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Putative role of invariant water molecules in the X-ray structures of family G fungal endoxylanases. J Biosci 2018. [DOI: 10.1007/s12038-018-9752-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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52
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Tabssum F, Irfan M, Shakir HA, Qazi JI. RSM based optimization of nutritional conditions for cellulase mediated Saccharification by Bacillus cereus. J Biol Eng 2018; 12:7. [PMID: 29755582 PMCID: PMC5934882 DOI: 10.1186/s13036-018-0097-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 04/03/2018] [Indexed: 11/10/2022] Open
Abstract
Background Cellulases are enzyme which have potential applications in various industries. Researchers are looking for potential cellulolytic bacterial strains for industrial exploitation. In this investigation, cellulase production of Bacillus cereus was explored while attacking poplar twigs. The bacterium was isolated from the gut of freshwater fish, Labeo rohita and identified by 16S rRNA gene sequencing technology. Various nutritional conditions were screened and optimized through response surface methodology. Initially, Plackett-Burman design was used for screening purpose and optimization was conducted through Box-Bhenken design. Results The maximum cellulase production occurred at 0.5% yeast extract, 0.09% MgSO4, 0.04% peptone, 2% poplar waste biomass, initial medium pH of 9.0, and inoculum size of 2% v/v at 37 °C with agitation speed of 120 rpm for 24 h of submerged fermentation. The proposed model for optimization of cellulase production was found highly significant. The indigenously produced cellulase enzyme was employed for saccharification purpose at 50 °C for various time periods. Maximum total sugars of 31.42 mg/ml were released after 6 h of incubation at 50 °C.The efficiency of this enzyme was compared with commercial cellulase enzyme revealing significant findings. Conclusion These results suggested potential utilization of this strain in biofuel industry.
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Affiliation(s)
- Fouzia Tabssum
- 1Microbial Biotechnology Laboratory, Department of Zoology, University of the Punjab, New Campus, Lahore, Pakistan
| | - Muhammad Irfan
- 2Department of Biotechnology, University of Sargodha, University road, Sargodha, Punjab Pakistan
| | - Hafiz Abdullah Shakir
- 1Microbial Biotechnology Laboratory, Department of Zoology, University of the Punjab, New Campus, Lahore, Pakistan
| | - Javed Iqbal Qazi
- 1Microbial Biotechnology Laboratory, Department of Zoology, University of the Punjab, New Campus, Lahore, Pakistan
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The workability of Escherichia coli BL21 (DE3) and Pseudomonas putida KT2440 expression platforms with autodisplayed cellulases: a comparison. Appl Microbiol Biotechnol 2018; 102:4829-4841. [DOI: 10.1007/s00253-018-8987-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 04/02/2018] [Accepted: 04/05/2018] [Indexed: 02/07/2023]
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Wojciechowski M, Różycki B, Huy PDQ, Li MS, Bayer EA, Cieplak M. Dual binding in cohesin-dockerin complexes: the energy landscape and the role of short, terminal segments of the dockerin module. Sci Rep 2018; 8:5051. [PMID: 29568013 PMCID: PMC5864761 DOI: 10.1038/s41598-018-23380-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 03/05/2018] [Indexed: 01/09/2023] Open
Abstract
The assembly of the polysaccharide degradating cellulosome machinery is mediated by tight binding between cohesin and dockerin domains. We have used an empirical model known as FoldX as well as molecular mechanics methods to determine the free energy of binding between a cohesin and a dockerin from Clostridium thermocellum in two possible modes that differ by an approximately 180° rotation. Our studies suggest that the full-length wild-type complex exhibits dual binding at room temperature, i.e., the two modes of binding have comparable probabilities at equilibrium. The ability to bind in the two modes persists at elevated temperatures. However, single-point mutations or truncations of terminal segments in the dockerin result in shifting the equilibrium towards one of the binding modes. Our molecular dynamics simulations of mechanical stretching of the full-length wild-type cohesin-dockerin complex indicate that each mode of binding leads to two kinds of stretching pathways, which may be mistakenly taken as evidence of dual binding.
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Affiliation(s)
- Michał Wojciechowski
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, PL-02668, Warsaw, Poland
| | - Bartosz Różycki
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, PL-02668, Warsaw, Poland
| | - Pham Dinh Quoc Huy
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, PL-02668, Warsaw, Poland
- Institute for Computational Sciences and Technology, SBI building, Quang Trung Software city, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Vietnam
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, PL-02668, Warsaw, Poland
| | - Edward A Bayer
- Department of Biomolecular Sciences, The Weizmann Institute of Science, 234 Herzl Street, Rehovot, 7610001, Israel
| | - Marek Cieplak
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, PL-02668, Warsaw, Poland.
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The features that distinguish lichenases from other polysaccharide-hydrolyzing enzymes and the relevance of lichenases for biotechnological applications. Appl Microbiol Biotechnol 2018; 102:3951-3965. [DOI: 10.1007/s00253-018-8904-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 02/23/2018] [Accepted: 02/26/2018] [Indexed: 01/16/2023]
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Enhanced features of Dictyoglomus turgidum Cellulase A engineered with carbohydrate binding module 11 from Clostridium thermocellum. Sci Rep 2018. [PMID: 29535356 PMCID: PMC5849603 DOI: 10.1038/s41598-018-22769-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Lignocellulosic biomass (LCB) is a low-cost and abundant source of fermentable sugars. Enzymatic hydrolysis is one of the main ways to obtain sugars from biomass, but most of the polysaccharide-degrading enzymes are poorly efficient on LCB and cellulases with higher performances are required. In this study, we designed a chimeric protein by adding the carbohydrate binding module (CBM) of the cellulosomal enzyme CtLic26A-Cel5E (endoglucanase H or CelH) from Clostridium (Ruminiclostridium) thermocellum to the C-terminus of Dtur CelA, an interesting hyperthermostable endoglucanase from Dictyoglomus turgidum. The activity and binding rate of both native and chimeric enzyme were evaluated on soluble and insoluble polysaccharides. The addition of a CBM resulted in a cellulase with enhanced stability at extreme pHs, higher affinity and activity on insoluble cellulose.
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Dey P, Roy A. Molecular structure and catalytic mechanism of fungal family G acidophilic xylanases. 3 Biotech 2018; 8:78. [PMID: 29430342 PMCID: PMC5799109 DOI: 10.1007/s13205-018-1091-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2017] [Accepted: 01/04/2018] [Indexed: 10/18/2022] Open
Abstract
Industrial applications of xylanases have made this enzyme an important subject of applied research work. Function of this particular enzyme is to degrade or hydrolyze the plentiful polysaccharide xylan, an important component of hemicellulose. It mainly cleaves the backbone of xylan that is made up of a number of xylose residues connected with β-1,4-glycosidic linkages. Fungi with mycelia are regarded as the best producer of xylanases. These varied xylanases not only differ in their sizes and shapes but also differ in their physicochemical properties. Depending on the optimum pH in which they work best, they have been classified into (1) acidophilic xylanases active at low pH or acidic pH range, (2) alkaliphilic xylanases that are active at high or alkaline pH range and (3) neutral xylanases having pH optima in the neutral range between pH 5 and 7. Other researchers have classified the xylanases also on the basis of their structural properties, kinetic parameters, etc. This review discusses the molecular structures of some acidophilic xylanases and the molecular basis of low pH optima observed for their activities. It also discusses their unique catalytic mechanism and actual role of the catalytic residues found in them. Apart from these, the review also discusses different applications of these acidophilic xylanases in different industries. The article concludes with brief suggestions about how these acidophilic xylanases can be created employing the techniques of genetic engineering and concepts of synthetic evolution, using the traits of the known acidophilic xylanases discussed in the review.
