap still exists in understanding the interaction between cellulosome and lignocellulosic substrate for those derived from biorefinery pretreatment of agricultural crops. The cellulosomic saccharification of lignocellulose is affected by various substrate-related physical and chemical factors, including native (untreated) wood lignin content, the extent of lignin and xylan removal by pretreatment, lignin structure, substrate size, and of course substrate pore surface area or substrate accessibility to cellulose. Herein, we summarize the cellulosome structure, substrate-related factors, and regulatory mechanisms in the host cells. We discuss the latest advances in specific strategies of cellulosome-induced hydrolysis, which can function in the reaction kinetics and the overall progress of biorefineries based on lignocellulosic feedstocks.
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Affiliation(s)
- Ying Wang
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-Environmental Science & Technology, Guangzhou 510650, China
- Department of Civil and Environmental Engineering, the Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China
| | - Ling Leng
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki 305-8566, Japan
| | - Md Khairul Islam
- Department of Civil and Environmental Engineering, the Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China
| | - Fanghua Liu
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-Environmental Science & Technology, Guangzhou 510650, China
| | - Carol Sze Ki Lin
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Shao-Yuan Leu
- Department of Civil and Environmental Engineering, the Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China.
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166
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Sheldon RA, Brady D. Broadening the Scope of Biocatalysis in Sustainable Organic Synthesis. CHEMSUSCHEM 2019; 12:2859-2881. [PMID: 30938093 DOI: 10.1002/cssc.201900351] [Citation(s) in RCA: 155] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 02/05/2019] [Accepted: 03/04/2019] [Indexed: 05/21/2023]
Abstract
This Review is aimed at synthetic organic chemists who may be familiar with organometallic catalysis but have no experience with biocatalysis, and seeks to provide an answer to the perennial question: if it is so attractive, why wasn't it extensively used in the past? The development of biocatalysis in industrial organic synthesis is traced from the middle of the last century. Advances in molecular biology in the last two decades, in particular genome sequencing, gene synthesis and directed evolution of proteins, have enabled remarkable improvements in scope and substantially reduced biocatalyst development times and cost contributions. Additionally, improvements in biocatalyst recovery and reuse have been facilitated by developments in enzyme immobilization technologies. Biocatalysis has become eminently competitive with chemocatalysis and the biocatalytic production of important pharmaceutical intermediates, such as enantiopure alcohols and amines, has become mainstream organic synthesis. The synthetic space of biocatalysis has significantly expanded and is currently being extended even further to include new-to-nature biocatalytic reactions.
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Affiliation(s)
- Roger A Sheldon
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg, 2050, South Africa
- Department of Biotechnology, Delft University of Technology, Section BOC, van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Dean Brady
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg, 2050, South Africa
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167
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Gunnoo M, Cazade PA, Orlowski A, Chwastyk M, Liu H, Ta DT, Cieplak M, Nash M, Thompson D. Steered molecular dynamics simulations reveal the role of Ca 2+ in regulating mechanostability of cellulose-binding proteins. Phys Chem Chem Phys 2019; 20:22674-22680. [PMID: 30132772 DOI: 10.1039/c8cp00925b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The conversion of cellulosic biomass into biofuels requires degradation of the biomass into fermentable sugars. The most efficient natural cellulase system for carrying out this conversion is an extracellular multi-enzymatic complex named the cellulosome. In addition to temperature and pH stability, mechanical stability is important for functioning of cellulosome domains, and experimental techniques such as Single Molecule Force Spectroscopy (SMFS) have been used to measure the mechanical strength of several cellulosomal proteins. Molecular dynamics computer simulations provide complementary atomic-resolution quantitative maps of domain mechanical stability for identification of experimental leads for protein stabilization. In this study, we used multi-scale steered molecular dynamics computer simulations, benchmarked against new SMFS measurements, to measure the intermolecular contacts that confer high mechanical stability to a family 3 Carbohydrate Binding Module protein (CBM3) derived from the archetypal Clostridium thermocellum cellulosome. Our data predicts that electrostatic interactions in the calcium binding pocket modulate the mechanostability of the cellulose-binding module, which provides an additional design rule for the rational re-engineering of designer cellulosomes for biotechnology. Our data offers new molecular insights into the origins of mechanostability in cellulose binding domains and gives leads for synthesis of more robust cellulose-binding protein modules. On the other hand, simulations predict that insertion of a flexible strand can promote alternative unfolding pathways and dramatically reduce the mechanostability of the carbohydrate binding module, which gives routes to rational design of tailormade fingerprint complexes for force spectroscopy experiments.
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Affiliation(s)
- Melissabye Gunnoo
- Department of Physics, Bernal Institute, University of Limerick, V94 T9PX, Ireland.
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Champreda V, Mhuantong W, Lekakarn H, Bunterngsook B, Kanokratana P, Zhao XQ, Zhang F, Inoue H, Fujii T, Eurwilaichitr L. Designing cellulolytic enzyme systems for biorefinery: From nature to application. J Biosci Bioeng 2019; 128:637-654. [PMID: 31204199 DOI: 10.1016/j.jbiosc.2019.05.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 05/06/2019] [Accepted: 05/11/2019] [Indexed: 12/14/2022]
Abstract
Cellulolytic enzymes play a key role on conversion of lignocellulosic plant biomass to biofuels and biochemicals in sugar platform biorefineries. In this review, we survey composite carbohydrate-active enzymes (CAZymes) among groups of cellulolytic fungi and bacteria that exist under aerobic and anaerobic conditions. Recent advances in designing effective cellulase mixtures are described, starting from the most complex microbial consortium-based enzyme preparations, to single-origin enzymes derived from intensively studied cellulase producers such as Trichoderma reesei, Talaromyces cellulolyticus, and Penicellium funiculosum, and the simplest minimal enzyme systems comprising selected sets of mono-component enzymes tailor-made for specific lignocellulosic substrates. We provide a comprehensive update on studies in developing high-performance cellulases for biorefineries.
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Affiliation(s)
- Verawat Champreda
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathumthani 12120, Thailand.
| | - Wuttichai Mhuantong
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathumthani 12120, Thailand
| | - Hataikarn Lekakarn
- Department of Biotechnology, Faculty of Science and Technology, Thammasat University, Rangsit Campus, Phahonyothin Road, Khlong Luang, Pathumthani 12120, Thailand
| | - Benjarat Bunterngsook
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathumthani 12120, Thailand
| | - Pattanop Kanokratana
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathumthani 12120, Thailand
| | - Xin-Qing Zhao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Fei Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hiroyuki Inoue
- Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology, 3-11-32 Kagamiyama, Hiroshima 739-0046, Japan
| | - Tatsuya Fujii
- Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology, 3-11-32 Kagamiyama, Hiroshima 739-0046, Japan
| | - Lily Eurwilaichitr
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathumthani 12120, Thailand
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169
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Grinberg IR, Yaniv O, de Ora LO, Muñoz-Gutiérrez I, Hershko A, Livnah O, Bayer EA, Borovok I, Frolow F, Lamed R, Voronov-Goldman M. Distinctive ligand-binding specificities of tandem PA14 biomass-sensory elements from Clostridium thermocellum and Clostridium clariflavum. Proteins 2019; 87:917-930. [PMID: 31162722 PMCID: PMC6852018 DOI: 10.1002/prot.25753] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 05/26/2019] [Accepted: 05/30/2019] [Indexed: 11/25/2022]
Abstract
Cellulolytic clostridia use a highly efficient cellulosome system to degrade polysaccharides. To regulate genes encoding enzymes of the multi‐enzyme cellulosome complex, certain clostridia contain alternative sigma I (σI) factors that have cognate membrane‐associated anti‐σI factors (RsgIs) which act as polysaccharide sensors. In this work, we analyzed the structure‐function relationship of the extracellular sensory elements of Clostridium (Ruminiclostridium) thermocellum and Clostridium clariflavum (RsgI3 and RsgI4, respectively). These elements were selected for comparison, as each comprised two tandem PA14‐superfamily motifs. The X‐ray structures of the PA14 modular dyads from the two bacterial species were determined, both of which showed a high degree of structural and sequence similarity, although their binding preferences differed. Bioinformatic approaches indicated that the DNA sequence of promoter of sigI/rsgI operons represents a strong signature, which helps to differentiate binding specificity of the structurally similar modules. The σI4‐dependent C. clariflavum promoter sequence correlates with binding of RsgI4_PA14 to xylan and was identified in genes encoding xylanases, whereas the σI3‐dependent C. thermocellum promoter sequence correlates with RsgI3_PA14 binding to pectin and regulates pectin degradation‐related genes. Structural similarity between clostridial PA14 dyads to PA14‐containing proteins in yeast helped identify another crucial signature element: the calcium‐binding loop 2 (CBL2), which governs binding specificity. Variations in the five amino acids that constitute this loop distinguish the pectin vs xylan specificities. We propose that the first module (PA14A) is dominant in directing the binding to the ligand in both bacteria. The two X‐ray structures of the different PA14 dyads represent the first reported structures of tandem PA14 modules.
