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Peng X, Qiao W, Mi S, Jia X, Su H, Han Y. Characterization of hemicellulase and cellulase from the extremely thermophilic bacterium Caldicellulosiruptor owensensis and their potential application for bioconversion of lignocellulosic biomass without pretreatment. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:131. [PMID: 26322125 PMCID: PMC4552416 DOI: 10.1186/s13068-015-0313-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 08/13/2015] [Indexed: 05/08/2023]
Abstract
BACKGROUND Pretreatment is currently the common approach for improving the efficiency of enzymatic hydrolysis on lignocellulose. However, the pretreatment process is expensive and will produce inhibitors such as furan derivatives and phenol derivatives. If the lignocellulosic biomass can efficiently be saccharified by enzymolysis without pretreatment, the bioconversion process would be simplified. The genus Caldicellulosiruptor, an obligatory anaerobic and extreme thermophile can produce a diverse set of glycoside hydrolases (GHs) for deconstruction of lignocellulosic biomass. It gives potential opportunities for improving the efficiency of converting native lignocellulosic biomass to fermentable sugars. RESULTS Both of the extracellular (extra-) and intracellular (intra-) enzymes of C. owensensis cultivated on corncob xylan or xylose had cellulase (including endoglucanase, cellobiohydrolase and β-glucosidase) and hemicellulase (including xylanase, xylosidase, arabinofuranosidase and acetyl xylan esterase) activities. The enzymes of C. owensensis had high ability for degrading hemicellulose of native corn stover and corncob with the conversion rates of xylan 16.7 % and araban 60.0 %. Moreover, they had remarkable synergetic function with the commercial enzyme cocktail Cellic CTec2 (Novoyzmes). When the native corn stover and corncob were respectively, sequentially hydrolyzed by the extra-enzymes of C. owensensis and CTec2, the glucan conversion rates were 31.2 and 37.9 %,which were 1.7- and 1.9-fold of each control (hydrolyzed by CTec2 alone), whereas the glucan conversion rates of the steam-exploded corn stover and corncob hydrolyzed by CTec2 alone on the same loading rate were 38.2 and 39.6 %, respectively. These results show that hydrolysis by the extra-enzyme of C. owensensis made almost the same contribution as steam-exploded pretreatment on degradation of native lignocellulosic biomass. A new process for saccharification of lignocellulosic biomass by sequential hydrolysis is demonstrated in the present research, namely hyperthermal enzymolysis (70-80 °C) by enzymes of C. owensensis followed with mesothermal enzymolysis (50-55 °C) by commercial cellulase. This process has the advantages of no sugar loss, few inhibitors generation and consolidated with sterilization. CONCLUSIONS The enzymes of C. owensensis demonstrated an enhanced ability to degrade the hemicellulose of native lignocellulose. The pretreatment and detoxification steps may be removed from the bioconversion process of the lignocellulosic biomass by using the enzymes from C. owensensis.
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Affiliation(s)
- Xiaowei Peng
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, China
| | - Weibo Qiao
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, China
| | - Shuofu Mi
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, China
| | - Xiaojing Jia
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, China
| | - Hong Su
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, China
| | - Yejun Han
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, China
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152
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Walker JA, Takasuka TE, Deng K, Bianchetti CM, Udell HS, Prom BM, Kim H, Adams PD, Northen TR, Fox BG. Multifunctional cellulase catalysis targeted by fusion to different carbohydrate-binding modules. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:220. [PMID: 26697109 PMCID: PMC4687162 DOI: 10.1186/s13068-015-0402-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 11/30/2015] [Indexed: 05/11/2023]
Abstract
BACKGROUND Carbohydrate binding modules (CBMs) bind polysaccharides and help target glycoside hydrolases catalytic domains to their appropriate carbohydrate substrates. To better understand how CBMs can improve cellulolytic enzyme reactivity, representatives from each of the 18 families of CBM found in Ruminoclostridium thermocellum were fused to the multifunctional GH5 catalytic domain of CelE (Cthe_0797, CelEcc), which can hydrolyze numerous types of polysaccharides including cellulose, mannan, and xylan. Since CelE is a cellulosomal enzyme, none of these fusions to a CBM previously existed. RESULTS CelEcc_CBM fusions were assayed for their ability to hydrolyze cellulose, lichenan, xylan, and mannan. Several CelEcc_CBM fusions showed enhanced hydrolytic activity with different substrates relative to the fusion to CBM3a from the cellulosome scaffoldin, which has high affinity for binding to crystalline cellulose. Additional binding studies and quantitative catalysis studies using nanostructure-initiator mass spectrometry (NIMS) were carried out with the CBM3a, CBM6, CBM30, and CBM44 fusion enzymes. In general, and consistent with observations of others, enhanced enzyme reactivity was correlated with moderate binding affinity of the CBM. Numerical analysis of reaction time courses showed that CelEcc_CBM44, a combination of a multifunctional enzyme domain with a CBM having broad binding specificity, gave the fastest rates for hydrolysis of both the hexose and pentose fractions of ionic-liquid pretreated switchgrass. CONCLUSION We have shown that fusions of different CBMs to a single multifunctional GH5 catalytic domain can increase its rate of reaction with different pure polysaccharides and with pretreated biomass. This fusion approach, incorporating domains with broad specificity for binding and catalysis, provides a new avenue to improve reactivity of simple combinations of enzymes within the complexity of plant biomass.
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Affiliation(s)
- Johnnie A. Walker
- />US Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706 USA
- />Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Taichi E. Takasuka
- />US Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706 USA
- />Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
- />Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589 Japan
| | - Kai Deng
- />US Department of Energy Joint BioEnergy Institute, Emeryville, CA 94608 USA
- />Sandia National Laboratories, Livermore, CA 94551 USA
| | - Christopher M. Bianchetti
- />US Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706 USA
- />Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
- />Department of Chemistry, University of Wisconsin-Oshkosh, Oshkosh, WI 54901 USA
| | - Hannah S. Udell
- />US Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Ben M. Prom
- />US Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Hyunkee Kim
- />US Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Paul D. Adams
- />US Department of Energy Joint BioEnergy Institute, Emeryville, CA 94608 USA
- />Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
- />Department of Bioengineering, University of California, Berkeley, CA 94720 USA
| | - Trent R. Northen
- />US Department of Energy Joint BioEnergy Institute, Emeryville, CA 94608 USA
- />Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Brian G. Fox
- />US Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706 USA
- />Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
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153
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Bunterngsook B, Eurwilaichitr L, Thamchaipenet A, Champreda V. Binding characteristics and synergistic effects of bacterial expansins on cellulosic and hemicellulosic substrates. BIORESOURCE TECHNOLOGY 2015; 176:129-35. [PMID: 25460993 DOI: 10.1016/j.biortech.2014.11.042] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 11/05/2014] [Accepted: 11/06/2014] [Indexed: 05/26/2023]
Abstract
Expansins are non-catalytic proteins which loosen plant cell wall structure. In this study, binding kinetics and synergistic action of five bacterial expansins on cellulosic and hemicellulosic polysaccharides were studied. The expansins differed in binding capacity (Bmax) and affinity (Kd) for different substrates. A common pattern of binding efficiency (Bmax/Kd) was found among the expansins tested, in which efficiency was greatest for the phosphoric acid-swollen cellulose (PASC), then the hemicellulose arabinoxylan followed by the microcrystalline cellulose (Avicel PH101). The expansins enhanced the action of Trichoderma reesei cellulase/hemicellulase mixture for degrading all three substrates to varying degrees. Among the substrates and expansins tested, BpEX from Bacillus pumilus and CmEX from Clavibacter michiganensis showed the greatest enhancement effect on arabinoxylan with 11.4 and 12.2-fold greater reducing sugar yield than the reaction with enzyme alone. The work gives insights into the wider application of expansins on enhancing polysaccharide hydrolysis, particularly on hemicellulosic substrates.
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Affiliation(s)
- Benjarat Bunterngsook
- Department of Genetics, Faculty of Sciences, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Lily Eurwilaichitr
- Enzyme Technology Laboratory, Bioresources Technology Unit, National Center for Genetic Engineering and Biotechnology, Thailand Science Park, Khlong Luang, Pathum Thani 12120, Thailand.
| | - Arinthip Thamchaipenet
- Department of Genetics, Faculty of Sciences, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Verawat Champreda
- Enzyme Technology Laboratory, Bioresources Technology Unit, National Center for Genetic Engineering and Biotechnology, Thailand Science Park, Khlong Luang, Pathum Thani 12120, Thailand
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154
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Wojciechowski M, Thompson D, Cieplak M. Mechanostability of cohesin-dockerin complexes in a structure-based model: anisotropy and lack of universality in the force profiles. J Chem Phys 2014; 141:245103. [PMID: 25554187 DOI: 10.1063/1.4904726] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We use a structure-based coarse grained model to elucidate stretching of three cohesin-dockerin complexes that are found in the cellulosome. The average strength of mechanostability is comparable to that of the I27 domain of titin, but the force profiles depend on the pulling direction and anisotropy effects can be substantial. Even though the force profiles for individual cohesins and dockerins are similar, those for their complexes are visibly distinct for any pulling direction.
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Affiliation(s)
- Michał Wojciechowski
- Institute of Physics, Polish Academy of Sciences, Aleja Lotników 32/46, 02-668 Warsaw, Poland
| | - Damien Thompson
- Materials and Surface Science Institute and Department of Physics and Energy, University of Limerick, Limerick, Ireland
| | - Marek Cieplak
- Institute of Physics, Polish Academy of Sciences, Aleja Lotników 32/46, 02-668 Warsaw, Poland
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155
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Bringing functions together with fusion enzymes—from nature’s inventions to biotechnological applications. Appl Microbiol Biotechnol 2014; 99:1545-56. [DOI: 10.1007/s00253-014-6315-1] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Revised: 12/04/2014] [Accepted: 12/09/2014] [Indexed: 12/18/2022]
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156
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Schoeler C, Malinowska KH, Bernardi RC, Milles LF, Jobst MA, Durner E, Ott W, Fried DB, Bayer EA, Schulten K, Gaub HE, Nash MA. Ultrastable cellulosome-adhesion complex tightens under load. Nat Commun 2014; 5:5635. [PMID: 25482395 PMCID: PMC4266597 DOI: 10.1038/ncomms6635] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 10/22/2014] [Indexed: 11/09/2022] Open
Abstract
Challenging environments have guided nature in the development of ultrastable protein complexes. Specialized bacteria produce discrete multi-component protein networks called cellulosomes to effectively digest lignocellulosic biomass. While network assembly is enabled by protein interactions with commonplace affinities, we show that certain cellulosomal ligand-receptor interactions exhibit extreme resistance to applied force. Here, we characterize the ligand-receptor complex responsible for substrate anchoring in the Ruminococcus flavefaciens cellulosome using single-molecule force spectroscopy and steered molecular dynamics simulations. The complex withstands forces of 600-750 pN, making it one of the strongest bimolecular interactions reported, equivalent to half the mechanical strength of a covalent bond. Our findings demonstrate force activation and inter-domain stabilization of the complex, and suggest that certain network components serve as mechanical effectors for maintaining network integrity. This detailed understanding of cellulosomal network components may help in the development of biocatalysts for production of fuels and chemicals from renewable plant-derived biomass.