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Affiliation(s)
- Protyusha Dey
- Department of Biotechnology, Visva-Bharati University, Santiniketan, 731235 West Bengal India
| | - Amit Roy
- Department of Biotechnology, Visva-Bharati University, Santiniketan, 731235 West Bengal India
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58
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Laluce C, Igbojionu LI, Dussán KJ. Fungal Enzymes Applied to Industrial Processes for Bioethanol Production. Fungal Biol 2018. [DOI: 10.1007/978-3-319-90379-8_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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59
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Ruginescu RM, Cojoc R, Enache M, Lazăr V. Preliminary Characterization of a Cellulase Producing Bacterial Strain Isolated from a Romanian Hypersaline Lake. ACTA ACUST UNITED AC 2018. [DOI: 10.4236/jep.2018.910066] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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60
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Effect of Different Pretreatment Conditions on Saccharum spontaneum for Cellulase Production by B. subtilis K-18 Through Box–Bhenken Design. IRANIAN JOURNAL OF SCIENCE AND TECHNOLOGY, TRANSACTIONS A: SCIENCE 2017. [DOI: 10.1007/s40995-017-0463-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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61
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Marden CL, McDonald R, Schreier HJ, Watts JEM. Investigation into the fungal diversity within different regions of the gastrointestinal tract of Panaque nigrolineatus, a wood-eating fish. AIMS Microbiol 2017; 3:749-761. [PMID: 29152603 PMCID: PMC5687512 DOI: 10.3934/microbiol.2017.4.749] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The Amazonian catfish, Panaque nigrolineatus have several physiological adaptions enabling the scraping and consumption of wood (xylivory), facilitating a detritivorous dietary strategy. Composed of lignocellulose, wood is a difficult substrate to degrade and as yet, it is unclear whether the fish obtains any direct nutritional benefits from wood ingestion and degradation. However, there are numerous systems that rely on microbial symbioses to provide energy and other nutritional benefits for host organisms via lignocellulose decomposition. While previous studies on the microbial community of P. nigrolineatus have focused upon the bacterial population, the role of fungi in lignocellulose degradation in the fish has not yet been examined. This study describes the detection of fungi within the fish gastrointestinal tract. Using next generation sequencing, the effects of diet on enteric fungal populations were examined in each gastrointestinal tract region. Fungal species were found to vary in different regions of the gastrointestinal tract as a function of diet. This study is the first to examine the fungal community in a xylivorous fish and results support the hypothesis that diet influences fungal distribution and diversity within the gastrointestinal tract of P. nigrolineatus.
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Affiliation(s)
- Caroline L Marden
- School of Biological Sciences, University of Portsmouth, Portsmouth, Hampshire, UK
| | - Ryan McDonald
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD, USA
| | - Harold J Schreier
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD, USA.,Department of Marine Biotechnology, University of Maryland Baltimore County, Baltimore, MD, USA
| | - Joy E M Watts
- School of Biological Sciences, University of Portsmouth, Portsmouth, Hampshire, UK
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62
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Homogenization of food samples for gamma spectrometry using tetramethylammonium hydroxide and enzymatic digestion. J Radioanal Nucl Chem 2017. [DOI: 10.1007/s10967-017-5434-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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63
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Chwastyk M, Vera AM, Galera-Prat A, Gunnoo M, Thompson D, Carrión-Vázquez M, Cieplak M. Non-local effects of point mutations on the stability of a protein module. J Chem Phys 2017; 147:105101. [DOI: 10.1063/1.4999703] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Mateusz Chwastyk
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, PL-02668 Warsaw, Poland
| | - Andrés M. Vera
- Instituto Cajal, Consejo Superior de Investigaciones Científicas, (CSIC), Ave. Doctor Arce, 37, 28002 Madrid, Spain
| | - Albert Galera-Prat
- Instituto Cajal, Consejo Superior de Investigaciones Científicas, (CSIC), Ave. Doctor Arce, 37, 28002 Madrid, Spain
| | - Melissabye Gunnoo
- Department of Physics, Bernal Institute, University of Limerick, Limerick V94 T9PX, Ireland
| | - Damien Thompson
- Department of Physics, Bernal Institute, University of Limerick, Limerick V94 T9PX, Ireland
| | - Mariano Carrión-Vázquez
- Instituto Cajal, Consejo Superior de Investigaciones Científicas, (CSIC), Ave. Doctor Arce, 37, 28002 Madrid, Spain
| | - Marek Cieplak
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, PL-02668 Warsaw, Poland
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Abstract
Fungi and fungal enzymes play important roles in the new bioeconomy. Enzymes from filamentous fungi can unlock the potential of recalcitrant lignocellulose structures of plant cell walls as a new resource, and fungi such as yeast can produce bioethanol from the sugars released after enzyme treatment. Such processes reflect inherent characteristics of the fungal way of life, namely, that fungi as heterotrophic organisms must break down complex carbon structures of organic materials to satisfy their need for carbon and nitrogen for growth and reproduction. This chapter describes major steps in the conversion of plant biomass to value-added products. These products provide a basis for substituting fossil-derived fuels, chemicals, and materials, as well as unlocking the biomass potential of the agricultural harvest to yield more food and feed. This article focuses on the mycological basis for the fungal contribution to biorefinery processes, which are instrumental for improved resource efficiency and central to the new bioeconomy. Which types of processes, inherent to fungal physiology and activities in nature, are exploited in the new industrial processes? Which families of the fungal kingdom and which types of fungal habitats and ecological specializations are hot spots for fungal biomass conversion? How can the best fungal enzymes be found and optimized for industrial use? How can they be produced most efficiently-in fungal expression hosts? How have industrial biotechnology and biomass conversion research contributed to mycology and environmental research? Future perspectives and approaches are listed, highlighting the importance of fungi in development of the bioeconomy.
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65
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Szczupak A, Aizik D, Moraïs S, Vazana Y, Barak Y, Bayer EA, Alfonta L. The Electrosome: A Surface-Displayed Enzymatic Cascade in a Biofuel Cell's Anode and a High-Density Surface-Displayed Biocathodic Enzyme. NANOMATERIALS (BASEL, SWITZERLAND) 2017; 7:E153. [PMID: 28644390 PMCID: PMC5535219 DOI: 10.3390/nano7070153] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 06/12/2017] [Accepted: 06/20/2017] [Indexed: 11/29/2022]
Abstract
The limitation of surface-display systems in biofuel cells to a single redox enzyme is a major drawback of hybrid biofuel cells, resulting in a low copy-number of enzymes per yeast cell and a limitation in displaying enzymatic cascades. Here we present the electrosome, a novel surface-display system based on the specific interaction between the cellulosomal scaffoldin protein and a cascade of redox enzymes that allows multiple electron-release by fuel oxidation. The electrosome is composed of two compartments: (i) a hybrid anode, which consists of dockerin-containing enzymes attached specifically to cohesin sites in the scaffoldin to assemble an ethanol oxidation cascade, and (ii) a hybrid cathode, which consists of a dockerin-containing oxygen-reducing enzyme attached in multiple copies to the cohesin-bearing scaffoldin. Each of the two compartments was designed, displayed, and tested separately. The new hybrid cell compartments displayed enhanced performance over traditional biofuel cells; in the anode, the cascade of ethanol oxidation demonstrated higher performance than a cell with just a single enzyme. In the cathode, a higher copy number per yeast cell of the oxygen-reducing enzyme copper oxidase has reduced the effect of competitive inhibition resulting from yeast oxygen consumption. This work paves the way for the assembly of more complex cascades using different enzymes and larger scaffoldins to further improve the performance of hybrid cells.