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Affiliation(s)
- Inna Rozman Grinberg
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel.,Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Oren Yaniv
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Lizett Ortiz de Ora
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel.,Department of Chemistry, University of California, Irvine, California
| | - Iván Muñoz-Gutiérrez
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel.,Outreach Research Training and Minority Science Programs, School of Biological Sciences, University of California, Irvine, California
| | - Almog Hershko
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Oded Livnah
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Wolfson Centre for Applied Structural Biology, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, Jerusalem, Israel
| | - Edward A Bayer
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Ilya Borovok
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Felix Frolow
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Raphael Lamed
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Milana Voronov-Goldman
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
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170
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Aburaya S, Aoki W, Kuroda K, Minakuchi H, Ueda M. Temporal proteome dynamics of Clostridium cellulovorans cultured with major plant cell wall polysaccharides. BMC Microbiol 2019; 19:118. [PMID: 31159733 PMCID: PMC6547498 DOI: 10.1186/s12866-019-1480-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 05/07/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Clostridium cellulovorans is a mesophilic, cellulosome-producing bacterium containing 57 genomic cellulosomal enzyme-encoding genes. In addition to cellulosomal proteins, C. cellulovorans also secretes non-cellulosomal proteins to degrade plant cell wall polysaccharides. Unlike other cellulosome-producing Clostridium species, C. cellulovorans can metabolize all major plant cell wall polysaccharides (cellulose, hemicelluloses, and pectins). In this study, we performed a temporal proteome analysis of C. cellulovorans to reveal strategies underlying plant cell wall polysaccharide degradation. RESULTS We cultured C. cellulovorans with five different carbon sources (glucose, cellulose, xylan, galactomannan, and pectin) and performed proteome analysis on cellular and secreted proteins. In total, we identified 1895 cellular proteins and 875 secreted proteins. The identified unique carbohydrate-degrading enzymes corresponding to each carbon source were annotated to have specific activity against each carbon source. However, we identified pectate lyase as a unique enzyme in C. cellulovorans cultivated on xylan, which was not previously associated with xylan degradation. We performed k-means clustering analysis for elucidation of temporal changes of the cellular and secreted proteins in each carbon sources. We found that cellular proteins in most of the k-means clusters are involved in carbohydrate metabolism, amino acid metabolism, translation, or membrane transport. When xylan and pectin were used as the carbon sources, the most increasing k-means cluster contained proteins involved in the metabolism of cofactors and vitamins. In case of secreted proteins of C. cellulovorans cultured either on cellulose or xylan, galactomannan, and pectin, the clusters with the most increasing trend contained either 25 cellulosomal proteins and five non-cellulosomal proteins or 8-19 cellulosomal proteins and 9-16 non-cellulosomal proteins, respectively. These differences might reflect mechanisms for degrading cellulose of other carbon source. Co-abundance analysis of the secreted proteins revealed that proteases and protease inhibitors accumulated coordinately. This observation implies that the secreted protease inhibitors and proteases protect carbohydrate-degrading enzymes from an attack from the plant. CONCLUSION In this study, we clarified, for the first time, the temporal proteome dynamics of cellular and secreted proteins in C. cellulovorans. This data will be valuable in understanding strategies employed by C. cellulovorans for degrading major plant cell wall polysaccharides.
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Affiliation(s)
- Shunsuke Aburaya
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan.,Research Fellow of the Japan Society for the Promotion of Science, Sakyo-ku, Kyoto, Japan
| | - Wataru Aoki
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan.,Kyoto Integrated Science and Technology Bio-Analysis Center, Shimogyo-ku, Kyoto, Japan.,JST-PRESTO, Chiyoda-ku, Tokyo, Japan
| | - Kouichi Kuroda
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Hiroshi Minakuchi
- Kyoto-monotech, 1095, Shuzei-cho, Kamigyo-ku, Kyoto-shi, Kyoto, 602-8155, Japan
| | - Mitsuyoshi Ueda
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan. .,Kyoto Integrated Science and Technology Bio-Analysis Center, Shimogyo-ku, Kyoto, Japan. .,JST-PRESTO, Chiyoda-ku, Tokyo, Japan.
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171
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Lu L, Zhang L, Yuan L, Zhu T, Chen W, Wang G, Wang Q. Artificial Cellulosome Complex from the Self-Assembly of Ni-NTA-Functionalized Polymeric Micelles and Cellulases. Chembiochem 2019; 20:1394-1399. [PMID: 30697892 DOI: 10.1002/cbic.201900061] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Indexed: 12/17/2023]
Abstract
Polymer-protein core-shell nanoparticles have been explored for enzyme immobilization. This work reports on the development of functional polymeric micelles for immobilizing His6 -tagged cellulases with controlled spatial orientation of enzymes, resulting in "artificial cellulosomes" for effective cellulose hydrolysis. Poly(styrene)-b-poly(styrene-alt-maleic anhydride) was prepared through one-pot reversible addition-fragmentation chain-transfer polymerization and modified with nitrilotriacetic acid (NTA) to afford an amphiphilic block copolymer. The self-assembled polymer was mixed with a solution of NiSO4 to form Ni-NTA-functionalized micelles, which could successfully capture His6 -tagged cellulases and form hierarchically structured core-shell nanoparticles with cellulases as the corona. Because the anchored enzymes are site-specifically oriented and in close proximity, synergistic catalysis that results in over twofold activity enhancement has been achieved.
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Affiliation(s)
- Lin Lu
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, SC, 29208, USA
| | - Libo Zhang
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, SC, 29208, USA
| | - Liang Yuan
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, SC, 29208, USA
| | - Tianyu Zhu
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, SC, 29208, USA
| | - Wilfred Chen
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, DE, 19716, USA
| | - Guiren Wang
- Department of Mechanical Engineering, University of South Carolina, 301 Main Street, Columbia, SC, 29208, USA
| | - Qian Wang
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, SC, 29208, USA
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172
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Zhivin-Nissan O, Dassa B, Morag E, Kupervaser M, Levin Y, Bayer EA. Unraveling essential cellulosomal components of the ( Pseudo) Bacteroides cellulosolvens reveals an extensive reservoir of novel catalytic enzymes. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:115. [PMID: 31086567 PMCID: PMC6507058 DOI: 10.1186/s13068-019-1447-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 04/20/2019] [Indexed: 05/23/2023]
Abstract
BACKGROUND (Pseudo)Bacteroides cellulosolvens is a cellulolytic bacterium that produces the most extensive and intricate cellulosomal system known in nature. Recently, the elaborate architecture of the B. cellulosolvens cellulosomal system was revealed from analysis of its genome sequence, and the first evidence regarding the interactions between its structural and enzymatic components were detected in vitro. Yet, the understanding of the cellulolytic potential of the bacterium in carbohydrate deconstruction is inextricably linked to its high-molecular-weight protein complexes, which are secreted from the bacterium. RESULTS The current proteome-wide work reveals patterns of protein expression of the various cellulosomal components, and explores the signature of differential expression upon growth of the bacterium on two major carbon sources-cellobiose and microcrystalline cellulose. Mass spectrometry analysis of the bacterial secretome revealed the expression of 24 scaffoldin structural units and 166 dockerin-bearing components (mainly enzymes), in addition to free enzymatic subunits. The dockerin-bearing components comprise cell-free and cell-bound cellulosomes for more efficient carbohydrate degradation. Various glycoside hydrolase (GH) family members were represented among 102 carbohydrate-degrading enzymes, including the omnipresent, most abundant GH48 exoglucanase. Specific cellulosomal components were found in different molecular-weight fractions associated with cell growth on different carbon sources. Overall, microcrystalline cellulose-derived cellulosomes showed markedly higher expression levels of the structural and enzymatic components, and exhibited the highest degradation activity on five different cellulosic and/or hemicellulosic carbohydrates. The cellulosomal activity of B. cellulosolvens showed high degradation rates that are very promising in biotechnological terms and were compatible with the activity levels exhibited by Clostridium thermocellum purified cellulosomes. CONCLUSIONS The current research demonstrates the involvement of key cellulosomal factors that participate in the mechanism of carbohydrate degradation by B. cellulosolvens. The powerful ability of the bacterium to exhibit different degradation strategies on various carbon sources was revealed. The novel reservoir of cellulolytic components of the cellulosomal degradation machineries may serve as a pool for designing new cellulolytic cocktails for biotechnological purposes.