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Affiliation(s)
- 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
| | - Rafael C Bernardi
- Theoretical and Computational Biophysics Group, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Lukas F Milles
- Lehrstuhl für Angewandte Physik and Center for Nanoscience, Ludwig-Maximilians-Universität, 80799 Munich, Germany
| | - Markus A Jobst
- Lehrstuhl für Angewandte Physik and Center for Nanoscience, Ludwig-Maximilians-Universität, 80799 Munich, Germany
| | - Ellis Durner
- Lehrstuhl für Angewandte Physik and Center for Nanoscience, Ludwig-Maximilians-Universität, 80799 Munich, Germany
| | - Wolfgang Ott
- Lehrstuhl für Angewandte Physik and Center for Nanoscience, Ludwig-Maximilians-Universität, 80799 Munich, Germany
| | - Daniel B Fried
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Edward A Bayer
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Klaus Schulten
- 1] Theoretical and Computational Biophysics Group, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA [2] Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Hermann E Gaub
- Lehrstuhl für Angewandte Physik and Center for Nanoscience, Ludwig-Maximilians-Universität, 80799 Munich, Germany
| | - Michael A Nash
- Lehrstuhl für Angewandte Physik and Center for Nanoscience, Ludwig-Maximilians-Universität, 80799 Munich, Germany
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157
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Khattak WA, Ullah MW, Ul-Islam M, Khan S, Kim M, Kim Y, Park JK. Developmental strategies and regulation of cell-free enzyme system for ethanol production: a molecular prospective. Appl Microbiol Biotechnol 2014; 98:9561-78. [PMID: 25359472 DOI: 10.1007/s00253-014-6154-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 10/09/2014] [Accepted: 10/12/2014] [Indexed: 10/24/2022]
Abstract
Most biomanufacturing systems developed for the production of biocommodities are based on whole-cell systems. However, with the advent of innovative technologies, the focus has shifted from whole-cell towards cell-free enzyme system. Since more than a century, researchers are using the cell-free extract containing the required enzymes and their respective cofactors in order to study the fundamental aspects of biological systems, particularly fermentation. Although yeast cell-free enzyme system is known since long ago, it is rarely been studied and characterized in detail. In this review, we hope to describe the major pitfalls encountered by whole-cell system and introduce possible solutions to them using cell-free enzyme systems. We have discussed the glycolytic and fermentative pathways and their regulation at both transcription and translational levels. Moreover, several strategies employed for development of cell-free enzyme system have been described with their potential merits and shortcomings associated with these developmental approaches. We also described in detail the various developmental approaches of synthetic cell-free enzyme system such as compartmentalization, metabolic channeling, protein fusion, and co-immobilization strategies. Additionally, we portrayed the novel cell-free enzyme technologies based on encapsulation and immobilization techniques and their development and commercialization. Through this review, we have presented the basics of cell-free enzyme system, the strategies involved in development and operation, and the advantages over conventional processes. Finally, we have addressed some potential directions for the future development and industrialization of cell-free enzyme system.
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Affiliation(s)
- Waleed Ahmad Khattak
- Department of Chemical Engineering, Kyungpook National University, Daegu, 7020-701, Korea
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158
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Bernardi RC, Melo MCR, Schulten K. Enhanced sampling techniques in molecular dynamics simulations of biological systems. Biochim Biophys Acta Gen Subj 2014; 1850:872-877. [PMID: 25450171 DOI: 10.1016/j.bbagen.2014.10.019] [Citation(s) in RCA: 410] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Revised: 10/17/2014] [Accepted: 10/20/2014] [Indexed: 01/29/2023]
Abstract
BACKGROUND Molecular dynamics has emerged as an important research methodology covering systems to the level of millions of atoms. However, insufficient sampling often limits its application. The limitation is due to rough energy landscapes, with many local minima separated by high-energy barriers, which govern the biomolecular motion. SCOPE OF REVIEW In the past few decades methods have been developed that address the sampling problem, such as replica-exchange molecular dynamics, metadynamics and simulated annealing. Here we present an overview over theses sampling methods in an attempt to shed light on which should be selected depending on the type of system property studied. MAJOR CONCLUSIONS Enhanced sampling methods have been employed for a broad range of biological systems and the choice of a suitable method is connected to biological and physical characteristics of the system, in particular system size. While metadynamics and replica-exchange molecular dynamics are the most adopted sampling methods to study biomolecular dynamics, simulated annealing is well suited to characterize very flexible systems. The use of annealing methods for a long time was restricted to simulation of small proteins; however, a variant of the method, generalized simulated annealing, can be employed at a relatively low computational cost to large macromolecular complexes. GENERAL SIGNIFICANCE Molecular dynamics trajectories frequently do not reach all relevant conformational substates, for example those connected with biological function, a problem that can be addressed by employing enhanced sampling algorithms. This article is part of a Special Issue entitled Recent developments of molecular dynamics.
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Affiliation(s)
| | - Marcelo C R Melo
- Center for Biophysics and Computational Biology, University of Illinois, Urbana, IL 61801, USA
| | - Klaus Schulten
- Beckman Institute, University of Illinois, Urbana, IL 61801, USA; Center for Biophysics and Computational Biology, University of Illinois, Urbana, IL 61801, USA; Department of Physics, University of Illinois, Urbana, IL 61801, USA.
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159
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von Schantz L, Håkansson M, Logan DT, Nordberg-Karlsson E, Ohlin M. Carbohydrate binding module recognition of xyloglucan defined by polar contacts with branching xyloses and CH-Π interactions. Proteins 2014; 82:3466-75. [PMID: 25302425 DOI: 10.1002/prot.24700] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2014] [Revised: 09/03/2014] [Accepted: 09/19/2014] [Indexed: 12/13/2022]
Abstract
Engineering of novel carbohydrate-binding proteins that can be utilized in various biochemical and biotechnical applications would benefit from a deeper understanding of the biochemical interactions that determine protein-carbohydrate specificity. In an effort to understand further the basis for specificity we present the crystal structure of the multi-specific carbohydrate-binding module (CBM) X-2 L110F bound to a branched oligomer of xyloglucan (XXXG). X-2 L110F is an engineered CBM that can recognize xyloglucan, xylans and β-glucans. The structural observations of the present study compared with previously reported structures of X-2 L110F in complex with linear oligomers, show that the π-surface of a phenylalanine, F110, allows for interactions with hydrogen atoms on both linear (xylopentaose and cellopentaose) and branched ligands (XXXG). Furthermore, X-2 L110F is shown to have a relatively flexible binding cleft, as illustrated in binding to XXXG. This branched ligand requires a set of reorientations of protein side chains Q72, N31, and R142, although these residues have previously been determined as important for binding to xylose oligomers by mediating polar contacts. The loss of these polar contacts is compensated for in binding to XXXG by polar interactions mediated by other protein residues, T74, R115, and Y149, which interact mainly with the branching xyloses of the xyloglucan oligomer. Taken together, the present study illustrates in structural detail how CH-π interactions can influence binding specificity and that flexibility is a key feature for the multi-specificity displayed by X-2 L110F, allowing for the accommodation of branched ligands.
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Affiliation(s)
- Laura von Schantz
- Department of Immunotechnology, Lund University, Medicon Village, SE-223 81 Lund, Sweden
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160
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Hyeon JE, Kang DH, Han SO. Signal amplification by a self-assembled biosensor system designed on the principle of dockerin-cohesin interactions in a cellulosome complex. Analyst 2014; 139:4790-3. [PMID: 25093214 DOI: 10.1039/c4an00856a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
To construct a self-assembled biosensor with signal amplification, a cellulosome system, comprising type I and type II dockerin-cohesin interactions with different specificities, from the anaerobic Clostridia bacterium was applied. The self-assembled biosensor was highly sensitive and achieved 128.1-fold increase in detection levels compared to the control.
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Affiliation(s)
- Jeong Eun Hyeon
- Department of Biotechnology, Korea University, Seoul 136-701, Republic of Korea.
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161
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Inoue I, Watanabe K, Yamauchi H, Ishikawa Y, Yasueda H, Uraoka Y, Yamashita I. Biological construction of single-walled carbon nanotube electron transfer pathways in dye-sensitized solar cells. CHEMSUSCHEM 2014; 7:2805-2810. [PMID: 25111295 DOI: 10.1002/cssc.201402514] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Indexed: 06/03/2023]
Abstract
We designed and mass-produced a versatile protein supramolecule that can be used to manufacture a highly efficient dye-sensitized solar cell (DSSC). Twelve single-walled carbon-nanotube (SWNT)-binding and titanium-mineralizing peptides were genetically integrated on a cage-shaped dodecamer protein (CDT1). A process involving simple mixing of highly conductive SWNTs with CDT1 followed by TiO2 biomineralization produces a high surface-area/weight TiO2 -(anatase)-coated intact SWNT nanocomposite under environmentally friendly conditions. A DSSC with a TiO2 photoelectrode containing 0.2 wt % of the SWNT-TiO2 nanocomposite shows a current density improvement by 80% and a doubling of the photoelectric conversion efficiency. The SWNT-TiO2 nanocomposite transfers photon-generated electrons from dye molecules adsorbed on the TiO2 to the anode electrode swiftly.