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Affiliation(s)
- Alon Szczupak
- Department of Life Sciences and the Ilse Katz Institute for Nanoscale Science and Technology, P.O. Box 653, 8410501 Beer-Sheva, Israel.
| | - Dror Aizik
- Department of Life Sciences and the Ilse Katz Institute for Nanoscale Science and Technology, P.O. Box 653, 8410501 Beer-Sheva, Israel.
| | - Sarah Moraïs
- Department of Biomolecular Sciences, Weizmann Institute of Science, 234 Herzl St., P.O. Box 26, 7610001 Rehovot, Israel.
| | - Yael Vazana
- Department of Biomolecular Sciences, Weizmann Institute of Science, 234 Herzl St., P.O. Box 26, 7610001 Rehovot, Israel.
| | - Yoav Barak
- Department of Chemical Research Support, Weizmann Institute of Science, 234 Herzl St., P.O. Box 26, 7610001 Rehovot, Israel.
| | - Edward A Bayer
- Department of Biomolecular Sciences, Weizmann Institute of Science, 234 Herzl St., P.O. Box 26, 7610001 Rehovot, Israel.
| | - Lital Alfonta
- Department of Life Sciences and the Ilse Katz Institute for Nanoscale Science and Technology, P.O. Box 653, 8410501 Beer-Sheva, Israel.
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Impact of Module-X2 and Carbohydrate Binding Module-3 on the catalytic activity of associated glycoside hydrolases towards plant biomass. Sci Rep 2017. [PMID: 28623337 PMCID: PMC5473887 DOI: 10.1038/s41598-017-03927-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Cellulolytic enzymes capable of hydrolyzing plant biomass are secreted by microbial cells specifically in response to the carbon substrate present in the environment. These enzymes consist of a catalytic domain, generally appended to one or more non-catalytic Carbohydrate Binding Module (CBM), which enhances their activity towards recalcitrant biomass. In the present study, the genome of a cellulolytic microbe Paenibacillus polymyxa A18 was annotated for the presence of CBMs and analyzed their expression in response to the plant biomass and model polysaccharides Avicel, CMC and xylan using quantitative PCR. A gene that encodes X2-CBM3 was found to be maximally induced in response to the biomass and crystalline substrate Avicel. Association of X2-CBM3 with xyloglucanase and endoglucanase led to up to 4.6-fold increase in activity towards insoluble substrates. In the substrate binding study, module X2 showed a higher affinity towards biomass and phosphoric acid swollen cellulose, whereas CBM3 showed a higher affinity towards Avicel. Further structural modeling of X2 also indicated its potential role in substrate binding. Our findings highlighted the role of module X2 along with CBM3 in assisting the enzyme catalysis of agricultural residue and paved the way to engineer glycoside hydrolases for superior activity.
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Tiwari R, Nain L, Labrou NE, Shukla P. Bioprospecting of functional cellulases from metagenome for second generation biofuel production: a review. Crit Rev Microbiol 2017; 44:244-257. [DOI: 10.1080/1040841x.2017.1337713] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Rameshwar Tiwari
- Department of Microbiology, Laboratory of Enzyme Technology and Protein Bioinformatics, Maharshi Dayanand University, Rohtak, India
- Division of Microbiology, Indian Agricultural Research Institute, New Delhi, India
| | - Lata Nain
- Division of Microbiology, Indian Agricultural Research Institute, New Delhi, India
| | - Nikolaos E. Labrou
- Department of Biotechnology, School of Food, Biotechnology and Development, Laboratory of Enzyme Technology, Agricultural University of Athens, Athens, Greece
| | - Pratyoosh Shukla
- Department of Microbiology, Laboratory of Enzyme Technology and Protein Bioinformatics, Maharshi Dayanand University, Rohtak, India
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Maruthamuthu M, van Elsas JD. Molecular cloning, expression, and characterization of four novel thermo-alkaliphilic enzymes retrieved from a metagenomic library. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:142. [PMID: 28588643 PMCID: PMC5457731 DOI: 10.1186/s13068-017-0808-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Accepted: 04/29/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Enzyme discovery is a promising approach to aid in the deconstruction of recalcitrant plant biomass in an industrial process. Novel enzymes can be readily discovered by applying metagenomics on whole microbiomes. Our goal was to select, examine, and characterize eight novel glycoside hydrolases that were previously detected in metagenomic libraries, to serve biotechnological applications with high performance. RESULTS Here, eight glycosyl hydrolase family candidate genes were selected from metagenomes of wheat straw-degrading microbial consortia using molecular cloning and subsequent gene expression studies in Escherichia coli. Four of the eight enzymes had significant activities on either pNP-β-d-galactopyranoside, pNP-β-d-xylopyranoside, pNP-α-l-arabinopyranoside or pNP-α-d-glucopyranoside. These proteins, denoted as proteins 1, 2, 5 and 6, were his-tag purified and their nature and activities further characterized using molecular and activity screens with the pNP-labeled substrates. Proteins 1 and 2 showed high homologies with (1) a β-galactosidase (74%) and (2) a β-xylosidase (84%), whereas the remaining two (5 and 6) were homologous with proteins reported as a diguanylate cyclase and an aquaporin, respectively. The β-galactosidase- and β-xylosidase-like proteins 1 and 2 were confirmed as being responsible for previously found thermo-alkaliphilic glycosidase activities of extracts of E. coli carrying the respective source fosmids. Remarkably, the β-xylosidase-like protein 2 showed activities with both pNP-Xyl and pNP-Ara in the temperature range 40-50 °C and pH range 8.0-10.0. Moreover, proteins 5 and 6 showed thermotolerant α-glucosidase activity at pH 10.0. In silico structure prediction of protein 5 revealed the presence of a potential "GGDEF" catalytic site, encoding α-glucosidase activity, whereas that of protein 6 showed a "GDSL" site, encoding a 'new family' α-glucosidase activity. CONCLUSION Using a rational screening approach, we identified and characterized four thermo-alkaliphilic glycosyl hydrolases that have the potential to serve as constituents of enzyme cocktails that produce sugars from lignocellulosic plant remains.