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Affiliation(s)
- Olga Zhivin-Nissan
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Bareket Dassa
- Bioinformatics Unit, Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Ely Morag
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Meital Kupervaser
- Proteomics Unit, Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Yishai Levin
- Proteomics Unit, Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Edward A. Bayer
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
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173
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Vita N, Borne R, Perret S, de Philip P, Fierobe HP. Turning a potent family-9 free cellulase into an operational cellulosomal component and vice versa. FEBS J 2019; 286:3359-3373. [PMID: 31004451 DOI: 10.1111/febs.14858] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 03/18/2019] [Accepted: 04/16/2019] [Indexed: 11/29/2022]
Abstract
Ruminiclostridium cellulolyticum and Lachnoclostridium phytofermentans are cellulolytic clostridia either producing extracellular multienzymatic complexes termed cellulosomes or secreting free cellulases respectively. In the free state, the cellulase Cel9A secreted by L. phytofermentans is much more active on crystalline cellulose than any cellulosomal family-9 enzyme produced by R. cellulolyticum. Nevertheless, the incorporation of Cel9A in vitro in hybrid cellulosomes was formerly shown to generate artificial complexes with altered activity, whereas its incorporation in vivo in native R. cellulolyticum cellulosomes resulted in a strain displaying a weakened cellulolytic phenotype. In this study, we investigated why Cel9A is so potent in the free state but functions poorly as a cellulosomal component, in contrast to the most similar enzyme synthesized by R. cellulolyticum, Cel9G, weakly active in the free state but whose activity on crystalline cellulose is drastically increased in cellulosomes. We show that the removal of the C-terminal moiety of Cel9A encompassing the two X2 modules and the family-3b carbohydrate binding module (CBM3b), reduces its activity on crystalline cellulose. Grafting a dockerin module further diminishes the activity, but this truncated cellulosomal form of Cel9A displays important synergies in hybrid cellulosomes with the pivotal family-48 cellulosomal enzyme of R. cellulolyticum. The exact inverse approach was applied to the cellulosomal Cel9G. Grafting the two X2 modules and the CBM3b of Cel9A to Cel9G strongly increases its activity on crystalline cellulose, to reach Cel9A activity levels. Altogether these data emphasize the specific features required to generate an efficient free or cellulosomal family-9 cellulase.
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174
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Lapébie P, Lombard V, Drula E, Terrapon N, Henrissat B. Bacteroidetes use thousands of enzyme combinations to break down glycans. Nat Commun 2019; 10:2043. [PMID: 31053724 PMCID: PMC6499787 DOI: 10.1038/s41467-019-10068-5] [Citation(s) in RCA: 221] [Impact Index Per Article: 44.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 04/18/2019] [Indexed: 01/21/2023] Open
Abstract
Unlike proteins, glycan chains are not directly encoded by DNA, but by the specificity of the enzymes that assemble them. Theoretical calculations have proposed an astronomical number of possible isomers (> 1012 hexasaccharides) but the actual diversity of glycan structures in nature is not known. Bacteria of the Bacteroidetes phylum are considered primary degraders of polysaccharides and they are found in all ecosystems investigated. In Bacteroidetes genomes, carbohydrate-degrading enzymes (CAZymes) are arranged in gene clusters termed polysaccharide utilization loci (PULs). The depolymerization of a given complex glycan by Bacteroidetes PULs requires bespoke enzymes; conversely, the enzyme composition in PULs can provide information on the structure of the targeted glycans. Here we group the 13,537 PULs encoded by 964 Bacteroidetes genomes according to their CAZyme composition. We find that collectively Bacteroidetes have elaborated a few thousand enzyme combinations for glycan breakdown, suggesting a global estimate of diversity of glycan structures much smaller than the theoretical one. Bacteroidetes genomes contain polysaccharide utilization loci (PULs), each of which encodes enzymes for the breakdown of one particular glycan. By analyzing the enzyme composition of 13,537 PULs, the authors suggest that the natural glycan diversity is orders of magnitude lower than previously proposed.
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Affiliation(s)
- Pascal Lapébie
- Architecture et Fonction des Macromolécules Biologiques (AFMB), Centre National de la Recherche Scientifique (CNRS, UMR7257), Institut National Agronomique (INRA, USC 1408) and Aix-Marseille Université (AMU), 13288 Marseille cedex 9, Marseille, France
| | - Vincent Lombard
- Architecture et Fonction des Macromolécules Biologiques (AFMB), Centre National de la Recherche Scientifique (CNRS, UMR7257), Institut National Agronomique (INRA, USC 1408) and Aix-Marseille Université (AMU), 13288 Marseille cedex 9, Marseille, France
| | - Elodie Drula
- Architecture et Fonction des Macromolécules Biologiques (AFMB), Centre National de la Recherche Scientifique (CNRS, UMR7257), Institut National Agronomique (INRA, USC 1408) and Aix-Marseille Université (AMU), 13288 Marseille cedex 9, Marseille, France
| | - Nicolas Terrapon
- Architecture et Fonction des Macromolécules Biologiques (AFMB), Centre National de la Recherche Scientifique (CNRS, UMR7257), Institut National Agronomique (INRA, USC 1408) and Aix-Marseille Université (AMU), 13288 Marseille cedex 9, Marseille, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques (AFMB), Centre National de la Recherche Scientifique (CNRS, UMR7257), Institut National Agronomique (INRA, USC 1408) and Aix-Marseille Université (AMU), 13288 Marseille cedex 9, Marseille, France. .,Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.
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175
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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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176
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Andrei AŞ, Salcher MM, Mehrshad M, Rychtecký P, Znachor P, Ghai R. Niche-directed evolution modulates genome architecture in freshwater Planctomycetes. THE ISME JOURNAL 2019; 13:1056-1071. [PMID: 30610231 PMCID: PMC6461901 DOI: 10.1038/s41396-018-0332-5] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 11/22/2018] [Accepted: 11/29/2018] [Indexed: 11/08/2022]
Abstract
Freshwater environments teem with microbes that do not have counterparts in culture collections or genetic data available in genomic repositories. Currently, our apprehension of evolutionary ecology of freshwater bacteria is hampered by the difficulty to establish organism models for the most representative clades. To circumvent the bottlenecks inherent to the cultivation-based techniques, we applied ecogenomics approaches in order to unravel the evolutionary history and the processes that drive genome architecture in hallmark freshwater lineages from the phylum Planctomycetes. The evolutionary history inferences showed that sediment/soil Planctomycetes transitioned to aquatic environments, where they gave rise to new freshwater-specific clades. The most abundant lineage was found to have the most specialised lifestyle (increased regulatory genetic circuits, metabolism tuned for mineralization of proteinaceous sinking aggregates, psychrotrophic behaviour) within the analysed clades and to harbour the smallest freshwater Planctomycetes genomes, highlighting a genomic architecture shaped by niche-directed evolution (through loss of functions and pathways not needed in the newly acquired freshwater niche).
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Affiliation(s)
- Adrian-Ştefan Andrei
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre CAS, Na Sádkách 702/7, 370 05 České Budějovice, Czech Republic.
| | - Michaela M Salcher
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre CAS, Na Sádkách 702/7, 370 05 České Budějovice, Czech Republic
- Limnological Station, Institute of Plant and Microbial Biology, University of Zurich, Seestrasse 187, 8802, Kilchberg, Switzerland
| | - Maliheh Mehrshad
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre CAS, Na Sádkách 702/7, 370 05 České Budějovice, Czech Republic
| | - Pavel Rychtecký
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre CAS, Na Sádkách 702/7, 370 05 České Budějovice, Czech Republic
| | - Petr Znachor
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre CAS, Na Sádkách 702/7, 370 05 České Budějovice, Czech Republic
| | - Rohit Ghai
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre CAS, Na Sádkách 702/7, 370 05 České Budějovice, Czech Republic.