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Affiliation(s)
- Ippei Inoue
- Frontier Research Labs., Institute for Innovation, Ajinomoto Co., Inc. (Japan)
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162
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Fan X, Bai L, Zhu L, Yang L, Zhang X. Marine algae-derived bioactive peptides for human nutrition and health. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2014; 62:9211-22. [PMID: 25179496 DOI: 10.1021/jf502420h] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Within the parent protein molecule, most peptides are inactive, and they are released with biofunctionalities after enzymatic hydrolysis. Marine algae have high protein content, up to 47% of the dry weight, depending on the season and the species. Recently, there is an increasing interest in using marine algae protein as a source of bioactive peptides due to their health promotion and disease therapy potentials. This review presents an overview of marine algae-derived bioactive peptides and especially highlights some key issues, such as in silico proteolysis and quantitative structure-activity relationship studies, in vivo fate of bioactive peptides, and novel technologies in bioactive peptides studies and production.
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Affiliation(s)
- Xiaodan Fan
- College of Light Industry and Food Sciences, South China University of Technology , Guangzhou, China
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163
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Purification and characterization of a cellulolytic multienzyme complex produced by Neocallimastix patriciarum J11. Biochem Biophys Res Commun 2014; 451:190-5. [PMID: 25073115 DOI: 10.1016/j.bbrc.2014.07.088] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 07/19/2014] [Indexed: 11/24/2022]
Abstract
Understanding the roles of the components of the multienzyme complex of the anaerobial cellulase system, acting on complex substrates, is crucial to the development of efficient cellulase systems for industrial applications such as converting lignocellulose to sugars for bioethanol production. In this study, we purified the multienzyme complex of Neocallimastix patriciarum J11 from a broth through cellulose affinity purification. The multienzyme complex is composed of at least 12 comprised proteins, based on sodium dodecyl sulfate polyacrylamide gel electrophoresis. Eight of these constituents have demonstrated β-glucanase activity on zymogram analysis. The multienzyme complex contained scaffoldings that respond to the gathering of the cellulolytic components. The levels and subunit ratio of the multienzyme complex from N. patriciarum J11 might have been affected by their utilized carbon sources, whereas the components of the complexes were consistent. The trypsin-digested peptides of six proteins were matched to the sequences of cellulases originating from rumen fungi, based on identification through liquid chromatography/mass spectrometry, revealing that at least three types of cellulase, including one endoglucanase and two exoglucanases, could be found in the multienzyme complex of N. patriciarum J11. The cellulolytic subunits could hydrolyze synergistically on both the internal bonds and the reducing and nonreducing ends of cellulose. Based on our research, our findings are the first to depict the composition of the multienzyme complex produced by N. patriciarum J11, and this complex is composed of scaffoldin and three types of cellulase.
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164
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Artzi L, Dassa B, Borovok I, Shamshoum M, Lamed R, Bayer EA. Cellulosomics of the cellulolytic thermophile Clostridium clariflavum. BIOTECHNOLOGY FOR BIOFUELS 2014; 7:100. [PMID: 26413154 PMCID: PMC4582956 DOI: 10.1186/1754-6834-7-100] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 06/12/2014] [Indexed: 05/23/2023]
Abstract
BACKGROUND Clostridium clariflavum is an anaerobic, thermophilic, Gram-positive bacterium, capable of growth on crystalline cellulose as a single carbon source. The genome of C. clariflavum has been sequenced to completion, and numerous cellulosomal genes were identified, including putative scaffoldin and enzyme subunits. RESULTS Bioinformatic analysis of the C. clariflavum genome revealed 49 cohesin modules distributed on 13 different scaffoldins and 79 dockerin-containing proteins, suggesting an abundance of putative cellulosome assemblies. The 13-scaffoldin system of C. clariflavum is highly reminiscent of the proposed cellulosome system of Acetivibrio cellulolyticus. Analysis of the C. clariflavum type I dockerin sequences indicated a very high level of conservation, wherein the putative recognition residues are remarkably similar to those of A. cellulolyticus. The numerous interactions among the cellulosomal components were elucidated using a standardized affinity ELISA-based fusion-protein system. The results revealed a rather simplistic recognition pattern of cohesin-dockerin interaction, whereby the type I and type II cohesins generally recognized the dockerins of the same type. The anticipated exception to this rule was the type I dockerin of the ScaB adaptor scaffoldin which bound selectively to the type I cohesins of ScaC and ScaJ. CONCLUSIONS The findings reveal an intricate picture of predicted cellulosome assemblies in C. clariflavum. The network of cohesin-dockerin pairs provides a thermophilic alternative to those of C. thermocellum and a basis for subsequent utilization of the C. clariflavum cellulosomal system for biotechnological application.
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Affiliation(s)
- Lior Artzi
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel
| | - Bareket Dassa
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel
| | - Ilya Borovok
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, Israel
| | - Melina Shamshoum
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel
| | - Raphael Lamed
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, Israel
| | - Edward A Bayer
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel
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165
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Ciric M, Moon CD, Leahy SC, Creevey CJ, Altermann E, Attwood GT, Rakonjac J, Gagic D. Metasecretome-selective phage display approach for mining the functional potential of a rumen microbial community. BMC Genomics 2014; 15:356. [PMID: 24886150 PMCID: PMC4035507 DOI: 10.1186/1471-2164-15-356] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Accepted: 04/29/2014] [Indexed: 11/22/2022] Open
Abstract
Background In silico, secretome proteins can be predicted from completely sequenced genomes using various available algorithms that identify membrane-targeting sequences. For metasecretome (collection of surface, secreted and transmembrane proteins from environmental microbial communities) this approach is impractical, considering that the metasecretome open reading frames (ORFs) comprise only 10% to 30% of total metagenome, and are poorly represented in the dataset due to overall low coverage of metagenomic gene pool, even in large-scale projects. Results By combining secretome-selective phage display and next-generation sequencing, we focused the sequence analysis of complex rumen microbial community on the metasecretome component of the metagenome. This approach achieved high enrichment (29 fold) of secreted fibrolytic enzymes from the plant-adherent microbial community of the bovine rumen. In particular, we identified hundreds of heretofore rare modules belonging to cellulosomes, cell-surface complexes specialised for recognition and degradation of the plant fibre. Conclusions As a method, metasecretome phage display combined with next-generation sequencing has a power to sample the diversity of low-abundance surface and secreted proteins that would otherwise require exceptionally large metagenomic sequencing projects. As a resource, metasecretome display library backed by the dataset obtained by next-generation sequencing is ready for i) affinity selection by standard phage display methodology and ii) easy purification of displayed proteins as part of the virion for individual functional analysis. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-356) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | - Jasna Rakonjac
- Animal Nutrition and Health, AgResearch Ltd, Palmerston North 4442, New Zealand.
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166
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Sermsathanaswadi J, Pianwanit S, Pason P, Waeonukul R, Tachaapaikoon C, Ratanakhanokchai K, Septiningrum K, Kosugi A. The C-terminal region of xylanase domain in Xyn11A from Paenibacillus curdlanolyticus B-6 plays an important role in structural stability. Appl Microbiol Biotechnol 2014; 98:8223-33. [DOI: 10.1007/s00253-014-5748-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 03/31/2014] [Accepted: 04/02/2014] [Indexed: 02/02/2023]
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167
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Stern J, Anbar M, Moraïs S, Lamed R, Bayer EA. Insights into enhanced thermostability of a cellulosomal enzyme. Carbohydr Res 2014; 389:78-84. [DOI: 10.1016/j.carres.2014.01.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Revised: 01/13/2014] [Accepted: 01/17/2014] [Indexed: 10/25/2022]
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168
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Xie S, Syrenne R, Sun S, Yuan JS. Exploration of Natural Biomass Utilization Systems (NBUS) for advanced biofuel--from systems biology to synthetic design. Curr Opin Biotechnol 2014; 27:195-203. [PMID: 24657913 DOI: 10.1016/j.copbio.2014.02.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2013] [Revised: 02/07/2014] [Accepted: 02/08/2014] [Indexed: 12/24/2022]
Abstract
Efficient degradation and utilization of lignocellulosic biomass remains a challenge for sustainable and affordable biofuels. Various natural biomass utilization systems (NBUS) evolved the capacity to combat the recalcitrance of plant cell walls. The study of these NBUS could enable the development of efficient and cost-effective biocatalysts, microorganisms, and bioprocesses for biofuels and bioproducts. Here, we reviewed the recent research progresses for several NBUS, ranging from single cell microorganisms to consortiums such as cattle rumen and insect guts. These studies aided the discovery of biomass-degrading enzymes and the elucidation of the evolutionary and functional relevance in these systems. In particular, advances in the next generation 'omics' technologies offered new opportunities to explore NBUS in a high-throughput manner. Systems biology helped to facilitate the rapid biocatalyst discovery and detailed mechanism analysis, which could in turn guide the reverse design of engineered microorganisms and bioprocesses for cost-effective and efficient biomass conversion.
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Affiliation(s)
- Shangxian Xie
- Texas A&M Agrilife Synthetic and Systems Biology Innovation Hub, Department of Plant Pathology and Microbiology, Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843, United States
| | - Ryan Syrenne
- Texas A&M Agrilife Synthetic and Systems Biology Innovation Hub, Department of Plant Pathology and Microbiology, Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843, United States; Molecular & Environmental Plant Sciences, Texas A&M University, College Station, TX 77843, United States
| | - Su Sun
- Texas A&M Agrilife Synthetic and Systems Biology Innovation Hub, Department of Plant Pathology and Microbiology, Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843, United States
| | - Joshua S Yuan
- Texas A&M Agrilife Synthetic and Systems Biology Innovation Hub, Department of Plant Pathology and Microbiology, Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843, United States.
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169
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O'Connell JD, Tsechansky M, Royal A, Boutz DR, Ellington AD, Marcotte EM. A proteomic survey of widespread protein aggregation in yeast. MOLECULAR BIOSYSTEMS 2014; 10:851-861. [PMID: 24488121 DOI: 10.1039/c3mb70508k] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Many normally cytosolic yeast proteins form insoluble intracellular bodies in response to nutrient depletion, suggesting the potential for widespread protein aggregation in stressed cells. Nearly 200 such bodies have been found in yeast by screening libraries of fluorescently tagged proteins. In order to more broadly characterize the formation of these bodies in response to stress, we employed a proteome-wide shotgun mass spectrometry assay in order to measure shifts in the intracellular solubilities of endogenous proteins following heat stress. As quantified by mass spectrometry, heat stress tended to shift the same proteins into insoluble form as did nutrient depletion; many of these proteins were also known to form foci in response to arsenic stress. Affinity purification of several foci-forming proteins showed enrichment for co-purifying chaperones, including Hsp90 chaperones. Tests of induction conditions and co-localization of metabolic enzymes participating in the same metabolic pathways suggested those foci did not correspond to multi-enzyme organizing centers. Thus, in yeast, the formation of stress bodies appears common across diverse, normally diffuse cytoplasmic proteins and is induced by multiple types of cell stress, including thermal, chemical, and nutrient stress.