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Affiliation(s)
- Mukil Maruthamuthu
- Department of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747AG Groningen, The Netherlands
| | - Jan Dirk van Elsas
- Department of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747AG Groningen, The Netherlands
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Ezeilo UR, Zakaria II, Huyop F, Wahab RA. Enzymatic breakdown of lignocellulosic biomass: the role of glycosyl hydrolases and lytic polysaccharide monooxygenases. BIOTECHNOL BIOTEC EQ 2017. [DOI: 10.1080/13102818.2017.1330124] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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Song JM, Hong SK, An YJ, Kang MH, Hong KH, Lee YH, Cha SS. Genetic and Structural Characterization of a Thermo-Tolerant, Cold-Active, and Acidic Endo-β-1,4-glucanase from Antarctic Springtail, Cryptopygus antarcticus. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:1630-1640. [PMID: 28156112 DOI: 10.1021/acs.jafc.6b05037] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The CaCel gene from Antarctic springtail Cryptopygus antarcticus codes for a cellulase belonging to the glycosyl hydrolase family 45 (GHF45). Phylogenetic, biochemical, and structural analyses revealed that the CaCel gene product (CaCel) is closely related to fungal GHF45 endo-β-1,4-glucanases. The organization of five introns within the open reading frame of the CaCel gene indicates its endogenous origin in the genome of the species, which suggests the horizontal transfer of the gene from fungi to the springtail. CaCel exhibited optimal activity at pH 3.5, retained 80% of its activity at 0-10 °C, and maintained a half-life of 4 h at 70 °C. Based on the structural comparison between CaCel and a fungal homologue, we deduced the structural basis for the unusual characteristics of CaCel. Under acidic conditions at 50 °C, CaCel was effective to digest the green algae (Ulva pertusa), suggesting that it could be exploited for biofuel production from seaweeds.
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Affiliation(s)
- Jung Min Song
- Korea Institute of Ocean Science and Technology , 787 Haean-Ro, Sangnok-Gu, Ansan 426-744, Republic of Korea
| | - Seung Kon Hong
- Department of Chemistry & Nano Science, Ewha Womans University , Seoul 03760, Republic of Korea
| | - Young Jun An
- Korea Institute of Ocean Science and Technology , 787 Haean-Ro, Sangnok-Gu, Ansan 426-744, Republic of Korea
| | - Mee Hye Kang
- Korea Institute of Ocean Science and Technology , 787 Haean-Ro, Sangnok-Gu, Ansan 426-744, Republic of Korea
| | - Kwon Ho Hong
- Institute for Therapeutics Discovery and Development, University of Minnesota , 717 Delaware Street SE, Minneapolis, Minnesota 55414, United States
| | - Youn-Ho Lee
- Korea Institute of Ocean Science and Technology , 787 Haean-Ro, Sangnok-Gu, Ansan 426-744, Republic of Korea
- University of Science and Technology , 217 Gajung-Ro Yuseong-Gu, Daejeon 305-333, Republic of Korea
| | - Sun-Shin Cha
- Department of Chemistry & Nano Science, Ewha Womans University , Seoul 03760, Republic of Korea
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Zichová M, Stratilová E, Omelková J, Vadkertiová R, Babák L, Rosenberg M. Production of ethanol from waste paper using immobilized yeasts. CHEMICAL PAPERS 2017. [DOI: 10.1007/s11696-016-0036-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Poudel S, Giannone RJ, Rodriguez M, Raman B, Martin MZ, Engle NL, Mielenz JR, Nookaew I, Brown SD, Tschaplinski TJ, Ussery D, Hettich RL. Integrated omics analyses reveal the details of metabolic adaptation of Clostridium thermocellum to lignocellulose-derived growth inhibitors released during the deconstruction of switchgrass. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:14. [PMID: 28077967 PMCID: PMC5223564 DOI: 10.1186/s13068-016-0697-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 12/24/2016] [Indexed: 05/03/2023]
Abstract
BACKGROUND Clostridium thermocellum is capable of solubilizing and converting lignocellulosic biomass into ethanol. Although much of the work-to-date has centered on characterizing this microbe's growth on model cellulosic substrates, such as cellobiose, Avicel, or filter paper, it is vitally important to understand its metabolism on more complex, lignocellulosic substrates to identify relevant industrial bottlenecks that could undermine efficient biofuel production. To this end, we have examined a time course progression of C. thermocellum grown on switchgrass to assess the metabolic and protein changes that occur during the conversion of plant biomass to ethanol. RESULTS The most striking feature of the metabolome was the observed accumulation of long-chain, branched fatty acids over time, implying an adaptive restructuring of C. thermocellum's cellular membrane as the culture progresses. This is undoubtedly a response to the gradual accumulation of lignocellulose-derived inhibitory compounds as the organism deconstructs the switchgrass to access the embedded cellulose. Corroborating the metabolomics data, proteomic analysis revealed a corresponding time-dependent increase in various enzymes, including those involved in the interconversion of branched amino acids valine, leucine, and isoleucine to iso- and anteiso-fatty acid precursors. Additionally, the metabolic accumulation of hemicellulose-derived sugars and sugar alcohols concomitant with increased abundance of enzymes involved in C5 sugar metabolism/pentose phosphate pathway indicates that C. thermocellum shifts glycolytic intermediates to alternate pathways to modulate overall carbon flux in response to C5 sugar metabolites that increase during lignocellulose deconstruction. CONCLUSIONS Integrated omic platforms provided complementary systems biological information that highlight C. thermocellum's specific response to cytotoxic inhibitors released during the deconstruction and utilization of switchgrass. These additional viewpoints allowed us to fully realize the level to which the organism adapts to an increasingly challenging culture environment-information that will prove critical to C. thermocellum's industrial efficacy.