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177
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Schmid-Dannert C, López-Gallego F. Advances and opportunities for the design of self-sufficient and spatially organized cell-free biocatalytic systems. Curr Opin Chem Biol 2019; 49:97-104. [DOI: 10.1016/j.cbpa.2018.11.021] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 11/16/2018] [Accepted: 11/27/2018] [Indexed: 11/29/2022]
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178
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Bashirova A, Pramanik S, Volkov P, Rozhkova A, Nemashkalov V, Zorov I, Gusakov A, Sinitsyn A, Schwaneberg U, Davari MD. Disulfide Bond Engineering of an Endoglucanase from Penicillium verruculosum to Improve Its Thermostability. Int J Mol Sci 2019; 20:E1602. [PMID: 30935060 PMCID: PMC6479618 DOI: 10.3390/ijms20071602] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 03/25/2019] [Accepted: 03/27/2019] [Indexed: 01/29/2023] Open
Abstract
Endoglucanases (EGLs) are important components of multienzyme cocktails used in the production of a wide variety of fine and bulk chemicals from lignocellulosic feedstocks. However, a low thermostability and the loss of catalytic performance of EGLs at industrially required temperatures limit their commercial applications. A structure-based disulfide bond (DSB) engineering was carried out in order to improve the thermostability of EGLII from Penicillium verruculosum. Based on in silico prediction, two improved enzyme variants, S127C-A165C (DSB2) and Y171C-L201C (DSB3), were obtained. Both engineered enzymes displayed a 15⁻21% increase in specific activity against carboxymethylcellulose and β-glucan compared to the wild-type EGLII (EGLII-wt). After incubation at 70 °C for 2 h, they retained 52⁻58% of their activity, while EGLII-wt retained only 38% of its activity. At 80 °C, the enzyme-engineered forms retained 15⁻22% of their activity after 2 h, whereas EGLII-wt was completely inactivated after the same incubation time. Molecular dynamics simulations revealed that the introduced DSB rigidified a global structure of DSB2 and DSB3 variants, thus enhancing their thermostability. In conclusion, this work provides an insight into DSB protein engineering as a potential rational design strategy that might be applicable for improving the stability of other enzymes for industrial applications.
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Affiliation(s)
- Anna Bashirova
- Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences, Moscow 119071, Russia.
| | - Subrata Pramanik
- Institute of Biotechnology, RWTH Aachen University, Aachen 52074, Worringerweg 3, Germany.
| | - Pavel Volkov
- Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences, Moscow 119071, Russia.
| | - Aleksandra Rozhkova
- Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences, Moscow 119071, Russia.
| | - Vitaly Nemashkalov
- G.K.Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino 142292, Moscow region, Russia.
| | - Ivan Zorov
- Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences, Moscow 119071, Russia.
- Department of Chemistry, M.V.Lomonosov Moscow State University, Moscow 119991, Russia.
| | - Alexander Gusakov
- Department of Chemistry, M.V.Lomonosov Moscow State University, Moscow 119991, Russia.
| | - Arkady Sinitsyn
- Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences, Moscow 119071, Russia.
- Department of Chemistry, M.V.Lomonosov Moscow State University, Moscow 119991, Russia.
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University, Aachen 52074, Worringerweg 3, Germany.
- DWI-Leibniz Institut für Interaktive Materialien, Forckenbeckstrasse 50, Aachen 52056, Germany.
| | - Mehdi D Davari
- Institute of Biotechnology, RWTH Aachen University, Aachen 52074, Worringerweg 3, Germany.
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179
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Kahn A, Moraïs S, Galanopoulou AP, Chung D, Sarai NS, Hengge N, Hatzinikolaou DG, Himmel ME, Bomble YJ, Bayer EA. Creation of a functional hyperthermostable designer cellulosome. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:44. [PMID: 30858881 PMCID: PMC6394049 DOI: 10.1186/s13068-019-1386-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 02/20/2019] [Indexed: 05/28/2023]
Abstract
BACKGROUND Renewable energy has become a field of high interest over the past decade, and production of biofuels from cellulosic substrates has a particularly high potential as an alternative source of energy. Industrial deconstruction of biomass, however, is an onerous, exothermic process, the cost of which could be decreased significantly by use of hyperthermophilic enzymes. An efficient way of breaking down cellulosic substrates can also be achieved by highly efficient enzymatic complexes called cellulosomes. The modular architecture of these multi-enzyme complexes results in substrate targeting and proximity-based synergy among the resident enzymes. However, cellulosomes have not been observed in hyperthermophilic bacteria. RESULTS Here, we report the design and function of a novel hyperthermostable "designer cellulosome" system, which is stable and active at 75 °C. Enzymes from Caldicellulosiruptor bescii, a highly cellulolytic hyperthermophilic anaerobic bacterium, were selected and successfully converted to the cellulosomal mode by grafting onto them divergent dockerin modules that can be inserted in a precise manner into a thermostable chimaeric scaffoldin by virtue of their matching cohesins. Three pairs of cohesins and dockerins, selected from thermophilic microbes, were examined for their stability at extreme temperatures and were determined stable at 75 °C for at least 72 h. The resultant hyperthermostable cellulosome complex exhibited the highest levels of enzymatic activity on microcrystalline cellulose at 75 °C, compared to those of previously reported designer cellulosome systems and the native cellulosome from Clostridium thermocellum. CONCLUSION The functional hyperthermophilic platform fulfills the appropriate physico-chemical properties required for exothermic processes. This system can thus be adapted for other types of thermostable enzyme systems and could serve as a basis for a variety of cellulolytic and non-cellulolytic industrial objectives at high temperatures.
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Affiliation(s)
- Amaranta Kahn
- Department of Biomolecular Sciences, The Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Sarah Moraïs
- Department of Biomolecular Sciences, The Weizmann Institute of Science, 7610001 Rehovot, Israel
- Faculty of Natural Sciences, Ben-Gurion University of the Negev, 8499000 Beer-Sheva, Israel
| | - Anastasia P. Galanopoulou
- Microbiology Group, Faculty of Biology, National and Kapodistrian University of Athens, Zografou Campus, 15784 Athens, Greece
| | - Daehwan Chung
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO USA
| | - Nicholas S. Sarai
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO USA
- Present Address: Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125 USA
| | - Neal Hengge
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO USA
| | - Dimitris G. Hatzinikolaou
- Microbiology Group, Faculty of Biology, National and Kapodistrian University of Athens, Zografou Campus, 15784 Athens, Greece
| | - Michael E. Himmel
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO USA
| | - Yannick J. Bomble
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO USA
| | - Edward A. Bayer
- Department of Biomolecular Sciences, The Weizmann Institute of Science, 7610001 Rehovot, Israel
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180
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Abstract
Enzymatic breakdown of plant biomass is an essential step for its utilization in biorefinery applications, and the products could serve as substrates for the sustainable and environmentally friendly production of fuels and chemicals. Toward this end, the incorporation of enzymes into polyenzymatic cellulosome complexes-able to specifically bind to and hydrolyze crystalline cellulosic materials, such as plant biomass-is known to increase the efficiency and the overall hydrolysis performance of a cellulase system. Despite their relative abundance in various mesophilic anaerobic cellulolytic bacteria, there are only a few reports of cellulosomes of thermophilic origin. However, since various biorefinery processes are favored by elevated temperatures, the development of thermophilic designer cellulosomes could be of great importance. Owing to the limited number of thermophilic cellulosomes, designer cellulosomes, composed of mixtures of mesophilic and thermophilic components, have been constructed. As a result, the overall thermal profile of the individual parts and the resulting complex has to be extensively evaluated. Here, we describe a practical guide for the determination of temperature stability for cellulases in the cellulosome complexes. The approach is also appropriate for other related enzymes, notably xylanases as well as other glycoside hydrolases. We provide detailed experimental procedures for the evaluation of the thermal stability of the individual designer cellulosome components and their complexes as well as protocols for the assessment of complex integrity at elevated temperatures.
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181
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Dou TY, Chen J, Hao YF, Qi X. Effects of Different Carbon Sources on Enzyme Production and Ultrastructure of Cellulosimicrobium cellulans. Curr Microbiol 2019; 76:355-360. [PMID: 30684027 DOI: 10.1007/s00284-019-01633-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 01/17/2019] [Indexed: 01/18/2023]
Abstract
The secretomes of the strain Cellulosimicrobium cellulans F16 grown on different carbon sources were analyzed by zymography, and the subcellular surface structures were extensively studied by electron microscope. The exo-cellulase and xylanase systems were sparse when cells were grown on soluble oligosaccharides, but were significantly increased when grown on complex and water-insoluble polysaccharides, such as Avicel, corn cob, and birchwood xylan. The cellulosome-like protuberant structures were clearly observed on the cell surfaces of strain F16 grown on cellulose, with diameters of 15-20 nm. Fibrous structures that connected the adjacent cells can be seen under microscope. Moreover, protuberances that adsorbed the cell to cellulose were also observed. As the adhesion of Cellulosimicrobium cellulans cells onto cellulose surfaces occurs via thick bacterial curdlan-type exopolysaccharides (EPS), such surface layer is potentially important in the digestion of insoluble substrates such as cellulose or hemicellulose, and the previously reported xylanosomes are part of such complex glycocalyx layer on the surface of the bacterial cell.