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Affiliation(s)
- Jeremy D O'Connell
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of America.,Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, United States of America
| | - Mark Tsechansky
- Department of Chemistry, Cambridge University, Lensfield Road, Cambridge, UK
| | - Ariel Royal
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of America
| | - Daniel R Boutz
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of America
| | - Andrew D Ellington
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of America.,Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, United States of America
| | - Edward M Marcotte
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of America.,Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, United States of America
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170
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de Lorenzo V. From theselfish genetoselfish metabolism: Revisiting the central dogma. Bioessays 2014; 36:226-35. [DOI: 10.1002/bies.201300153] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Víctor de Lorenzo
- Systems & Synthetic Biology Program; Centro Nacional de Biotecnología CSIC Cantoblanco; Madrid Spain
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171
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Xu T, Li Y, He Z, Zhou J. Dockerin-containing protease inhibitor protects key cellulosomal cellulases from proteolysis inClostridium cellulolyticum. Mol Microbiol 2014; 91:694-705. [DOI: 10.1111/mmi.12488] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/07/2013] [Indexed: 11/28/2022]
Affiliation(s)
- Tao Xu
- Institute for Environmental Genomics; University of Oklahoma; Norman OK 73071 USA
- Department of Microbiology and Plant Biology; University of Oklahoma; Norman OK 73071 USA
| | - Yongchao Li
- Institute for Environmental Genomics; University of Oklahoma; Norman OK 73071 USA
- Department of Microbiology and Plant Biology; University of Oklahoma; Norman OK 73071 USA
| | - Zhili He
- Institute for Environmental Genomics; University of Oklahoma; Norman OK 73071 USA
- Virtual Institute for Microbial Stress and Survival; Berkeley USA
| | - Jizhong Zhou
- Institute for Environmental Genomics; University of Oklahoma; Norman OK 73071 USA
- Virtual Institute for Microbial Stress and Survival; Berkeley USA
- Earth Sciences Division; Lawrence Berkeley National Laboratory; Berkeley CA 94720 USA
- Department of Environmental Science and Engineering; Tsinghua University; Beijing 100084 China
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172
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Affiliation(s)
- Hisashi Kimoto
- Department of Bioscience, Faculty of Biotechnology, Fukui Prefectural University
| | - Takafumi Itoh
- Department of Bioscience, Faculty of Biotechnology, Fukui Prefectural University
| | - Takao Hibi
- Department of Bioscience, Faculty of Biotechnology, Fukui Prefectural University
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173
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Sun Q, Madan B, Tsai SL, DeLisa MP, Chen W. Creation of artificial cellulosomes on DNA scaffolds by zinc finger protein-guided assembly for efficient cellulose hydrolysis. Chem Commun (Camb) 2014; 50:1423-5. [DOI: 10.1039/c3cc47215a] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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174
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Geng X, Henderson WA. Impact of non-solvents on the structural features and enzymatic digestibility of cellulose regenerated from an ionic liquid. RSC Adv 2014. [DOI: 10.1039/c4ra05019c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The choice of non-solvent used to precipitate cellulose after dissolution in an ionic liquid strongly influence the resulting cellulose structure.
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Affiliation(s)
- Xinglian Geng
- Ionic Liquids & Electrolytes for Energy Technologies (ILEET) Laboratory
- Department of Chemical & Biomolecular Engineering
- North Carolina State University
- Raleigh, USA
| | - Wesley A. Henderson
- Ionic Liquids & Electrolytes for Energy Technologies (ILEET) Laboratory
- Department of Chemical & Biomolecular Engineering
- North Carolina State University
- Raleigh, USA
- Energy & Environment Directorate
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175
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Chen R, Chen Q, Kim H, Siu KH, Sun Q, Tsai SL, Chen W. Biomolecular scaffolds for enhanced signaling and catalytic efficiency. Curr Opin Biotechnol 2013; 28:59-68. [PMID: 24832076 DOI: 10.1016/j.copbio.2013.11.007] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 11/18/2013] [Accepted: 11/19/2013] [Indexed: 11/16/2022]
Abstract
Proteins inherently are not designed to be standalone entities. Whether it is a multi-step biochemical reaction or a signaling event that triggers several other cascading events, proteins are naturally designed to function cohesively. Several natural systems have been developed through evolution to co-localize the functional proteins of the same pathway in order to ensure efficient communication of signals or intermediates. This review focuses on some selected examples of where synthetic scaffolds inspired by nature have been used to enhance the overall biological pathway performance. Applications encompass both in vivo and in vitro systems that address two key biological events in cell signaling and biosynthesis will be discussed.
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Affiliation(s)
- Rebecca Chen
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, United States
| | - Qi Chen
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, United States
| | - Heejae Kim
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, United States
| | - Ka-Hei Siu
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, United States
| | - Qing Sun
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, United States
| | - Shen-Long Tsai
- Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei City, Taiwan
| | - Wilfred Chen
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, United States.
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176
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Prawitwong P, Waeonukul R, Tachaapaikoon C, Pason P, Ratanakhanokchai K, Deng L, Sermsathanaswadi J, Septiningrum K, Mori Y, Kosugi A. Direct glucose production from lignocellulose using Clostridium thermocellum cultures supplemented with a thermostable β-glucosidase. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:184. [PMID: 24359557 PMCID: PMC3878107 DOI: 10.1186/1754-6834-6-184] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Accepted: 12/05/2013] [Indexed: 05/04/2023]
Abstract
BACKGROUND Cellulases continue to be one of the major costs associated with the lignocellulose hydrolysis process. Clostridium thermocellum is an anaerobic, thermophilic, cellulolytic bacterium that produces cellulosomes capable of efficiently degrading plant cell walls. The end-product cellobiose, however, inhibits degradation. To maximize the cellulolytic ability of C. thermocellum, it is important to eliminate this end-product inhibition. RESULTS This work describes a system for biological saccharification that leads to glucose production following hydrolysis of lignocellulosic biomass. C. thermocellum cultures supplemented with thermostable beta-glucosidases make up this system. This approach does not require any supplementation with cellulases and hemicellulases. When C. thermocellum strain S14 was cultured with a Thermoanaerobacter brockii beta-glucosidase (CglT with activity 30 U/g cellulose) in medium containing 100 g/L cellulose (617 mM initial glucose equivalents), we observed not only high degradation of cellulose, but also accumulation of 426 mM glucose in the culture broth. In contrast, cultures without CglT, or with less thermostable beta-glucosidases, did not efficiently hydrolyze cellulose and accumulated high levels of glucose. Glucose production required a cellulose load of over 10 g/L. When alkali-pretreated rice straw containing 100 g/L glucan was used as the lignocellulosic biomass, approximately 72% of the glucan was saccharified, and glucose accumulated to 446 mM in the culture broth. The hydrolysate slurry containing glucose was directly fermented to 694 mM ethanol by addition of Saccharomyces cerevisiae, giving an 85% theoretical yield without any inhibition. CONCLUSIONS Our process is the first instance of biological saccharification with exclusive production and accumulation of glucose from lignocellulosic biomass. The key to its success was the use of C. thermocellum supplemented with a thermostable beta-glucosidase and cultured under a high cellulose load. We named this approach biological simultaneous enzyme production and saccharification (BSES). BSES may resolve a significant barrier to economical production by providing a platform for production of fermentable sugars with reduced enzyme amounts.
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Affiliation(s)
- Panida Prawitwong
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
| | - Rattiya Waeonukul
- Pilot Plant Development and Training Institute (PDTI), King Mongkut’s University of Technology Thonburi (KMUTT), Bangkok, Thailand
| | - Chakrit Tachaapaikoon
- Pilot Plant Development and Training Institute (PDTI), King Mongkut’s University of Technology Thonburi (KMUTT), Bangkok, Thailand
| | - Patthra Pason
- Pilot Plant Development and Training Institute (PDTI), King Mongkut’s University of Technology Thonburi (KMUTT), Bangkok, Thailand
| | - Khanok Ratanakhanokchai
- School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi (KMUTT), Bangkok, Thailand
| | - Lan Deng
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
| | - Junjarus Sermsathanaswadi
- School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi (KMUTT), Bangkok, Thailand
| | - Krisna Septiningrum
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
- University of Tsukuba Graduate School of Life and Environmental Sciences, 1-1-1 Ten-noudai, Tsukuba, Ibaraki 305-8572, Japan
| | - Yutaka Mori
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
| | - Akihiko Kosugi
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
- University of Tsukuba Graduate School of Life and Environmental Sciences, 1-1-1 Ten-noudai, Tsukuba, Ibaraki 305-8572, Japan
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177
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Brunecky R, Alahuhta M, Xu Q, Donohoe BS, Crowley MF, Kataeva IA, Yang SJ, Resch MG, Adams MWW, Lunin VV, Himmel ME, Bomble YJ. Revealing Nature's Cellulase Diversity: The Digestion Mechanism of Caldicellulosiruptor bescii CelA. Science 2013; 342:1513-6. [PMID: 24357319 DOI: 10.1126/science.1244273] [Citation(s) in RCA: 229] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Roman Brunecky
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA
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178
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Cheng X, Hiras J, Deng K, Bowen B, Simmons BA, Adams PD, Singer SW, Northen TR. High throughput nanostructure-initiator mass spectrometry screening of microbial growth conditions for maximal β-glucosidase production. Front Microbiol 2013; 4:365. [PMID: 24367356 PMCID: PMC3854461 DOI: 10.3389/fmicb.2013.00365] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 11/17/2013] [Indexed: 11/13/2022] Open
Abstract
Production of biofuels via enzymatic hydrolysis of complex plant polysaccharides is a subject of intense global interest. Microbial communities are known to express a wide range of enzymes necessary for the saccharification of lignocellulosic feedstocks and serve as a powerful reservoir for enzyme discovery. However, the growth temperature and conditions that yield high cellulase activity vary widely, and the throughput to identify optimal conditions has been limited by the slow handling and conventional analysis. A rapid method that uses small volumes of isolate culture to resolve specific enzyme activity is needed. In this work, a high throughput nanostructure-initiator mass spectrometry (NIMS)-based approach was developed for screening a thermophilic cellulolytic actinomycete, Thermobispora bispora, for β-glucosidase production under various growth conditions. Media that produced high β-glucosidase activity were found to be I/S + glucose or microcrystalline cellulose (MCC), Medium 84 + rolled oats, and M9TE + MCC at 45°C. Supernatants of cell cultures grown in M9TE + 1% MCC cleaved 2.5 times more substrate at 45°C than at all other temperatures. While T. bispora is reported to grow optimally at 60°C in Medium 84 + rolled oats and M9TE + 1% MCC, approximately 40% more conversion was observed at 45°C. This high throughput NIMS approach may provide an important tool in discovery and characterization of enzymes from environmental microbes for industrial and biofuel applications.