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Affiliation(s)
- Suresh Poudel
- Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN 37831 USA
- Department of Genome Science and Technology, University of Tennessee, Knoxville, TN 37996 USA
| | | | - Miguel Rodriguez
- Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN 37831 USA
| | - Babu Raman
- Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN 37831 USA
- Dow AgroSciences, 9330 Zionsville Road, Indianapolis, IN 46268 USA
| | - Madhavi Z. Martin
- Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN 37831 USA
| | - Nancy L. Engle
- Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN 37831 USA
| | | | - Intawat Nookaew
- Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN 37831 USA
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR 72205 USA
| | - Steven D. Brown
- Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN 37831 USA
- Department of Genome Science and Technology, University of Tennessee, Knoxville, TN 37996 USA
| | | | - David Ussery
- Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN 37831 USA
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR 72205 USA
| | - Robert L. Hettich
- Chemical Sciences Division, Oak Ridge National Lab, Oak Ridge, TN 37831 USA
- Department of Genome Science and Technology, University of Tennessee, Knoxville, TN 37996 USA
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73
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Willis JD, Grant JN, Mazarei M, Kline LM, Rempe CS, Collins AG, Turner GB, Decker SR, Sykes RW, Davis MF, Labbe N, Jurat-Fuentes JL, Stewart CN. The TcEG1 beetle ( Tribolium castaneum) cellulase produced in transgenic switchgrass is active at alkaline pH and auto-hydrolyzes biomass for increased cellobiose release. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:230. [PMID: 29213306 PMCID: PMC5707894 DOI: 10.1186/s13068-017-0918-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 09/28/2017] [Indexed: 05/17/2023]
Abstract
BACKGROUND Genetically engineered biofuel crops, such as switchgrass (Panicum virgatum L.), that produce their own cell wall-digesting cellulase enzymes would reduce costs of cellulosic biofuel production. To date, non-bioenergy plant models have been used in nearly all studies assessing the synthesis and activity of plant-produced fungal and bacterial cellulases. One potential source for cellulolytic enzyme genes is herbivorous insects adapted to digest plant cell walls. Here we examine the potential of transgenic switchgrass-produced TcEG1 cellulase from Tribolium castaneum (red flour beetle). This enzyme, when overproduced in Escherichia coli and Saccharomyces cerevisiae, efficiently digests cellulose at optima of 50 °C and pH 12.0. RESULTS TcEG1 that was produced in green transgenic switchgrass tissue had a range of endoglucanase activity of 0.16-0.05 units (µM glucose release/min/mg) at 50 °C and pH 12.0. TcEG1 activity from air-dried leaves was unchanged from that from green tissue, but when tissue was dried in a desiccant oven (46 °C), specific enzyme activity decreased by 60%. When transgenic biomass was "dropped-in" into an alkaline buffer (pH 12.0) and allowed to incubate at 50 °C, cellobiose release was increased up to 77% over non-transgenic biomass. Saccharification was increased in one transgenic event by 28%, which had a concurrent decrease in lignin content of 9%. Histological analysis revealed an increase in cell wall thickness with no change to cell area or perimeter. Transgenic plants produced more, albeit narrower, tillers with equivalent dry biomass as the control. CONCLUSIONS This work describes the first study in which an insect cellulase has been produced in transgenic plants; in this case, the dedicated bioenergy crop switchgrass. Switchgrass overexpressing the TcEG1 gene appeared to be morphologically similar to its non-transgenic control and produced equivalent dry biomass. Therefore, we propose TcEG1 transgenics could be bred with other transgenic germplasm (e.g., low-lignin lines) to yield new switchgrass with synergistically reduced recalcitrance to biofuel production. In addition, transgenes for other cell wall degrading enzymes may be stacked with TcEG1 in switchgrass to yield complementary cell wall digestion features and complete auto-hydrolysis.
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Affiliation(s)
- Jonathan D. Willis
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996 USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Joshua N. Grant
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996 USA
| | - Mitra Mazarei
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996 USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Lindsey M. Kline
- Center for Renewable Carbon, University of Tennessee, Knoxville, TN 37996 USA
| | - Caroline S. Rempe
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996 USA
- UT-ORNL Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37996 USA
| | - A. Grace Collins
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996 USA
| | - Geoffrey B. Turner
- The National Research Energy Laboratory, Golden, CO 80401 USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Stephen R. Decker
- The National Research Energy Laboratory, Golden, CO 80401 USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Robert W. Sykes
- The National Research Energy Laboratory, Golden, CO 80401 USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Mark F. Davis
- The National Research Energy Laboratory, Golden, CO 80401 USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Nicole Labbe
- Center for Renewable Carbon, University of Tennessee, Knoxville, TN 37996 USA
| | - Juan L. Jurat-Fuentes
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996 USA
| | - C. Neal Stewart
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996 USA
- UT-ORNL Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37996 USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
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74
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Wang X, Rong L, Wang M, Pan Y, Zhao Y, Tao F. Improving the activity of endoglucanase I (EGI) from Saccharomyces cerevisiae by DNA shuffling. RSC Adv 2017. [DOI: 10.1039/c6ra26508a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
To enhance the endo-β-1,4-glucanase activity of three mixedTrichodermasp. (Trichoderma reesei, Trichoderma longibrachiatum, andTrichoderma pseudokoningii), we optimized the efficiency of the encoding gene using DNA shuffling andSaccharomyces cerevisiaeINVSc1 as a host.
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Affiliation(s)
- Xu Wang
- College of Food Science and Technology
- Shanghai Ocean University
- Shanghai
- China
- School of Life Sciences
| | - Liang Rong
- USC School of Pharmacy
- University of Southern California
- Los Angeles
- USA
| | - Mingfu Wang
- College of Food Science and Technology
- Shanghai Ocean University
- Shanghai
- China
| | - Yingjie Pan
- College of Food Science and Technology
- Shanghai Ocean University
- Shanghai
- China
| | - Yong Zhao
- College of Food Science and Technology
- Shanghai Ocean University
- Shanghai
- China
| | - Fang Tao
- School of Life Sciences
- Anhui Agricultural University
- China
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75
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Prakash Menon M, Selvakumar R, Suresh kumar P, Ramakrishna S. Extraction and modification of cellulose nanofibers derived from biomass for environmental application. RSC Adv 2017. [DOI: 10.1039/c7ra06713e] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Cellulose nanofibers obtained from various plants and microbial sources, their extraction methods and various environmental applications are discussed.
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Affiliation(s)
| | - R. Selvakumar
- Nanobiotechnology Laboratory
- PSG Institute of Advanced Studies
- Coimbatore
- India-641004
| | - Palaniswamy Suresh kumar
- Environmental & Water Technology Centre of Innovation (EWTCOI)
- Ngee Ann Polytechnic
- Singapore-599489
| | - Seeram Ramakrishna
- Center for Nanofibers and Nanotechnology
- Department of Mechanical Engineering
- National University of Singapore
- Singapore 117576
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76
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Auxenfans T, Husson E, Sarazin C. Simultaneous pretreatment and enzymatic saccharification of (ligno) celluloses in aqueous-ionic liquid media: A compromise. Biochem Eng J 2017. [DOI: 10.1016/j.bej.2016.10.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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77
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Abstract
For modern biotechnology there is a steady need to identify novel enzymes. In biotechnological applications, however, enzymes often must function under extreme and nonnatural conditions (i.e., in the presence of solvents, high temperature and/or at extreme pH values). Cellulases have many industrial applications from the generation of bioethanol, a realistic long-term energy source, to the finishing of textiles. These industrial processes require cellulolytic activity under a wide range of pH, temperature, and ionic conditions, and they are usually carried out by mixtures of cellulases. Investigation of the broad diversity of cellulolytic enzymes involved in the natural degradation of cellulose is necessary for optimizing these processes.
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Affiliation(s)
- Nele Ilmberger
- Microbiology & Biotechnology, Biocenter Klein Flottbek, University of Hamburg, Ohnhorststr. 18, 22609, Hamburg, Germany
| | - Wolfgang R Streit
- Microbiology & Biotechnology, Biocenter Klein Flottbek, University of Hamburg, Ohnhorststr. 18, 22609, Hamburg, Germany.