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Affiliation(s)
- Tong-Yi Dou
- School of Life Science and Medicine, Dalian University of Technology, Dagong Road No. 2, LiaoDongWan New District, Panjin, 124221, China.
| | - Jing Chen
- School of Life Science and Medicine, Dalian University of Technology, Dagong Road No. 2, LiaoDongWan New District, Panjin, 124221, China
| | - Yi-Fu Hao
- School of Life Science and Medicine, Dalian University of Technology, Dagong Road No. 2, LiaoDongWan New District, Panjin, 124221, China
| | - Xiaohui Qi
- College of Life Science, Dalian Minzu University, Dalian, 116600, China
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182
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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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183
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Ren Z, You W, Wu S, Poetsch A, Xu C. Secretomic analyses of Ruminiclostridium papyrosolvens reveal its enzymatic basis for lignocellulose degradation. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:183. [PMID: 31338125 PMCID: PMC6628489 DOI: 10.1186/s13068-019-1522-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 07/05/2019] [Indexed: 05/07/2023]
Abstract
BACKGROUND Efficient biotechnological conversion of lignocellulosic biomass to valuable products, such as transportation biofuels, is ecologically attractive, yet requires substantially improved mechanistic understanding and optimization to become economically feasible. Cellulolytic clostridia, such as Ruminiclostridium papyrosolvens (previously Clostridium papyrosolvens), produce a wide variety of carbohydrate-active enzymes (CAZymes) including extracellular multienzyme complexes-cellulosomes with different specificities for enhanced cellulosic biomass degradation. Identification of the secretory components, especially CAZymes, during bacterial growth on lignocellulose and their influence on bacterial catalytic capabilities provide insight into construction of potent cellulase systems of cell factories tuned or optimized for the targeted substrate by matching the type and abundance of enzymes and corresponding transporters. RESULTS In this study, we firstly predicted a total of 174 putative CAZymes from the genome of R. papyrosolvens, including 74 cellulosomal components. To explore profile of secreted proteins involved in lignocellulose degradation, we compared the secretomes of R. papyrosolvens grown on different substrates using label-free quantitative proteomics. CAZymes, extracellular solute-binding proteins (SBPs) of transport systems and proteins involved in spore formation were enriched in the secretome of corn stover for lignocellulose degradation. Furthermore, compared with free CAZymes, complex CAZymes (cellulosomal components) had larger fluctuations in variety and abundance of enzymes among four carbon sources. In particular, cellulosomal proteins encoded by the cip-cel operon and the xyl-doc gene cluster had the highest abundance with corn stover as substrate. Analysis of differential expression of CAZymes revealed a substrate-dependent secretion pattern of CAZymes, which was consistent with their catalytic activity from each secretome determined on different cellulosic substrates. The results suggest that the expression of CAZymes is regulated by the type of substrate in the growth medium. CONCLUSIONS In the present study, our results demonstrated the complexity of the lignocellulose degradation systems of R. papyrosolvens and showed the potency of its biomass degradation activity. Differential proteomic analyses and activity assays of CAZymes secreted by R. papyrosolvens suggested a distinct environment-sensing strategy for cellulose utilization in which R. papyrosolvens modulated the composition of the CAZymes, especially cellulosome, according to the degradation state of its natural substrate.
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Affiliation(s)
- Zhenxing Ren
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, 030006 Shanxi China
- Institute of Applied Chemistry, Shanxi University, Taiyuan, 030006 Shanxi China
| | - Wuxin You
- Department of Plant Biochemistry, Ruhr University Bochum, 44801 Bochum, Germany
| | - Shasha Wu
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, 030006 Shanxi China
| | - Ansgar Poetsch
- Department of Plant Biochemistry, Ruhr University Bochum, 44801 Bochum, Germany
- School of Biomedical and Healthcare Sciences, University of Plymouth, Plymouth, PL48AA UK
| | - Chenggang Xu
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, 030006 Shanxi China
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184
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Dong M, Wang S, Xu F, Wang J, Yang N, Li Q, Chen J, Li W. Pretreatment of sweet sorghum straw and its enzymatic digestion: insight into the structural changes and visualization of hydrolysis process. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:276. [PMID: 31768194 PMCID: PMC6874820 DOI: 10.1186/s13068-019-1613-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 11/10/2019] [Indexed: 05/03/2023]
Abstract
BACKGROUND The efficient utilization of lignocellulosic biomass for biofuel production has received increasing attention. Previous studies have investigated the pretreatment process of biomass, but the detailed enzymatic hydrolysis process of pretreated biomass remains largely unclear. Thus, this study investigated the pretreatment efficiency of dilute alkali, acid, hydrogen peroxide and its ultimate effects on enzymatic hydrolysis. Furthermore, to better understand the enzymatic digestion process of alkali-pretreated sweet sorghum straw (SSS), multimodal microscopy techniques were used to visualize the enzymatic hydrolysis process. RESULT After pretreatment with alkali, an enzymatic hydrolysis efficiency of 86.44% was obtained, which increased by 99.54% compared to the untreated straw (43.23%). The FTIR, XRD and SEM characterization revealed a sequence of microstructural changes occurring in plant cell walls after pretreatment, including the destruction of lignin-polysaccharide interactions, the increase of porosity and crystallinity, and reduction of recalcitrance. During the course of hydrolysis, the cellulase dissolved the cell walls in the same manner and the digestion firstly occurred from the middle of cell walls and then toward the cell wall corners. The CLSM coupled with fluorescent labeling demonstrated that the sclerenchyma cells and vascular bundles in natural SSS were highly lignified, which caused the nonproductive bindings of cellulase on lignin. However, the efficient delignification significantly increased the accessibility and digestibility of cellulase to biomass, thereby improving the saccharification efficiency. CONCLUSION This work will be helpful in investigating the biomass pretreatment and its structural characterization. In addition, the visualization results of the enzymatic hydrolysis process of pretreated lignocellulose could be used for guidance to explore the lignocellulosic biomass processing and large-scale biofuel production.