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Affiliation(s)
- Xiaoliang Cheng
- 1Technology Division, Joint BioEnergy Institute Emeryville, CA, USA ; 2Department of Bioenergy/GTL & Structural Biology, Life Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Jennifer Hiras
- 3Deconstruction Division, Joint BioEnergy Institute Emeryville, CA, USA ; 4Physical Biosciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Kai Deng
- 1Technology Division, Joint BioEnergy Institute Emeryville, CA, USA ; 5Biological and Materials Science Center, Sandia National Laboratories Livermore, CA, USA
| | - Benjamin Bowen
- 2Department of Bioenergy/GTL & Structural Biology, Life Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Blake A Simmons
- 3Deconstruction Division, Joint BioEnergy Institute Emeryville, CA, USA ; 5Biological and Materials Science Center, Sandia National Laboratories Livermore, CA, USA
| | - Paul D Adams
- 1Technology Division, Joint BioEnergy Institute Emeryville, CA, USA ; 4Physical Biosciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Steven W Singer
- 3Deconstruction Division, Joint BioEnergy Institute Emeryville, CA, USA ; 6Department of Geochemistry, Earth Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA ; 7Department of Ecology, Earth Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Trent R Northen
- 1Technology Division, Joint BioEnergy Institute Emeryville, CA, USA ; 2Department of Bioenergy/GTL & Structural Biology, Life Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
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179
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Bae D, Seo KS, Zhang T, Wang C. Characterization of a potential Listeria monocytogenes virulence factor associated with attachment to fresh produce. Appl Environ Microbiol 2013; 79:6855-61. [PMID: 23974144 PMCID: PMC3811550 DOI: 10.1128/aem.01006-13] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Accepted: 08/14/2013] [Indexed: 11/20/2022] Open
Abstract
A study to determine the attachment of L. monocytogenes serotype 4b strain F2365 on vegetables and fruits was conducted. In an initial study, we screened 32 genes encoding surface proteins and lipases of the strain to find highly expressed genes on lettuce leaves. The results showed that transcription levels of LMOf2365_0413, LMOf2365_0498, LMOf2365_0859, LMOf2365_2052, and LMOf2365_2812 were significantly upregulated on lettuce leaves. In silico analysis showed that LMOf2365_0859 contains a putative cellulose binding domain. Thus, we hypothesized that this gene may be involved in an attachment to vegetables, and named it lcp (gene encoding Listeria cellulose binding protein [LCP]). lcp mutant (Δlcp) and lcp complement (F2365::pMAD::cat::lcp) strains were generated by homologous recombination. The abilities of a wild-type (WT) strain, the Δlcp strain, and the complemented strain to attach to lettuce leaves were evaluated, which indicated that the attachment of the Δlcp strain to lettuce was significantly less than that of the WT and the complemented strains. Similar results were observed for baby spinach and cantaloupe. Fluorescence microscopy and field emission scanning microscopy analysis further supported these findings. The binding of L. monocytogenes to cellulose was determined using cellulose acetate-coated plates. The results showed that a binding ability of the Δlcp strain was significantly lower than that of the wild type. Combined, these results strongly suggest that LCP plays an important role in an attachment to vegetables and fruits.
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Affiliation(s)
- Dongryeoul Bae
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi, USA
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180
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Hyeon JE, Jeon SD, Han SO. Cellulosome-based, Clostridium-derived multi-functional enzyme complexes for advanced biotechnology tool development: advances and applications. Biotechnol Adv 2013; 31:936-44. [PMID: 23563098 DOI: 10.1016/j.biotechadv.2013.03.009] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Revised: 03/22/2013] [Accepted: 03/25/2013] [Indexed: 12/20/2022]
Abstract
The cellulosome is one of nature's most elegant and elaborate nanomachines and a key biological and biotechnological macromolecule that can be used as a multi-functional protein complex tool. Each protein module in the cellulosome system is potentially useful in an advanced biotechnology application. The high-affinity interactions between the cohesin and dockerin domains can be used in protein-based biosensors to improve both sensitivity and selectivity. The scaffolding protein includes a carbohydrate-binding module (CBM) that attaches strongly to cellulose substrates and facilitates the purification of proteins fused with the dockerin module through a one-step CBM purification method. Although the surface layer homology (SLH) domain of CbpA is not present in other strains, replacement of the cell surface anchoring domain allows a foreign protein to be displayed on the surface of other strains. The development of a hydrolysis enzyme complex is a useful strategy for consolidated bioprocessing (CBP), enabling microorganisms with biomass hydrolysis activity. Thus, the development of various configurations of multi-functional protein complexes for use as tools in whole-cell biocatalyst systems has drawn considerable attention as an attractive strategy for bioprocess applications. This review provides a detailed summary of the current achievements in Clostridium-derived multi-functional complex development and the impact of these complexes in various areas of biotechnology.
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Affiliation(s)
- Jeong Eun Hyeon
- School of Life Sciences and Biotechnology, Korea University, Seoul, 136-701, Republic of Korea
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181
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Thompson C, Beys-da-Silva W, Santi L, Berger M, Vainstein M, Guima rães J, Vasconcelos AT. A potential source for cellulolytic enzyme discovery and environmental aspects revealed through metagenomics of Brazilian mangroves. AMB Express 2013; 3:65. [PMID: 24160319 PMCID: PMC3922913 DOI: 10.1186/2191-0855-3-65] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Accepted: 10/21/2013] [Indexed: 11/19/2022] Open
Abstract
The mangroves are among the most productive and biologically important environments. The possible presence of cellulolytic enzymes and microorganisms useful for biomass degradation as well as taxonomic and functional aspects of two Brazilian mangroves were evaluated using cultivation and metagenomic approaches. From a total of 296 microorganisms with visual differences in colony morphology and growth (including bacteria, yeast and filamentous fungus), 179 (60.5%) and 117 (39.5%) were isolated from the Rio de Janeiro (RJ) and Bahia (BA) samples, respectively. RJ metagenome showed the higher number of microbial isolates, which is consistent with its most conserved state and higher diversity. The metagenomic sequencing data showed similar predominant bacterial phyla in the BA and RJ mangroves with an abundance of Proteobacteria (57.8% and 44.6%), Firmicutes (11% and 12.3%) and Actinobacteria (8.4% and 7.5%). A higher number of enzymes involved in the degradation of polycyclic aromatic compounds were found in the BA mangrove. Specific sequences involved in the cellulolytic degradation, belonging to cellulases, hemicellulases, carbohydrate binding domains, dockerins and cohesins were identified, and it was possible to isolate cultivable fungi and bacteria related to biomass decomposition and with potential applications for the production of biofuels. These results showed that the mangroves possess all fundamental molecular tools required for building the cellulosome, which is required for the efficient degradation of cellulose material and sugar release.
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182
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Smith SP, Bayer EA. Insights into cellulosome assembly and dynamics: from dissection to reconstruction of the supramolecular enzyme complex. Curr Opin Struct Biol 2013; 23:686-94. [PMID: 24080387 DOI: 10.1016/j.sbi.2013.09.002] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Accepted: 09/11/2013] [Indexed: 11/23/2022]
Abstract
Cellulosomes are multi-enzyme complexes produced by anaerobic bacteria for the efficient deconstruction of plant cell wall polysaccharides. The assembly of enzymatic subunits onto a central non-catalytic scaffoldin subunit is mediated by a highly specific interaction between the enzyme-bearing dockerin modules and the resident cohesin modules of the scaffoldin, which affords their catalytic activities to work synergistically. The scaffoldin also imparts substrate-binding and bacterial-anchoring properties, the latter of which involves a second cohesin-dockerin interaction. Recent structure-function studies reveal an ever-growing array of unique and increasingly complex cohesin-dockerin complexes and cellulosomal enzymes with novel activities. A 'build' approach involving multimodular cellulosomal segments has provided a structural model of an organized yet conformationally dynamic supramolecular assembly with the potential to form higher order structures.
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Affiliation(s)
- Steven P Smith
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada.
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183
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A useful method integrating production and immobilization of recombinant cellulase. Appl Microbiol Biotechnol 2013; 97:9185-92. [PMID: 24042477 DOI: 10.1007/s00253-013-5238-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 08/30/2013] [Accepted: 09/04/2013] [Indexed: 10/26/2022]
Abstract
The development of cellulase-based bioprocess is afflicted by the processing efficiency of enzymes. To address this issue, a method based on artificial oil bodies (AOBs) was proposed to integrate production and immobilization of recombinant cellulase. First, the heterologous endoglucanase (celA), cellobiohydrolase (celK), and β-glucosidase (gls) genes were individually fused with oleosin, a structural protein of plant seed oils. After expression in Escherichia coli, each fusion protein of insolubility was mixed together with plant oils. AOBs were assembled by subjecting the mixture to sonication. Consequently, active CelA, CelK, and Gls were resumed and co-immobilized on AOBs surface. Finally, the assembly condition (including the protein ratio) and the reaction condition were further optimized by response surface methodology. The resulting AOBs-bound cellulase remained stable for 4 cycles of cellulose-hydrolyzed reactions. Overall, the result shows a promise of this proposed approach for processing recombinant cellulase, which may provide a facile method to investigate optimum combination of cellulase components towards various cellulosic materials.