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78
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Xiong W, Yang JK, Chen FY, Han ZG. The catalytic domain of Penicillium crustosum endoglucanase EGL1 has cellulose-binding capacity and cellulolytic activity. Enzyme Microb Technol 2016; 97:71-81. [PMID: 28010775 DOI: 10.1016/j.enzmictec.2016.11.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Revised: 10/30/2016] [Accepted: 11/18/2016] [Indexed: 12/20/2022]
Abstract
The cellulase-mediated degradation of cellulosic materials, which is initiated by endoglucanases by the random cleavage of the glycosidic bonds between glucose units to break long cellulose molecules into shorter ones, represents a major carbon flow in the global carbon cycle. The structure of a typical endoglucanase contains a classical (α/β)8 barrel fold catalytic domain, a linker region and a cellulose-binding domain. In this study, we found that both the full-length enzyme and the catalytic domain of endoglucanase EGL1 cloned from Penicillium crustosum strain 601 have CMCase and FPase activity. A cellulose-binding assay using green fluorescent protein as a marker further showed that the catalytic domain could also bind the cellulose substrate. The three-dimensional structure of the catalytic domain of EGL1 revealed that this cellulose substrate-binding capacity of the catalytic domain may come from the hydrophobic core formed by aromatic amino acids distributed in or outside the (α/β)8 barrel fold. A glycine scanning mutagenesis assay further found that the aromatic amino acids at the bottom of the barrel fold and those adjacent to the catalytic site significantly affect the cellulolytic activity and the cellulose binding affinity of the catalytic domain. Thus, it could be speculated that the aromatic amino acids in the bottom of the barrel fold might be the main contributors in the binding capacity of the catalytic domain with the cellulose substrate, and those distributed around the active sites on the top of the enzyme might participate in moving the cellulose substrate to the active site in the barrel fold or releasing the hydrolysis products.
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Affiliation(s)
- Wei Xiong
- College of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Jiang-Ke Yang
- College of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan 430023, China.
| | - Fang-Yuan Chen
- College of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Zheng-Gang Han
- College of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan 430023, China
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79
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Characterization of a Cellulomonas fimi exoglucanase/xylanase-endoglucanase gene fusion which improves microbial degradation of cellulosic biomass. Enzyme Microb Technol 2016; 93-94:113-121. [DOI: 10.1016/j.enzmictec.2016.08.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 08/04/2016] [Accepted: 08/05/2016] [Indexed: 11/17/2022]
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80
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Tiwari R, Kumar K, Singh S, Nain L, Shukla P. Molecular Detection and Environment-Specific Diversity of Glycosyl Hydrolase Family 1 β-Glucosidase in Different Habitats. Front Microbiol 2016; 7:1597. [PMID: 27790196 PMCID: PMC5062022 DOI: 10.3389/fmicb.2016.01597] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Accepted: 09/26/2016] [Indexed: 12/23/2022] Open
Abstract
β-glucosidase is a crucial element of the microbial cellulose multienzyme complex since it is responsible for the regulation of the entire cellulose hydrolysis process. Therefore, the aim of the present work was to explore the diversity and distribution of glycosyl hydrolase family 1 β-glucosidase genes in three different environmental niches including, Himalayan soil, cow dung and compost by metagenomic approach. Preliminary evaluation through metabolic profiling using BIOLOG based utilization patterns of carbon, nitrogen, phosphorus and sulfur revealed the environment and substrate specific nature of the indigenous microbial population. Furthermore, clonal library selection, screening and sequence analysis revealed that most of the GH1 β-glucosidase proteins had low identities with the available database. Analysis of the distribution of GH1 β-glucosidase gene fragments and β-glucosidase producing microbial community revealed the environment specific nature. The OTUs obtained from Himalayan soil and compost metagenomic libraries were grouped into 19 different genera comprising 6 groups. The cow dung sample displayed the least diversity of GH1 β-glucosidase sequences, with only 14 genera, distributed among three groups- Bacteroidetes, Firmicutes, and Actinobacteria. The metagenomic study coupled with metabolic profiling of GH1 β-glucosidase illustrated the existence of intricate relationship between the geochemical environmental factors and inherent microbial community.
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Affiliation(s)
- Rameshwar Tiwari
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand UniversityRohtak, India; Division of Microbiology, ICAR-Indian Agricultural Research InstituteNew Delhi, India
| | - Kanika Kumar
- ICAR-National Research Centre on Plant Biotechnology, LBS Centre, Indian Agricultural Research Institute New Delhi, India
| | - Surender Singh
- Division of Microbiology, ICAR-Indian Agricultural Research Institute New Delhi, India
| | - Lata Nain
- Division of Microbiology, ICAR-Indian Agricultural Research Institute New Delhi, India
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University Rohtak, India
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81
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Wendisch VF, Brito LF, Gil Lopez M, Hennig G, Pfeifenschneider J, Sgobba E, Veldmann KH. The flexible feedstock concept in Industrial Biotechnology: Metabolic engineering of Escherichia coli, Corynebacterium glutamicum, Pseudomonas, Bacillus and yeast strains for access to alternative carbon sources. J Biotechnol 2016; 234:139-157. [DOI: 10.1016/j.jbiotec.2016.07.022] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 07/25/2016] [Accepted: 07/28/2016] [Indexed: 11/28/2022]
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82
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Li M, Yue Y, Zhang ZJ, Wang ZY, Tan TW, Fan LH. Site-Specific and High-Loading Immobilization of Proteins by Using Cohesin-Dockerin and CBM-Cellulose Interactions. Bioconjug Chem 2016; 27:1579-83. [PMID: 27357145 DOI: 10.1021/acs.bioconjchem.6b00282] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Immobilization of enzymes enhances their properties for application in industrial processes as reusable and robust biocatalysts. Here, we developed a new immobilization method by mimicking the natural cellulosome system. A group of cohesin and carbohydrate-binding module (CBM)-containing scaffoldins were genetically engineered, and their length was controlled by cohesin number. To use green fluorescent protein (GFP) as an immobilization model, its C-terminus was fused with a dockerin domain. GFP was able to specifically bind to scaffoldin via cohesin-dockerin interaction, while the scaffoldin could attach to cellulose by CBM-cellulose interaction. Our results showed that this mild and convenient approach was able to achieve site-specific immobilization, and the maximum GFP loading capacity reached ∼0.508 μmol/g cellulose.