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Affiliation(s)
- Miaoyin Dong
- Institute of Modern Physics, Chinese Academy of Sciences, 509 Nanchang Rd., Lanzhou, 730000 Gansu People’s Republic of China
- College of Life Sciences, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049 People’s Republic of China
| | - Shuyang Wang
- Institute of Modern Physics, Chinese Academy of Sciences, 509 Nanchang Rd., Lanzhou, 730000 Gansu People’s Republic of China
- Institute of Biology, Gansu Academy of Sciences, 197 Dingxi South Rd., Lanzhou, 730000 Gansu People’s Republic of China
- College of Life Sciences, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049 People’s Republic of China
| | - Fuqiang Xu
- Institute of Modern Physics, Chinese Academy of Sciences, 509 Nanchang Rd., Lanzhou, 730000 Gansu People’s Republic of China
- College of Life Sciences, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049 People’s Republic of China
| | - Junkai Wang
- College of Physics and Electronic Engineering, Northwest Normal University, Anning Rd., Lanzhou, 730000 Gansu People’s Republic of China
| | - Ning Yang
- College of Life Sciences, Northwest Normal University, Anning Rd., Lanzhou, 730000 Gansu People’s Republic of China
| | - Qiaoqiao Li
- Institute of Modern Physics, Chinese Academy of Sciences, 509 Nanchang Rd., Lanzhou, 730000 Gansu People’s Republic of China
- College of Life Sciences, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049 People’s Republic of China
| | - Jihong Chen
- Institute of Modern Physics, Chinese Academy of Sciences, 509 Nanchang Rd., Lanzhou, 730000 Gansu People’s Republic of China
- College of Life Sciences, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049 People’s Republic of China
| | - Wenjian Li
- Institute of Modern Physics, Chinese Academy of Sciences, 509 Nanchang Rd., Lanzhou, 730000 Gansu People’s Republic of China
- College of Life Sciences, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049 People’s Republic of China
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185
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Holwerda EK, Worthen RS, Kothari N, Lasky RC, Davison BH, Fu C, Wang ZY, Dixon RA, Biswal AK, Mohnen D, Nelson RS, Baxter HL, Mazarei M, Muchero W, Tuskan GA, Cai CM, Gjersing EE, Davis MF, Himmel ME, Wyman CE, Gilna P, Lynd LR. Multiple levers for overcoming the recalcitrance of lignocellulosic biomass. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:15. [PMID: 30675183 PMCID: PMC6335785 DOI: 10.1186/s13068-019-1353-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 01/04/2019] [Indexed: 05/03/2023]
Abstract
BACKGROUND The recalcitrance of cellulosic biomass is widely recognized as a key barrier to cost-effective biological processing to fuels and chemicals, but the relative impacts of physical, chemical and genetic interventions to improve biomass processing singly and in combination have yet to be evaluated systematically. Solubilization of plant cell walls can be enhanced by non-biological augmentation including physical cotreatment and thermochemical pretreatment, the choice of biocatalyst, the choice of plant feedstock, genetic engineering of plants, and choosing feedstocks that are less recalcitrant natural variants. A two-tiered combinatoric investigation of lignocellulosic biomass deconstruction was undertaken with three biocatalysts (Clostridium thermocellum, Caldicellulosiruptor bescii, Novozymes Cellic® Ctec2 and Htec2), three transgenic switchgrass plant lines (COMT, MYB4, GAUT4) and their respective nontransgenic controls, two Populus natural variants, and augmentation of biological attack using either mechanical cotreatment or cosolvent-enhanced lignocellulosic fractionation (CELF) pretreatment. RESULTS In the absence of augmentation and under the conditions tested, increased total carbohydrate solubilization (TCS) was observed for 8 of the 9 combinations of switchgrass modifications and biocatalysts tested, and statistically significant for five of the combinations. Our results indicate that recalcitrance is not a trait determined by the feedstock only, but instead is coequally determined by the choice of biocatalyst. TCS with C. thermocellum was significantly higher than with the other two biocatalysts. Both CELF pretreatment and cotreatment via continuous ball milling enabled TCS in excess of 90%. CONCLUSION Based on our results as well as literature studies, it appears that some form of non-biological augmentation will likely be necessary for the foreseeable future to achieve high TCS for most cellulosic feedstocks. However, our results show that this need not necessarily involve thermochemical processing, and need not necessarily occur prior to biological conversion. Under the conditions tested, the relative magnitude of TCS increase was augmentation > biocatalyst choice > plant choice > plant modification > plant natural variants. In the presence of augmentation, plant modification, plant natural variation, and plant choice exhibited a small, statistically non-significant impact on TCS.
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Affiliation(s)
- Evert K. Holwerda
- Thayer School of Engineering, Dartmouth College, 14 Engineering drive, Hanover, NH 03755 USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Robert S. Worthen
- Thayer School of Engineering, Dartmouth College, 14 Engineering drive, Hanover, NH 03755 USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Ninad Kothari
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Department of Chemical and Environmental Engineering and Center for Environmental Research and Technology, Bourns College of Engineering, University of California Riverside, Riverside, CA 92521 USA
| | - Ronald C. Lasky
- Thayer School of Engineering, Dartmouth College, 14 Engineering drive, Hanover, NH 03755 USA
| | - Brian H. Davison
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Chunxiang Fu
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Genomics Division, Noble Research Institute, Ardmore, OK 73401 USA
| | - Zeng-Yu Wang
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Genomics Division, Noble Research Institute, Ardmore, OK 73401 USA
| | - Richard A. Dixon
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Department of Biological Sciences, University of North Texas, Denton, TX 76203 USA
| | - Ajaya K. Biswal
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602 USA
| | - Debra Mohnen
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602 USA
| | - Richard S. Nelson
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Genomics Division, Noble Research Institute, Ardmore, OK 73401 USA
| | - Holly L. Baxter
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Department of Plant Sciences, University of Tennessee at Knoxville, Knoxville, TN 37996 USA
| | - Mitra Mazarei
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Department of Plant Sciences, University of Tennessee at Knoxville, Knoxville, TN 37996 USA
| | - Wellington Muchero
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Gerald A. Tuskan
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Charles M. Cai
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Department of Chemical and Environmental Engineering and Center for Environmental Research and Technology, Bourns College of Engineering, University of California Riverside, Riverside, CA 92521 USA
| | - Erica E. Gjersing
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Bioenergy Science and Technology, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Mark F. Davis
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Bioenergy Science and Technology, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Michael E. Himmel
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Bioenergy Science and Technology, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Charles E. Wyman
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Department of Chemical and Environmental Engineering and Center for Environmental Research and Technology, Bourns College of Engineering, University of California Riverside, Riverside, CA 92521 USA
| | - Paul Gilna
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Lee R. Lynd
- Thayer School of Engineering, Dartmouth College, 14 Engineering drive, Hanover, NH 03755 USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
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186
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Abstract
Cooperative enzyme catalysis in nature has long inspired the application of engineered multi-enzyme assemblies for industrial biocatalysis. Despite considerable interest, efforts to harness the activity of cell-surface displayed multi-enzyme assemblies have been based on trial and error rather than rational design due to a lack of quantitative tools. In this study, we developed a quantitative approach to whole-cell biocatalyst characterization enabling a comprehensive study of how yeast-surface displayed multi-enzyme assemblies form. Here we show that the multi-enzyme assembly efficiency is limited by molecular crowding on the yeast cell surface, and that maximizing enzyme density is the most important parameter for enhancing cellulose hydrolytic performance. Interestingly, we also observed that proximity effects are only synergistic when the average inter-enzyme distance is > ~130 nm. The findings and the quantitative approach developed in this work should help to advance the field of biocatalyst engineering from trial and error to rational design.
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187
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Hydrogenosomes of Anaerobic Fungi: An Alternative Way to Adapt to Anaerobic Environments. HYDROGENOSOMES AND MITOSOMES: MITOCHONDRIA OF ANAEROBIC EUKARYOTES 2019. [DOI: 10.1007/978-3-030-17941-0_7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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188
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Yin YR, Sang P, Xian WD, Li X, Jiao JY, Liu L, Hozzein WN, Xiao M, Li WJ. Expression and Characteristics of Two Glucose-Tolerant GH1 β-glucosidases From Actinomadura amylolytica YIM 77502 T for Promoting Cellulose Degradation. Front Microbiol 2018; 9:3149. [PMID: 30619214 PMCID: PMC6305311 DOI: 10.3389/fmicb.2018.03149] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 12/04/2018] [Indexed: 01/25/2023] Open
Abstract
The bioconversion of lignocellulose in various industrial processes, such as biofuel production, requires the degradation of cellulose. Actinomadura amylolytica YIM 77502T is an aerobic, Gram-positive actinomycete that can efficiently degrade crystalline cellulose by extracellular cellulases. Genomic analysis of A. amylolytica identified 9 cellulase and 11 β-glucosidase genes that could potentially encode proteins that digest cellulose. Extracellular proteome characterization of A. amylolytica cell-free culture supernatant by liquid chromatography tandem mass spectrometry analysis revealed that 4 of these cellulases and 2 of these β-glucosidases functioned during cellulose hydrolysis. Thin-layer chromatography analysis revealed extracellular β-glucosidases play a major role in carboxyl methyl cellulose (CMC) degradation of products in culture supernatants. In this study, 2 of the identified secreted β-glucosidases, AaBGL1 and AaBGL2, were functionally expressed in Escherichia coli and found to have β-glucosidase activity with wide substrate specificities, including for p-nitrophenyl β-D-glucopyranoside (pNPG), p-nitrophenyl-beta-D-cellobioside (pNPC), and cellobiose. Moreover, AaBGL1 and AaBGL2 had high tolerances for glucose. After adding these β-glucosidases to commercial cellulases, the degradation rates of CMC, Avicel, birch sawdust, and corncob powder increased by 37, 42, 33, and 9%, respectively. Overall, this work identifies an alternative potential source of β-glucosidases with potential applications in commercial cellulose utilization and the bioenergy industry.