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184
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Kamat RK, Ma W, Yang Y, Zhang Y, Wang C, Kumar CV, Lin Y. Adsorption and hydrolytic activity of the polycatalytic cellulase nanocomplex on cellulose. ACS APPLIED MATERIALS & INTERFACES 2013; 5:8486-8494. [PMID: 23968137 DOI: 10.1021/am401916k] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The formation of polycatalytic enzyme complexes may enhance the effectiveness of enzymes due to improved substrate interaction and synergistic actions of multiple enzymes in proximity. Much effort has been made to develop highly efficient polycatalytic cellulase complexes by immobilizing cellulases on low-cost polymer or nanoparticle scaffolds, aiming at their potential applications in biomass conversion to fuels. However, some key cellulases carry out the hydrolytic reaction on crystalline cellulose in a directional, processive manner. A large, artificial polycatalytic complex is unlikely to undergo a highly coordinated motion to slide on the cellulose surface as a whole unit. The mechanism underlying the activity enhancements observed in some artificial cellulase complexes and the limit of this approach remain elusive. Herein, we report the synthesis of polycatalytic cellulase complexes bound to colloidal polymer nanoparticles with a magnetic core and describe their unique adsorption, hydrolytic activities, and motions on cellulose. The polycatalytic clusters of cellulases on colloidal polymers show an increased rate of hydrolytic reactions on cellulose, but this was observed mainly at relatively low cellulase-to-cellulose ratios. Enhanced efficiency is mainly attributed to increased local concentrations of cellulases on the scaffolds and their polyvalent interactions with cellulose. However, once bound, the polycatalytic complexes can only carry out reactions locally and are not capable of relocating to new sites rapidly due to their lack of long-range surface mobility and their extremely tight binding. The development of highly optimized polycatalytic complexes may arise by developing novel nanoscaffolds that induce concerted motion of the complex as a whole.
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Affiliation(s)
- Ranjan K Kamat
- Polymer Program, Institute of Material Science, §Department of Chemistry, and ∥Department of Molecular and Cellular Biology, University of Connecticut , Storrs, Connecticut 06269, United States
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185
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Xu Q, Ding SY, Brunecky R, Bomble YJ, Himmel ME, Baker JO. Improving activity of minicellulosomes by integration of intra- and intermolecular synergies. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:126. [PMID: 23987588 PMCID: PMC3766687 DOI: 10.1186/1754-6834-6-126] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Accepted: 08/28/2013] [Indexed: 05/20/2023]
Abstract
BACKGROUND Complete hydrolysis of cellulose to glucose requires the synergistic action of three general types of glycoside hydrolases; endoglucanases, exoglucanases, and cellobiases. Cellulases that are found in Nature vary considerably in their modular diversity and architecture. They include: non-complexed enzymes with single catalytic domains, independent single peptide chains incorporating multiple catalytic modules, and complexed, scaffolded structures, such as the cellulosome. The discovery of the latter two enzyme architectures has led to a generally held hypothesis that these systems take advantage of intramolecular and intermolecular proximity synergies, respectively, to enhance cellulose degradation. We use domain engineering to exploit both of these concepts to improve cellulase activity relative to the activity of mixtures of the separate catalytic domains. RESULTS We show that engineered minicellulosomes can achieve high levels of cellulose conversion on crystalline cellulose by taking advantage of three types of synergism; (1) a complementary synergy produced by interaction of endo- and exo-cellulases, (2) an intramolecular synergy of multiple catalytic modules in a single gene product (this type of synergism being introduced for the first time to minicellulosomes targeting crystalline cellulose), and (3) an intermolecular proximity synergy from the assembly of these cellulases into larger multi-molecular structures called minicellulosomes. The binary minicellulosome constructed in this study consists of an artificial multicatalytic cellulase (CBM4-Ig-GH9-X11-X12-GH8-Doc) and one cellulase with a single catalytic domain (a modified Cel48S with the structure CBM4-Ig-GH48-Doc), connected by a non-catalytic scaffoldin protein. The high level endo-exo synergy and intramolecular synergies within the artificial multifunctional cellulase have been combined with an additional proximity-dependent synergy produced by incorporation into a minicellulosome demonstrating high conversion of crystalline cellulose (Avicel). Our minicellulosome is the first engineered enzyme system confirmed by test to be capable of both operating at temperatures as high as 60°C and converting over 60% of crystalline cellulose to fermentable sugars. CONCLUSION When compared to previously reported minicellulosomes assembled from cellulases containing only one catalytic module each, our novel minicellulosome demonstrates a method for substantial reduction in the number of peptide chains required, permitting improved heterologous expression of minicellulosomes in microbial hosts. In addition, it has been shown to be capable of substantial conversion of actual crystalline cellulose, as well as of the less-well-ordered and more easily digestible fraction of nominally crystalline cellulose.
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Affiliation(s)
- Qi Xu
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, USA
| | - Shi-You Ding
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, USA
| | - Roman Brunecky
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, USA
| | - Yannick J Bomble
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, USA
| | - Michael E Himmel
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, USA
| | - John O Baker
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, USA
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186
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Exoproteome profiles of Clostridium cellulovorans grown on various carbon sources. Appl Environ Microbiol 2013; 79:6576-84. [PMID: 23956399 DOI: 10.1128/aem.02137-13] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
The cellulosome is a complex of cellulosomal proteins bound to scaffolding proteins. This complex is considered the most efficient system for cellulose degradation. Clostridium cellulovorans, which is known to produce cellulosomes, changes the composition of its cellulosomes depending on the growth substrates. However, studies have investigated only cellulosomal proteins; profile changes in noncellulosomal proteins have rarely been examined. In this study, we performed a quantitative proteome analysis of the whole exoproteome of C. cellulovorans, including cellulosomal and noncellulosomal proteins, to illustrate how various substrates are efficiently degraded. C. cellulovorans was cultured with cellobiose, xylan, pectin, or phosphoric acid-swollen cellulose (PASC) as the sole carbon source. PASC was used as a cellulose substrate for more accurate quantitative analysis. Using an isobaric tag method and a liquid chromatography mass spectrometer equipped with a long monolithic silica capillary column, 639 proteins were identified and quantified in all 4 samples. Among these, 79 proteins were involved in saccharification, including 35 cellulosomal and 44 noncellulosomal proteins. We compared protein abundance by spectral count and found that cellulosomal proteins were more abundant than noncellulosomal proteins. Next, we focused on the fold change of the proteins depending on the growth substrates. Drastic changes were observed mainly among the noncellulosomal proteins. These results indicate that cellulosomal proteins were primarily produced to efficiently degrade any substrate and that noncellulosomal proteins were specifically produced to optimize the degradation of a particular substrate. This study highlights the importance of noncellulosomal proteins as well as cellulosomes for the efficient degradation of various substrates.
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187
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Kanokratana P, Mhuantong W, Laothanachareon T, Tangphatsornruang S, Eurwilaichitr L, Pootanakit K, Champreda V. Phylogenetic analysis and metabolic potential of microbial communities in an industrial bagasse collection site. MICROBIAL ECOLOGY 2013; 66:322-34. [PMID: 23504022 DOI: 10.1007/s00248-013-0209-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2012] [Accepted: 03/05/2013] [Indexed: 05/05/2023]
Abstract
Industrial bagasse collection sites at sugar mills are an important resource for biomass-based industries and represent a unique ecological niche in lignocellulose degradation. In this study, microbial community structures at regions with varying microenvironmental conditions contained within a bagasse collection site were explored using tagged 16S rRNA gene pyrosequencing. Overall, remarkable differences in microbial community structures were found in aerobic surface and oxygen-limited interior regions of the pile. A variety of Alphaproteobacteria and Gammaproteobacteria represented the majority of bacteria in the aerobic upper-pile regions with the predominance of acetic acid bacteria towards the outer surface. Diverse Proteobacteria, Bacteroidetes, and Acidobacteria represented the predominant phyla at the exterior soil-contact pile base with an increasing abundance of anaerobic Spirochaetes with the increasing depth, where it shared similar community structures to that in the open-field soil from decomposed bagasse. Using complementary shotgun pyrosequencing, a variety of genes encoding various glycosyl hydrolases targeting cellulose and hemicellulose degradation were identified in the oxygen-limited interior pile base. Most were relevant to orders Clostridiales, Bacteroidales, Sphingobacteriales, and Cytophagales, suggesting their role in lignocellulose degradation in this region, as evidenced by the decrease in cellulose and respective increase in lignin fractions of the biomass. Partial carbon flux in the anoxic region was metabolized through mixed methanogenesis pathways as suggested by the annotated functional genes in methane synthesis. This study gives insights into native microbial community structures and functions in this unique lignocellulose degrading environment and provides the basis for controlling microbial processes important for utilization of bagasse in bio-industries.
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Affiliation(s)
- Pattanop Kanokratana
- Enzyme Technology Laboratory, Bioresources Technology Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Paholyothin Road, Klong Luang, Pathumthani, 12120, Thailand
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188
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Kadam SU, Tiwari BK, O'Donnell CP. Application of novel extraction technologies for bioactives from marine algae. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2013; 61:4667-75. [PMID: 23634989 DOI: 10.1021/jf400819p] [Citation(s) in RCA: 212] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Marine algae are a rich source of bioactive compounds. This paper outlines the main bioactive compounds in marine algae and recent advances in novel technologies for extracting them. Novel extraction technologies reviewed include enzyme-assisted extraction, microwave-assisted extraction, ultrasound-assisted extraction, supercritical fluid extraction, and pressurized liquid extraction. These technologies are reviewed with respect to principles, benefits, and potential applications for marine algal bioactives. Advantages of novel technologies include higher yield, reduced treatment time, and lower cost compared to traditional solvent extraction techniques. Moreover, different combinations of novel techniques used for extraction and technologies suitable for thermolabile compounds are identified. The limitations of and challenges to employing these novel extraction technologies in industry are also highlighted.