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Affiliation(s)
- Mei Li
- Beijing Key Laboratory of Bioprocess. College of Life Science and Technology, Beijing University of Chemical Technology , Beisanhuan East Road #15, Beijing, China 100029
| | - Yi Yue
- Beijing Key Laboratory of Bioprocess. College of Life Science and Technology, Beijing University of Chemical Technology , Beisanhuan East Road #15, Beijing, China 100029
| | - Zi-Jian Zhang
- Beijing Key Laboratory of Bioprocess. College of Life Science and Technology, Beijing University of Chemical Technology , Beisanhuan East Road #15, Beijing, China 100029
| | - Zai-Yu Wang
- Beijing Key Laboratory of Bioprocess. College of Life Science and Technology, Beijing University of Chemical Technology , Beisanhuan East Road #15, Beijing, China 100029
| | - Tian-Wei Tan
- Beijing Key Laboratory of Bioprocess. College of Life Science and Technology, Beijing University of Chemical Technology , Beisanhuan East Road #15, Beijing, China 100029
| | - Li-Hai Fan
- Beijing Key Laboratory of Bioprocess. College of Life Science and Technology, Beijing University of Chemical Technology , Beisanhuan East Road #15, Beijing, China 100029
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83
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Cunha ES, Hatem CL, Barrick D. Synergistic enhancement of cellulase pairs linked by consensus ankyrin repeats: Determination of the roles of spacing, orientation, and enzyme identity. Proteins 2016; 84:1043-54. [PMID: 27071357 DOI: 10.1002/prot.25047] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 03/09/2016] [Accepted: 03/25/2016] [Indexed: 12/22/2022]
Abstract
Biomass deconstruction to small simple sugars is a potential approach to biofuels production; however, the highly recalcitrant nature of biomass limits the economic viability of this approach. Thus, research on efficient biomass degradation is necessary to achieve large-scale production of biofuels. Enhancement of cellulolytic activity by increasing synergism between cellulase enzymes holds promise in achieving high-yield biofuels production. Here we have inserted cellulase pairs from extremophiles into hyperstable α-helical consensus ankyrin repeat domain scaffolds. Such chimeric constructs allowed us to optimize arrays of enzyme pairs against a variety of cellulolytic substrates. We found that endocellulolytic domains CelA (CA) and Cel12A (C12A) act synergistically in the context of ankyrin repeats, with both three and four repeat spacing. The extent of synergy differs for different substrates. Also, having C12A N-terminal to CA provides greater synergy than the reverse construct, especially against filter paper. In contrast, we do not see synergy for these enzymes in tandem with CelK (CK) catalytic domain, a larger exocellulase, demonstrating the importance of enzyme identity in synergistic enhancement. Furthermore, we found endocellulases CelD and CA with three repeat spacing to act synergistically against filter paper. Importantly, connecting CA and C12A with a disordered linker of similar contour length shows no synergistic enhancement, indicating that synergism results from connecting these domains with folded ankyrin repeats. These results show that ankyrin arrays can be used to vary spacing and orientation between enzymes, helping to design and optimize artificial cellulosomes, providing a novel architecture for synergistic enhancement of enzymatic cellulose degradation. Proteins 2016; 84:1043-1054. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Eva S Cunha
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St, Baltimore, Maryland, 21218.,Department of Structural Biology, Max Plank Institute of Biophysics, Max-von-Laue-Str. 3, Frankfurt am Main, D-60438, Germany
| | - Christine L Hatem
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St, Baltimore, Maryland, 21218
| | - Doug Barrick
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St, Baltimore, Maryland, 21218
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84
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Zhang Q, Li H, Zhu X, Lai F, Zhai Z, Wang Y. Exploration of the key functional proteins from an efficient cellulolytic microbial consortium using dilution-to-extinction approach. J Environ Sci (China) 2016; 43:199-207. [PMID: 27155425 DOI: 10.1016/j.jes.2015.09.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 09/21/2015] [Accepted: 09/23/2015] [Indexed: 06/05/2023]
Abstract
In the present study, the cellulose binding proteins (CBPs) secreted by a putative cellulolytic microbial consortium were isolated and purified by affinity digestion. The purified CBPs were subsequently separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). Using mass spectrometric analyses, eight CBPs were identified and annotated to be similar to known proteins secreted by Clostridium clariflavum DSM 19732 and Paenibacillus sp. W-61. In addition, in combination with dilution-to-extinction approach and zymogram analysis technique, CBPs 6 (97kDa) and 12 (52kDa) were confirmed to be the key functional proteins that influence cellulolytic activities. Moreover, structural domain analyses and enzymatic activity detection indicated that CBPs 6 and 12 contained glycoside hydrolase families (GH) 9 and 48 catalytic modules, which both revealed endoglucandase and xylanase activities. It was suggested that the coexistence of GH9 and GH48 catalytic domains present in these two proteins could synergistically promote the efficient degradation of cellulose.
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Affiliation(s)
- Qinghua Zhang
- College of Bioscience and Engineering, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China.
| | - Hanguang Li
- College of Bioscience and Engineering, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China.
| | - Xiangdong Zhu
- College of Bioscience and Engineering, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
| | - Fenju Lai
- College of Bioscience and Engineering, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
| | - Zhijun Zhai
- College of Bioscience and Engineering, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
| | - Yuanxiu Wang
- College of Bioscience and Engineering, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
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85
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Poszytek K, Ciezkowska M, Sklodowska A, Drewniak L. Microbial Consortium with High Cellulolytic Activity (MCHCA) for Enhanced Biogas Production. Front Microbiol 2016; 7:324. [PMID: 27014244 PMCID: PMC4791528 DOI: 10.3389/fmicb.2016.00324] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 02/29/2016] [Indexed: 11/26/2022] Open
Abstract
The use of lignocellulosic biomass as a substrate in agricultural biogas plants is very popular and yields good results. However, the efficiency of anaerobic digestion, and thus biogas production, is not always satisfactory due to the slow or incomplete degradation (hydrolysis) of plant matter. To enhance the solubilization of the lignocellulosic biomass various physical, chemical and biological pretreatment methods are used. The aim of this study was to select and characterize cellulose-degrading bacteria, and to construct a microbial consortium, dedicated for degradation of maize silage and enhancing biogas production from this substrate. Over 100 strains of cellulose-degrading bacteria were isolated from: sewage sludge, hydrolyzer from an agricultural biogas plant, cattle slurry and manure. After physiological characterization of the isolates, 16 strains (representatives of Bacillus, Providencia, and Ochrobactrum genera) were chosen for the construction of a Microbial Consortium with High Cellulolytic Activity, called MCHCA. The selected strains had a high endoglucanase activity (exceeding 0.21 IU/mL CMCase activity) and a wide range of tolerance to various physical and chemical conditions. Lab-scale simulation of biogas production using the selected strains for degradation of maize silage was carried out in a two-bioreactor system, similar to those used in agricultural biogas plants. The obtained results showed that the constructed MCHCA consortium is capable of efficient hydrolysis of maize silage, and increases biogas production by even 38%, depending on the inoculum used for methane fermentation. The results in this work indicate that the mesophilic MCHCA has a great potential for application on industrial scale in agricultural biogas plants.
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Affiliation(s)
- Krzysztof Poszytek
- Laboratory of Environmental Pollution Analysis, Faculty of Biology, University of Warsaw Warsaw, Poland
| | - Martyna Ciezkowska
- Laboratory of Environmental Pollution Analysis, Faculty of Biology, University of Warsaw Warsaw, Poland
| | - Aleksandra Sklodowska
- Laboratory of Environmental Pollution Analysis, Faculty of Biology, University of Warsaw Warsaw, Poland
| | - Lukasz Drewniak
- Laboratory of Environmental Pollution Analysis, Faculty of Biology, University of Warsaw Warsaw, Poland
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86
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Artzi L, Morag E, Shamshoum M, Bayer EA. Cellulosomal expansin: functionality and incorporation into the complex. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:61. [PMID: 26973715 PMCID: PMC4788839 DOI: 10.1186/s13068-016-0474-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 03/02/2016] [Indexed: 05/24/2023]
Abstract
BACKGROUND Expansins are relatively small proteins that lack enzymatic activity and are found in plants and microorganisms. The function of these proteins is to disrupt the plant cell walls by interfering with the non-covalent interchain bonding of the polysaccharides. Expansins were found to be important for plant growth, but they are also expressed by various bacteria known to have interactions with plants. Clostridium clariflavum is a plant cell wall-degrading bacterium with a highly elaborate cellulosomal system. Among its numerous dockerin-containing genes, two expansin-like proteins, Clocl_1862 and Clocl_1298 (termed herein CclEXL1 and CclEXL2) were identified, and CclEXL1 was found to be expressed as part of the cellulosome system. This is the first time that an expansin-like protein is identified in a cellulosome complex, which implicates its possible role in biomass deconstruction. RESULTS In the present article, we analyzed the functionality of CclEXL1. Its dockerin was characterized and shown to bind selectively to type-I cohesins of C. clariflavum, with preferential binding to the cohesin of ScaG, and additionally to a type-I cohesin of C. cellulolyticum. We demonstrated experimentally that the expansin-like protein binds preferentially to microcrystalline cellulose, but it also binds to acid-swollen cellulose, xylan, and wheat straw. CclEXL1 exhibited a pronounced loosening effect on filter paper, which resulted in substantial decrease in tensile stress. The C. clariflavum expansin-like protein thus enhances significantly enzymatic hydrolysis of cellulose, both by C. clariflavum cellulosomes and two major cellulosomal cellulases from this bacterium: GH48 (exoglucanase) and GH9 (endoglucanase). Finally, we demonstrated CclEXL1-mediated enhancement of microcrystalline cellulose degradation by different cellulosome fractions and the two enzymes. CONCLUSIONS The results of this study confirm that the C. clariflavum expansin-like protein is part of the elaborate cellulosome system of this bacterium with capabilities of cellulose creeping. The data suggest that pretreatment of cellulosic materials with CclEXL1 can bring about substantial improvement of hydrolysis by cellulases.