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Affiliation(s)
- Yi-Rui Yin
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Peng Sang
- College of Agriculture and Biological Science, Dali University, Dali, China
| | - Wen-Dong Xian
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xin Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jian-Yu Jiao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Lan Liu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Wael N Hozzein
- Bioproducts Research Chair, Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia.,Department of Botany and Microbiology, Faculty of Science, Beni-Suef University, Beni-Suef, Egypt
| | - Min Xiao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi, China
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189
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de Araújo EA, de Oliveira Neto M, Polikarpov I. Biochemical characterization and low-resolution SAXS structure of two-domain endoglucanase BlCel9 from Bacillus licheniformis. Appl Microbiol Biotechnol 2018; 103:1275-1287. [PMID: 30547217 DOI: 10.1007/s00253-018-9508-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Revised: 10/03/2018] [Accepted: 11/07/2018] [Indexed: 12/16/2022]
Abstract
Lignocellulose feedstock constitutes the most abundant carbon source in the biosphere; however, its recalcitrance remains a challenge for microbial conversion into biofuel and bioproducts. Bacillus licheniformis is a microbial mesophilic bacterium capable of secreting a large number of glycoside hydrolase (GH) enzymes, including a glycoside hydrolase from GH family 9 (BlCel9). Here, we conducted biochemical and biophysical studies of recombinant BlCel9, and its low-resolution molecular shape was retrieved from small angle X-ray scattering (SAXS) data. BlCel9 is an endoglucanase exhibiting maximum catalytic efficiency at pH 7.0 and 60 °C. Furthermore, it retains 80% of catalytic activity within a broad range of pH values (5.5-8.5) and temperatures (up to 50 °C) for extended periods of time (over 48 h). It exhibits the highest hydrolytic activity against phosphoric acid swollen cellulose (PASC), followed by bacterial cellulose (BC), filter paper (FP), and to a lesser extent carboxymethylcellulose (CMC). The HPAEC-PAD analysis of the hydrolytic products demonstrated that the end product of the enzymatic hydrolysis is primarily cellobiose, and also small amounts of glucose, cellotriose, and cellotetraose are produced. SAXS data analysis revealed that the enzyme adopts a monomeric state in solution and has a molecular mass of 65.8 kDa as estimated from SAXS data. The BlCel9 has an elongated shape composed of an N-terminal family 3 carbohydrate-binding module (CBM3c) and a C-terminal GH9 catalytic domain joined together by 20 amino acid residue long linker peptides. The domains are closely juxtaposed in an extended conformation and form a relatively rigid structure in solution, indicating that the interactions between the CBM3c and GH9 catalytic domains might play a key role in cooperative cellulose biomass recognition and hydrolysis.
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Affiliation(s)
- Evandro Ares de Araújo
- Instituto de Física de São Carlos, Universidade de São Paulo, Av. Trabalhador Saocarlense 400, São Carlos, SP, 13560-970, Brazil
| | - Mário de Oliveira Neto
- Departmento de Física e Biofísica, Universidade Estadual Paulista "Júlio de Mesquita Filho", R. Prof. Dr. Antonio Celso Wagner Zanin 689, Jardim Sao Jose, Botucatu, SP, 18618-970, Brazil
| | - Igor Polikarpov
- Instituto de Física de São Carlos, Universidade de São Paulo, Av. Trabalhador Saocarlense 400, São Carlos, SP, 13560-970, Brazil.
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190
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Xylanosomes produced by Cellulosimicrobium cellulans F16 were diverse in size, but resembled in subunit composition. Arch Microbiol 2018; 201:163-170. [PMID: 30539263 DOI: 10.1007/s00203-018-1606-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 11/30/2018] [Accepted: 12/03/2018] [Indexed: 12/31/2022]
Abstract
The hemicellulolytic enzyme system produced by Cellulosimicrobium cellulans strain F16 was resolved by ultracentrifugation and size exclusion chromatography. The particle size and molecular weight were determined by both dynamic light scattering and negative stain electron microscopy. The results showed that xylanosomes produced by strain F16 were found to have an apparent sedimentation coefficient of 28 S, were diverse in size (18-70 nm), molecular weight (11-78 MDa) and morphology, but resembled in subunit composition (SDS-PAGE and proteomic results). It is proposed that particles of 22 nm may be the basic unit, while 43 nm and 60 nm particles observed may be dimer and trimer of the basic unit, or xylanosomes with smaller size might be degradation products of larger size xylanosomes. Moreover, such xylanosomes are also found to have strong binding affinity toward water-insoluble substrates such as Avicel, birchwood xylan, and corn cob.
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191
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McMillan JR, Hayes OG, Remis JP, Mirkin CA. Programming Protein Polymerization with DNA. J Am Chem Soc 2018; 140:15950-15956. [PMID: 30407003 DOI: 10.1021/jacs.8b10011] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
A strategy that utilizes DNA for controlling the association pathway of proteins is described. This strategy uses sequence-specific DNA interactions to program energy barriers for polymerization, allowing for either step-growth or chain-growth pathways to be accessed. Two sets of mutant green fluorescent protein (mGFP)-DNA monomers with single DNA modifications have been synthesized and characterized. Depending on the deliberately controlled sequence and conformation of the appended DNA, these monomers can be polymerized through either a step-growth or chain-growth pathway. Cryo-electron microscopy with Volta phase plate technology enables the visualization of the distribution of the oligomer and polymer products, and even the small mGFP-DNA monomers. Whereas cyclic and linear polymer distributions were observed for the step-growth DNA design, in the case of the chain-growth system linear chains exclusively were observed, and a dependence of the chain length on the concentration of the initiator strand was noted. Importantly, the chain-growth system possesses a living character whereby chains can be extended with the addition of fresh monomer. This work represents an important and early example of mechanistic control over protein assembly, thereby establishing a robust methodology for synthesizing oligomeric and polymeric protein-based materials with exceptional control over architecture.
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192
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Podell S, Blanton JM, Neu A, Agarwal V, Biggs JS, Moore BS, Allen EE. Pangenomic comparison of globally distributed Poribacteria associated with sponge hosts and marine particles. ISME JOURNAL 2018; 13:468-481. [PMID: 30291328 DOI: 10.1038/s41396-018-0292-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 09/12/2018] [Accepted: 09/15/2018] [Indexed: 01/10/2023]
Abstract
Candidatus Poribacteria is a little-known bacterial phylum, previously characterized by partial genomes from a single sponge host, but never isolated in culture. We have reconstructed multiple genome sequences from four different sponge genera and compared them to recently reported, uncharacterized Poribacteria genomes from the open ocean, discovering shared and unique functional characteristics. Two distinct, habitat-linked taxonomic lineages were identified, designated Entoporibacteria (sponge-associated) and Pelagiporibacteria (free-living). These lineages differed in flagellar motility and chemotaxis genes unique to Pelagiporibacteria, and highly expanded families of restriction endonucleases, DNA methylases, transposases, CRISPR repeats, and toxin-antitoxin gene pairs in Entoporibacteria. Both lineages shared pathways for facultative anaerobic metabolism, denitrification, fermentation, organosulfur compound utilization, type IV pili, cellulosomes, and bacterial proteosomes. Unexpectedly, many features characteristic of eukaryotic host association were also shared, including genes encoding the synthesis of eukaryotic-like cell adhesion molecules, extracellular matrix digestive enzymes, phosphoinositol-linked membrane glycolipids, and exopolysaccharide capsules. Complete Poribacteria 16S rRNA gene sequences were found to contain multiple mismatches to "universal" 16S rRNA gene primer sets, substantiating concerns about potential amplification failures in previous studies. A newly designed primer set corrects these mismatches, enabling more accurate assessment of Poribacteria abundance in diverse marine habitats where it may have previously been overlooked.
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Affiliation(s)
- Sheila Podell
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, La Jolla, San Diego, CA, USA
| | - Jessica M Blanton
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, La Jolla, San Diego, CA, USA
| | - Alexander Neu
- Division of Biological Sciences, University of California, La Jolla, San Diego, CA, USA
| | - Vinayak Agarwal
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA.,Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, La Jolla, San Diego, CA, USA
| | - Jason S Biggs
- University of Guam Marine Laboratory, UOG Station, Mangilao, Guam, USA
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, La Jolla, San Diego, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, La Jolla, San Diego, CA, USA
| | - Eric E Allen
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, La Jolla, San Diego, CA, USA. .,Division of Biological Sciences, University of California, La Jolla, San Diego, CA, USA. .,Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, La Jolla, San Diego, CA, USA.