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Affiliation(s)
- Shekhar U Kadam
- School of Biosystems Engineering, Agriculture and Food Science Centre, University College Dublin, Belfield, Dublin 4, Ireland
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189
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Nakazawa H, Kim DM, Matsuyama T, Ishida N, Ikeuchi A, Ishigaki Y, Kumagai I, Umetsu M. Hybrid Nanocellulosome Design from Cellulase Modules on Nanoparticles: Synergistic Effect of Catalytically Divergent Cellulase Modules on Cellulose Degradation Activity. ACS Catal 2013. [DOI: 10.1021/cs400012v] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hikaru Nakazawa
- Department of Biomolecular Engineering,
Graduate school of Engineering, Tohoku University, 6-6-11 Aoba, Aramaki, Aoba-ku, Sendai 980-8579, Japan
| | - Do-Myoung Kim
- Department of Biomolecular Engineering,
Graduate school of Engineering, Tohoku University, 6-6-11 Aoba, Aramaki, Aoba-ku, Sendai 980-8579, Japan
| | - Takashi Matsuyama
- Toyota Central R&D Laboratories, Yokomichi 41-1, Oaza Nagakute, Nagakute-cho, Aichi-gun, 480-1192, Japan
| | - Nobuhiro Ishida
- Toyota Central R&D Laboratories, Yokomichi 41-1, Oaza Nagakute, Nagakute-cho, Aichi-gun, 480-1192, Japan
| | - Akinori Ikeuchi
- Toyota Central R&D Laboratories, Yokomichi 41-1, Oaza Nagakute, Nagakute-cho, Aichi-gun, 480-1192, Japan
| | - Yuri Ishigaki
- Department of Biomolecular Engineering,
Graduate school of Engineering, Tohoku University, 6-6-11 Aoba, Aramaki, Aoba-ku, Sendai 980-8579, Japan
| | - Izumi Kumagai
- Department of Biomolecular Engineering,
Graduate school of Engineering, Tohoku University, 6-6-11 Aoba, Aramaki, Aoba-ku, Sendai 980-8579, Japan
| | - Mitsuo Umetsu
- Department of Biomolecular Engineering,
Graduate school of Engineering, Tohoku University, 6-6-11 Aoba, Aramaki, Aoba-ku, Sendai 980-8579, Japan
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190
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An efficient proteomic approach to analyze agriculture crop biomass. Protein J 2013; 32:365-72. [PMID: 23681363 DOI: 10.1007/s10930-013-9495-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
While a plant cell wall is formed by a complex of various components, including polysaccharides and structural proteins, its composition and representation may vary during cell growth. Currently, plant research targets the proteins participating in wall loosening. Multiple classes of enzymes, including various hemicellulases and cellulases, are required for plant material degradation to achieve the maximum decomposition. Identifying the set of proteins involved in the breakdown of cell-wall polymers is important to understand plant material conversion into suitable products. The objective of this study was to describe a method which can be used to carry out proteomics analysis of complex plant samples and identify enzymes degrading biomass. For this purpose we used proteomic techniques including gel electrophoresis, high pressure liquid chromatography combinated with mass spectrometry followed by data evaluation using databases searching. Results show that more than 50 % of these activities correspond to enzymes with proteolytic function. This study was focused primarily on enzymes able to breakdown the lignocellulosic and hemicellulosic parts that are very important for the material conversion into required products of degradation.
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191
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Xu C, Huang R, Teng L, Wang D, Hemme CL, Borovok I, He Q, Lamed R, Bayer EA, Zhou J, Xu J. Structure and regulation of the cellulose degradome in Clostridium cellulolyticum. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:73. [PMID: 23657055 PMCID: PMC3656788 DOI: 10.1186/1754-6834-6-73] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2013] [Accepted: 05/01/2013] [Indexed: 05/20/2023]
Abstract
BACKGROUND Many bacteria efficiently degrade lignocellulose yet the underpinning genome-wide metabolic and regulatory networks remain elusive. Here we revealed the "cellulose degradome" for the model mesophilic cellulolytic bacterium Clostridium cellulolyticum ATCC 35319, via an integrated analysis of its complete genome, its transcriptomes under glucose, xylose, cellobiose, cellulose, xylan or corn stover and its extracellular proteomes under glucose, cellobiose or cellulose. RESULTS Proteins for core metabolic functions, environment sensing, gene regulation and polysaccharide metabolism were enriched in the cellulose degradome. Analysis of differentially expressed genes revealed a "core" set of 48 CAZymes required for degrading cellulose-containing substrates as well as an "accessory" set of 76 CAZymes required for specific non-cellulose substrates. Gene co-expression analysis suggested that Carbon Catabolite Repression (CCR) related regulators sense intracellular glycolytic intermediates and control the core CAZymes that mainly include cellulosomal components, whereas 11 sets of Two-Component Systems (TCSs) respond to availability of extracellular soluble sugars and respectively regulate most of the accessory CAZymes and associated transporters. Surprisingly, under glucose alone, the core cellulases were highly expressed at both transcript and protein levels. Furthermore, glucose enhanced cellulolysis in a dose-dependent manner, via inducing cellulase transcription at low concentrations. CONCLUSION A molecular model of cellulose degradome in C. cellulolyticum (Ccel) was proposed, which revealed the substrate-specificity of CAZymes and the transcriptional regulation of core cellulases by CCR where the glucose acts as a CCR inhibitor instead of a trigger. These features represent a distinct environment-sensing strategy for competing while collaborating for cellulose utilization, which can be exploited for process and genetic engineering of microbial cellulolysis.
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Affiliation(s)
- Chenggang Xu
- BioEnergy Genome Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
| | - Ranran Huang
- BioEnergy Genome Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
| | - Lin Teng
- BioEnergy Genome Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
| | - Dongmei Wang
- BioEnergy Genome Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
| | - Christopher L Hemme
- Institute for Environmental Genomics, Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73072, USA
| | - Ilya Borovok
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Qiang He
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996, USA
| | - Raphael Lamed
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Edward A Bayer
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Jizhong Zhou
- Institute for Environmental Genomics, Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73072, USA
| | - Jian Xu
- BioEnergy Genome Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
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192
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Gao ZM, Xu X, Ruan LW. Enrichment and characterization of an anaerobic cellulolytic microbial consortium SQD-1.1 from mangrove soil. Appl Microbiol Biotechnol 2013; 98:465-74. [PMID: 23529681 DOI: 10.1007/s00253-013-4857-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Revised: 03/09/2013] [Accepted: 03/12/2013] [Indexed: 11/29/2022]
Abstract
Enrichment of microbial consortia provides an approach to simulate and investigate microbial communities in natural environments. In this study, a cellulolytic microbial consortium SQD-1.1 was enriched from mangrove soil of Qinglan port (Hainan, China) by 27 times continuous subcultivation under anaerobic static conditions. The consortium could completely degrade 0.2% (w/v) filter paper within 3 days and utilized it as the sole carbon source. PCR-denaturing gradient gel electrophoresis analysis revealed a stable microbial community structure in the incubation process of 10 days and in the procedure of subcultivation. Twenty-four operational taxonomic units belonging to seven phyla were obtained from the full-length 16S rRNA gene library. Five clones, closest related to the genera Alkaliflexus, Clostridium, Alistipes, Spirochaeta, and Trichococcus, were the predominant ones. Among them, M117, phylogeneticly showing high similarity (16S rRNA gene identity, 95.3%) with the cellulolytic anaerobic bacterium Clostridium straminisolvens CSK1(T), was the potential key cellulolytic bacterium. Using the plate cultivation method, 12 strains, including one potential new species and four potential new species of new genera, were isolated. The strain P2, corresponding to the most frequently detected clone (M05) in the 16S rRNA gene library, showed both CMCase and xylanase activity and may be another important cellulolytic bacterium. The findings of cellulase activity in cell pellet and cohesion and dockerin domains in metagenome data further suggested the potential of utilization of cellulosomes by the consortium to degrade cellulose. Consortium SQD-1.1 provides a candidate for investigating the mechanism of cellulose degradation under anoxic conditions in natural environments.
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Affiliation(s)
- Zhao-Ming Gao
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration (SOA), Xiamen, 361005, People's Republic of China
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193
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You C, Zhang YHP. Self-assembly of synthetic metabolons through synthetic protein scaffolds: one-step purification, co-immobilization, and substrate channeling. ACS Synth Biol 2013; 2:102-10. [PMID: 23656373 DOI: 10.1021/sb300068g] [Citation(s) in RCA: 115] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
One-step purification of a multi-enzyme complex was developed based on a mixture of cell extracts containing three dockerin-containing enzymes and one family 3 cellulose-binding module (CBM3)-containing scaffoldin through high-affinity adsorption on low-cost solid regenerated amorphous cellulose (RAC). The three-enzyme complex, called synthetic metabolon, was self-assembled through the high-affinity interaction between the dockerin in each enzyme and three cohesins in the synthetic scaffoldin. The metabolons were either immobilized on the external surface of RAC or free when the scaffoldin contained an intein between the CBM3 and three cohesins. The immobilized and free metabolons containing triosephosphate isomerase, aldolase, and fructose 1,6-biphosphatase exhibited initial reaction rates 48 and 38 times, respectively, that of the non-complexed three-enzyme mixture at the same enzyme loading. Such reaction rate enhancements indicated strong substrate channeling among synthetic metabolons due to the close spatial organization among cascade enzymes. These results suggested that the construction of synthetic metabolons by using cohesins, dockerins, and cellulose-binding modules from cellulosomes not only decreased protein purification labor and cost for in vitro synthetic biology projects but also accelerated reaction rates by 1 order of magnitude compared to non-complexed enzymes. Synthetic metabolons would be an important biocatalytic module for in vitro and in vivo synthetic biology projects.
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Affiliation(s)
- Chun You
- Biological Systems Engineering Department, Virginia Tech, Blacksburg, VA 24061, USA
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194
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Currie MA, Cameron K, Dias FMV, Spencer HL, Bayer EA, Fontes CMGA, Smith SP, Jia Z. Small angle X-ray scattering analysis of Clostridium thermocellum cellulosome N-terminal complexes reveals a highly dynamic structure. J Biol Chem 2013; 288:7978-7985. [PMID: 23341454 DOI: 10.1074/jbc.m112.408757] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Clostridium thermocellum produces the prototypical cellulosome, a large multienzyme complex that efficiently hydrolyzes plant cell wall polysaccharides into fermentable sugars. This ability has garnered great interest in its potential application in biofuel production. The core non-catalytic scaffoldin subunit, CipA, bears nine type I cohesin modules that interact with the type I dockerin modules of secreted hydrolytic enzymes and promotes catalytic synergy. Because the large size and flexibility of the cellulosome preclude structural determination by traditional means, the structural basis of this synergy remains unclear. Small angle x-ray scattering has been successfully applied to the study of flexible proteins. Here, we used small angle x-ray scattering to determine the solution structure and to analyze the conformational flexibility of two overlapping N-terminal cellulosomal scaffoldin fragments comprising two type I cohesin modules and the cellulose-specific carbohydrate-binding module from CipA in complex with Cel8A cellulases. The pair distribution functions, ab initio envelopes, and rigid body models generated for these two complexes reveal extended structures. These two N-terminal cellulosomal fragments are highly dynamic and display no preference for extended or compact conformations. Overall, our work reveals structural and dynamic features of the N terminus of the CipA scaffoldin that may aid in cellulosome substrate recognition and binding.