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193
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Chen H, Huang R, Kim EJ, Zhang YHPJ. Building a Thermostable Metabolon for Facilitating Coenzyme Transport and In Vitro Hydrogen Production at Elevated Temperature. CHEMSUSCHEM 2018; 11:3120-3130. [PMID: 30014617 DOI: 10.1002/cssc.201801141] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 07/12/2018] [Indexed: 06/08/2023]
Abstract
To facilitate coenzyme transport and in vitro enzymatic hydrogen production, a multi-enzyme metabolon comprising a miniscaffoldin containing three cohesins, a dockerin-containing mutant dehydrogenase, a dockerin-containing diaphorase, and a Histidine-tagged (His-tagged) NiFe hydrogenase was constructed. As the NiFe hydrogenase has very complicated structure and cannot be fused directly with a dockerin, a bifunctional peptide was designed. The bifunctional peptide, in which one terminus contains a modified dockerin binding the cohesin of the miniscaffoldin and the other, after chemical modification, binds the His-tag of NiFe hydrogenase, enabled His-tagged proteins to be integrated into the cohesin-dockerin-based metabolon. The metabolon exhibited an initial reaction rate 4.5 times that of the enzyme cocktail at the same enzyme loading, which indicated enhanced coenzyme transport of the metabolon. However, this metabolon was unstable owing to the degradation of the miniscaffoldin at elevated temperature. Glutaraldehyde was used to cross-link the metabolon for locking its spatial organization. The cross-linked metabolon not only exhibited 2.5 times the reaction rate of the enzyme cocktail, but also retained its stability at 70 °C. The amount of hydrogen production catalyzed by the cross-linked metabolon was nearly twice that of the metabolon without glutaraldehyde cross-linking and four times that of the enzyme cocktail at 70 °C after 22 h of reaction.
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Affiliation(s)
- Hui Chen
- Biological Systems Engineering Department, Virginia Tech, 304 Seitz Hall, Blacksburg, Virginia, 24061, USA
| | - Rui Huang
- Biological Systems Engineering Department, Virginia Tech, 304 Seitz Hall, Blacksburg, Virginia, 24061, USA
| | - Eui-Jin Kim
- Biological Systems Engineering Department, Virginia Tech, 304 Seitz Hall, Blacksburg, Virginia, 24061, USA
| | - Yi-Heng P Job Zhang
- Biological Systems Engineering Department, Virginia Tech, 304 Seitz Hall, Blacksburg, Virginia, 24061, USA
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, P. R. China
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194
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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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195
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Comparative Biochemical Analysis of Cellulosomes Isolated from Clostridium clariflavum DSM 19732 and Clostridium thermocellum ATCC 27405 Grown on Plant Biomass. Appl Biochem Biotechnol 2018; 187:994-1010. [DOI: 10.1007/s12010-018-2864-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 08/13/2018] [Indexed: 12/12/2022]
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196
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Kaushik P, Rawat K, Aswal VK, Kohlbrecher J, Bohidar HB. Mixing ratio dependent complex coacervation versus bicontinuous gelation of pectin with in situ formed zein nanoparticles. SOFT MATTER 2018; 14:6463-6475. [PMID: 30051132 DOI: 10.1039/c8sm00809d] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We report on the competitive phenomenon of complex coacervation versus bicontinuous gelation between pectin (P, a polyanionic carbohydrate, [P] = 0.01-2% (w/v)) and zein nanoparticles (Z, a hydrophobic protein and a weak polyampholyte, [Z] = 0.1 and 0.5% (w/v), in an ethanolic solution of effective concentration 4 and 27% (v/v)), which was studied below (pH ≈ 4), and above (pH ≈ 7.4) the pI (≈ 6.2) of zein at room temperature, 25 °C. The uniqueness of this study arises from the interaction protocol used, where the pectin used was in the extended polyelectrolyte (persistence length ≈ 10 nm) conformation while zein was used as a charged globular nanoparticle (size ≈ 80-120 nm) that was formed in situ. Their mixing ratio, r = [P] : [Z] (w/w), was varied from 0.02 to 4.0 (for [Z] = 0.5% (w/v)), and from 0.1 to 7.5 (for [Z] = 0.1% (w/v)) in the ionic strength range 10-4 to 10-2 M NaCl. Zeta potential data revealed that at pH ≈ 4, the complementary binding condition, r = 1 : 1 (equivalent to 1 : 5 molecule/nanoparticle) demarcated the coacervate from the gel region. The measured rigidity (G0, low frequency storage modulus) of these materials revealed the following: for r < 1, (low pectin content samples, coacervate region) the material had lower values of Gcoac0, whereas for r > 1, an excess of pectin facilitated gelation with Ggel0 ≫ Gcoac0. Above pI, surface patch binding caused associative interactions and complex coacervation though both biopolymers had similar net charge. The network density was used as a descriptor to distinguish between the coacervate and gel samples. Their microstructures were probed by small angle neutron scattering (SANS), and viscoelastic properties by rheology. Simple modeling shows that formation of the interpolymer complex was favored in higher protein containing samples. Mixing ratio dependent selective coacervation (a kinetic process) and bicontinuous gelation (a thermodynamic process) are rarely seen to coexist in biopolymer interactions.
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Affiliation(s)
- Priyanka Kaushik
- School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
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197
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Steven J. VD, Richard M. L. Chitins and chitinase activity in airway diseases. J Allergy Clin Immunol 2018; 142:364-369. [PMID: 29959948 PMCID: PMC6078791 DOI: 10.1016/j.jaci.2018.06.017] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 06/19/2018] [Accepted: 06/22/2018] [Indexed: 01/04/2023]
Abstract
Chitin, one of the most abundant biopolymers on Earth, is bound and degraded by chitinases, specialized enzymes that are similarly widespread in nature. Chitin catabolism affects global carbon and nitrogen cycles through a host of diverse biological processes, but recent work has focused attention on systems of chitin recognition and degradation conserved in mammals, connecting an ancient pathway of polysaccharide processing to human diseases influenced by persistent immune triggering. Here we review current advances in our understanding of how chitin-chitinase interactions affect mucosal immune feedback mechanisms essential to maintaining homeostasis and organ health.
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Affiliation(s)
- Van Dyken Steven J.
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO USA.
| | - Locksley Richard M.
- Howard Hughes Medical Institute, Departments of Medicine and Microbiology / Immuology, University of California San Francisco, San Francisco, CA, USA.
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198
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Ortiz de Ora L, Lamed R, Liu YJ, Xu J, Cui Q, Feng Y, Shoham Y, Bayer EA, Muñoz-Gutiérrez I. Regulation of biomass degradation by alternative σ factors in cellulolytic clostridia. Sci Rep 2018; 8:11036. [PMID: 30038431 PMCID: PMC6056542 DOI: 10.1038/s41598-018-29245-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 07/04/2018] [Indexed: 11/28/2022] Open
Abstract
Bacteria can adjust their genetic programs via alternative σ factors to face new environmental pressures. Here, we analyzed a unique set of paralogous alternative σ factors, termed σIs, which fine-tune the regulation of one of the most intricate cellulolytic systems in nature, the bacterial cellulosome, that is involved in degradation of environmental polysaccharides. We combined bioinformatics with experiments to decipher the regulatory networks of five σIs in Clostridium thermocellum, the epitome of cellulolytic microorganisms, and one σI in Pseudobacteroides cellulosolvens which produces the cellulosomal system with the greatest known complexity. Despite high homology between different σIs, our data suggest limited cross-talk among them. Remarkably, the major cross-talk occurs within the main cellulosomal genes which harbor the same σI-dependent promoter elements, suggesting a promoter-based mechanism to guarantee the expression of relevant genes. Our findings provide insights into the mechanisms used by σIs to differentiate among their corresponding regulons, representing a comprehensive overview of the regulation of the cellulosome to date. Finally, we show the advantage of using a heterologous host system for analysis of multiple σIs, since information generated by their analysis in their natural host can be misinterpreted owing to a cascade of interactions among the different σIs.
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Affiliation(s)
- Lizett Ortiz de Ora
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Raphael Lamed
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Ya-Jun Liu
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
| | - Jian Xu
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
| | - Qiu Cui
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
| | - Yingang Feng
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
| | - Yuval Shoham
- Department of Biotechnology and Food Engineering, Technion-IIT, Haifa, Israel
| | - Edward A Bayer
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Iván Muñoz-Gutiérrez
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel. .,Outreach Research Training and Minority Science Programs, Francisco Ayala School of Biological Sciences, University of California, Irvine, California, USA.
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199
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Bugada LF, Smith MR, Wen F. Engineering Spatially Organized Multienzyme Assemblies for Complex Chemical Transformation. ACS Catal 2018. [DOI: 10.1021/acscatal.8b01883] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Luke F. Bugada
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Mason R. Smith
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Fei Wen
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
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200
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Hitschler L, Kuntz M, Langschied F, Basen M. Thermoanaerobacter species differ in their potential to reduce organic acids to their corresponding alcohols. Appl Microbiol Biotechnol 2018; 102:8465-8476. [DOI: 10.1007/s00253-018-9210-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 06/14/2018] [Accepted: 06/28/2018] [Indexed: 11/28/2022]
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