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Affiliation(s)
- Mark A Currie
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Kate Cameron
- Centro Interdisciplinar de Investigacao em Sanidade Animal, Faculdade de Medincina Veterinaria, Universidade Tecnica de Lisboa, 1300-477 Lisbon, Portugal
| | - Fernando M V Dias
- Centro Interdisciplinar de Investigacao em Sanidade Animal, Faculdade de Medincina Veterinaria, Universidade Tecnica de Lisboa, 1300-477 Lisbon, Portugal
| | - Holly L Spencer
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Edward A Bayer
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Carlos M G A Fontes
- Centro Interdisciplinar de Investigacao em Sanidade Animal, Faculdade de Medincina Veterinaria, Universidade Tecnica de Lisboa, 1300-477 Lisbon, Portugal
| | - Steven P Smith
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario K7L 3N6, Canada; Protein Function Discovery Group, Queen's University, Kingston, Ontario K7L 3N6, Canada.
| | - Zongchao Jia
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario K7L 3N6, Canada; Protein Function Discovery Group, Queen's University, Kingston, Ontario K7L 3N6, Canada.
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195
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Tsai SL, DaSilva NA, Chen W. Functional display of complex cellulosomes on the yeast surface via adaptive assembly. ACS Synth Biol 2013; 2:14-21. [PMID: 23656322 DOI: 10.1021/sb300047u] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
A new adaptive strategy was developed for the ex vivo assembly of a functional tetravalent designer cellulosome on the yeast cell surface. The design is based on the use of (1) a surface-bound anchoring scaffoldin composed of two divergent cohesin domains, (2) two dockerin-tagged adaptor scaffoldins to amplify the number of enzyme loading sites based on the specific dockerin-cohesin interaction with the anchoring scaffoldin, and (3) two dockerin-tagged enzymatic subunits (the endoglucanse Gt and the β-glucosidase Bglf) for cellulose hydrolysis. Cells displaying the tetravalent cellulosome on the surface exhibited a 4.2-fold enhancement in the hydrolysis of phosphoric acid swollen cellulose (PASC) compared with free enzymes. More importantly, cells displaying the tetravalent celluosome also exhibited an ~2-fold increase in ethanol production compared with cells displaying a divalent cellulosome using a similar enzyme loading. These results clearly indicate the more crucial role of enzyme proximity than just simply increasing the enzyme loading on the overall cellulosomal synergy. To the best of our knowledge, this is the first report that exploits the natural adaptive assembly strategy in creating artificial cellulosome structures. The unique feature of the anchoring and the adaptor scaffoldin strategy to amplify the number of enzymatic subunits can be easily extended to more complex cellulosomal structures to achieve an even higher level of enzyme synergy.
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Affiliation(s)
- Shen-Long Tsai
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA
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196
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The genome sequences of Cellulomonas fimi and "Cellvibrio gilvus" reveal the cellulolytic strategies of two facultative anaerobes, transfer of "Cellvibrio gilvus" to the genus Cellulomonas, and proposal of Cellulomonas gilvus sp. nov. PLoS One 2013; 8:e53954. [PMID: 23342046 PMCID: PMC3544764 DOI: 10.1371/journal.pone.0053954] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Accepted: 12/04/2012] [Indexed: 11/19/2022] Open
Abstract
Actinobacteria in the genus Cellulomonas are the only known and reported cellulolytic facultative anaerobes. To better understand the cellulolytic strategy employed by these bacteria, we sequenced the genome of the Cellulomonas fimi ATCC 484(T). For comparative purposes, we also sequenced the genome of the aerobic cellulolytic "Cellvibrio gilvus" ATCC 13127(T). An initial analysis of these genomes using phylogenetic and whole-genome comparison revealed that "Cellvibrio gilvus" belongs to the genus Cellulomonas. We thus propose to assign "Cellvibrio gilvus" to the genus Cellulomonas. A comparative genomics analysis between these two Cellulomonas genome sequences and the recently completed genome for Cellulomonas flavigena ATCC 482(T) showed that these cellulomonads do not encode cellulosomes but appear to degrade cellulose by secreting multi-domain glycoside hydrolases. Despite the minimal number of carbohydrate-active enzymes encoded by these genomes, as compared to other known cellulolytic organisms, these bacteria were found to be proficient at degrading and utilizing a diverse set of carbohydrates, including crystalline cellulose. Moreover, they also encode for proteins required for the fermentation of hexose and xylose sugars into products such as ethanol. Finally, we found relatively few significant differences between the predicted carbohydrate-active enzymes encoded by these Cellulomonas genomes, in contrast to previous studies reporting differences in physiological approaches for carbohydrate degradation. Our sequencing and analysis of these genomes sheds light onto the mechanism through which these facultative anaerobes degrade cellulose, suggesting that the sequenced cellulomonads use secreted, multidomain enzymes to degrade cellulose in a way that is distinct from known anaerobic cellulolytic strategies.
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197
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Compartmentalization and metabolic channeling for multienzymatic biosynthesis: practical strategies and modeling approaches. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2013; 137:41-65. [PMID: 23934361 DOI: 10.1007/10_2013_221] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
: The construction of efficient enzyme complexes for multienzymatic biosynthesis is of increasing interest in order to achieve maximum yield and to minimize the interference due to shortcomings that are typical for straightforward one-pot multienzyme catalysis. These include product or intermediate feedback inhibition, degeneration, and diffusive losses of reaction intermediates, consumption of co-factors, and others. The main mechanisms in nature to tackle these effects in transient or stable protein associations are the formation of metabolic channeling and microcompartments, processes that are desirable also for multienzymatic biosynthesis in vitro. This chapter provides an overview over two main aspects. First, numerous recent strategies for establishing compartmentalized multienzyme associations and constructed synthetic enzyme complexes are reviewed. Second, the computational methods at hand to investigate and optimize such associations systematically, especially with focus on large multienzyme complexes and metabolic channeling, are discussed. Perspectives on future studies of multienzymatic biosynthesis concerning compartmentalization and metabolic channeling are presented.
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198
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Chauvigné-Hines LM, Anderson LN, Weaver HM, Brown JN, Koech PK, Nicora CD, Hofstad BA, Smith RD, Wilkins MJ, Callister SJ, Wright AT. Suite of activity-based probes for cellulose-degrading enzymes. J Am Chem Soc 2012; 134:20521-32. [PMID: 23176123 PMCID: PMC3538167 DOI: 10.1021/ja309790w] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Microbial glycoside hydrolases play a dominant role in the biochemical conversion of cellulosic biomass to high-value biofuels. Anaerobic cellulolytic bacteria are capable of producing multicomplex catalytic subunits containing cell-adherent cellulases, hemicellulases, xylanases, and other glycoside hydrolases to facilitate the degradation of highly recalcitrant cellulose and other related plant cell wall polysaccharides. Clostridium thermocellum is a cellulosome-producing bacterium that couples rapid reproduction rates to highly efficient degradation of crystalline cellulose. Herein, we have developed and applied a suite of difluoromethylphenyl aglycone, N-halogenated glycosylamine, and 2-deoxy-2-fluoroglycoside activity-based protein profiling (ABPP) probes to the direct labeling of the C. thermocellum cellulosomal secretome. These activity-based probes (ABPs) were synthesized with alkynes to harness the utility and multimodal possibilities of click chemistry and to increase enzyme active site inclusion for liquid chromatography-mass spectrometry (LC-MS) analysis. We directly analyzed ABP-labeled and unlabeled global MS data, revealing ABP selectivity for glycoside hydrolase (GH) enzymes, in addition to a large collection of integral cellulosome-containing proteins. By identifying reactivity and selectivity profiles for each ABP, we demonstrate our ability to widely profile the functional cellulose-degrading machinery of the bacterium. Derivatization of the ABPs, including reactive groups, acetylation of the glycoside binding groups, and mono- and disaccharide binding groups, resulted in considerable variability in protein labeling. Our probe suite is applicable to aerobic and anaerobic microbial cellulose-degrading systems and facilitates a greater understanding of the organismal role associated with biofuel development.
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Affiliation(s)
| | | | - Holly M. Weaver
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, Washington, 99352
| | - Joseph N. Brown
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, Washington, 99352
| | - Phillip K. Koech
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, Washington, 99352
| | - Carrie D. Nicora
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, Washington, 99352
| | - Beth A. Hofstad
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, Washington, 99352
| | - Richard D. Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, Washington, 99352
| | - Michael J. Wilkins
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, Washington, 99352
| | - Stephen J. Callister
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, Washington, 99352
| | - Aaron T. Wright
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, Washington, 99352
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199
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Abstract
Lignocellulosic biomass is a promising feedstock to produce biofuels and other valuable biocommodities. A major obstacle to its commercialization is the high cost of degrading biomass into fermentable sugars, which is typically achieved using cellulolytic enzymes from Trichoderma reesei. Here, we explore the use of microbes to break down biomass. Bacillus subtilis was engineered to display a multicellulase-containing minicellulosome. The complex contains a miniscaffoldin protein that is covalently attached to the cell wall and three noncovalently associated cellulase enzymes derived from Clostridium cellulolyticum (Cel48F, Cel9E, and Cel5A). The minicellulosome spontaneously assembles, thus increasing the practicality of the cells. The recombinant bacteria are highly cellulolytic and grew in minimal medium containing industrially relevant forms of biomass as the primary nutrient source (corn stover, hatched straw, and switch grass). Notably, growth did not require dilute acid pretreatment of the biomass and the cells achieved densities approaching those of cells cultured with glucose. An analysis of the sugars released from acid-pretreated corn stover indicates that the cells have stable cellulolytic activity that enables them to break down 62.3% ± 2.6% of the biomass. When supplemented with beta-glucosidase, the cells liberated 21% and 33% of the total available glucose and xylose in the biomass, respectively. As the cells display only three types of enzymes, increasing the number of displayed enzymes should lead to even more potent cellulolytic microbes. This work has important implications for the efficient conversion of lignocellulose to value-added biocommodities.
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200
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Rizk M, Antranikian G, Elleuche S. End-to-end gene fusions and their impact on the production of multifunctional biomass degrading enzymes. Biochem Biophys Res Commun 2012; 428:1-5. [DOI: 10.1016/j.bbrc.2012.09.142] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Accepted: 09/30/2012] [Indexed: 11/29/2022]
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