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Affiliation(s)
- Lior Artzi
- Department of Molecular Biosciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Ely Morag
- Department of Molecular Biosciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Melina Shamshoum
- Department of Molecular Biosciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Edward A. Bayer
- Department of Molecular Biosciences, The Weizmann Institute of Science, Rehovot, Israel
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87
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Identification of an Extracellular Endoglucanase That Is Required for Full Virulence in Xanthomonas citri subsp. citri. PLoS One 2016; 11:e0151017. [PMID: 26950296 PMCID: PMC4780785 DOI: 10.1371/journal.pone.0151017] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Accepted: 02/23/2016] [Indexed: 01/04/2023] Open
Abstract
Xanthomonas citri subsp. citri causes citrus canker disease, which is characterized by the formation of water-soaked lesions, white or yellow spongy pustules and brown corky canker. In this work, we report the contribution of extracellular endoglucanase to canker development during infection. The ectopic expression of nine putative cellulases in Escherichia coli indicated that two endoglucanases, BglC3 and EngXCA, show carboxymethyl cellulase activity. Both bglC3 and engXCA genes were transcribed in X. citri subsp. citri, however, only BglC3 protein was detected outside the cell in western blot analysis. The deletion of bglC3 gene resulted in complete loss of extracellular carboxymethyl cellulase activity and delayed the onset of canker symptoms in both infiltration- and wound-inoculation assays. When growing in plant tissue, the cell density of bglC3 mutant was lower than that of the wild type. Our data demonstrated that BglC3 is an extracellular endoglucanase required for the full virulence of X. citri subsp. citri.
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88
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Xu Q, Resch MG, Podkaminer K, Yang S, Baker JO, Donohoe BS, Wilson C, Klingeman DM, Olson DG, Decker SR, Giannone RJ, Hettich RL, Brown SD, Lynd LR, Bayer EA, Himmel ME, Bomble YJ. Dramatic performance of Clostridium thermocellum explained by its wide range of cellulase modalities. SCIENCE ADVANCES 2016; 2:e1501254. [PMID: 26989779 PMCID: PMC4788478 DOI: 10.1126/sciadv.1501254] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 11/30/2015] [Indexed: 05/18/2023]
Abstract
Clostridium thermocellum is the most efficient microorganism for solubilizing lignocellulosic biomass known to date. Its high cellulose digestion capability is attributed to efficient cellulases consisting of both a free-enzyme system and a tethered cellulosomal system wherein carbohydrate active enzymes (CAZymes) are organized by primary and secondary scaffoldin proteins to generate large protein complexes attached to the bacterial cell wall. This study demonstrates that C. thermocellum also uses a type of cellulosomal system not bound to the bacterial cell wall, called the "cell-free" cellulosomal system. The cell-free cellulosome complex can be seen as a "long range cellulosome" because it can diffuse away from the cell and degrade polysaccharide substrates remotely from the bacterial cell. The contribution of these two types of cellulosomal systems in C. thermocellum was elucidated by characterization of mutants with different combinations of scaffoldin gene deletions. The primary scaffoldin, CipA, was found to play the most important role in cellulose degradation by C. thermocellum, whereas the secondary scaffoldins have less important roles. Additionally, the distinct and efficient mode of action of the C. thermocellum exoproteome, wherein the cellulosomes splay or divide biomass particles, changes when either the primary or secondary scaffolds are removed, showing that the intact wild-type cellulosomal system is necessary for this essential mode of action. This new transcriptional and proteomic evidence shows that a functional primary scaffoldin plays a more important role compared to secondary scaffoldins in the proper regulation of CAZyme genes, cellodextrin transport, and other cellular functions.
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Affiliation(s)
- Qi Xu
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
- BioEnergy Science Center, Oak Ridge, TN 37831, USA
| | - Michael G. Resch
- BioEnergy Science Center, Oak Ridge, TN 37831, USA
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Kara Podkaminer
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
- BioEnergy Science Center, Oak Ridge, TN 37831, USA
| | - Shihui Yang
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - John O. Baker
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
- BioEnergy Science Center, Oak Ridge, TN 37831, USA
| | - Bryon S. Donohoe
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
- BioEnergy Science Center, Oak Ridge, TN 37831, USA
| | - Charlotte Wilson
- BioEnergy Science Center, Oak Ridge, TN 37831, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Dawn M. Klingeman
- BioEnergy Science Center, Oak Ridge, TN 37831, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Daniel G. Olson
- BioEnergy Science Center, Oak Ridge, TN 37831, USA
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA
| | - Stephen R. Decker
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
- BioEnergy Science Center, Oak Ridge, TN 37831, USA
| | - Richard J. Giannone
- BioEnergy Science Center, Oak Ridge, TN 37831, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Robert L. Hettich
- BioEnergy Science Center, Oak Ridge, TN 37831, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Steven D. Brown
- BioEnergy Science Center, Oak Ridge, TN 37831, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Lee R. Lynd
- BioEnergy Science Center, Oak Ridge, TN 37831, USA
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA
| | | | - Michael E. Himmel
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
- BioEnergy Science Center, Oak Ridge, TN 37831, USA
| | - Yannick J. Bomble
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
- BioEnergy Science Center, Oak Ridge, TN 37831, USA
- Corresponding author. E-mail:
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89
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2,3-Butanediol production from cellobiose using exogenous beta-glucosidase-expressing Bacillus subtilis. Appl Microbiol Biotechnol 2016; 100:5781-9. [DOI: 10.1007/s00253-016-7326-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 01/12/2016] [Accepted: 01/14/2016] [Indexed: 01/04/2023]
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90
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Zarafeta D, Kissas D, Sayer C, Gudbergsdottir SR, Ladoukakis E, Isupov MN, Chatziioannou A, Peng X, Littlechild JA, Skretas G, Kolisis FN. Discovery and Characterization of a Thermostable and Highly Halotolerant GH5 Cellulase from an Icelandic Hot Spring Isolate. PLoS One 2016; 11:e0146454. [PMID: 26741138 PMCID: PMC4704807 DOI: 10.1371/journal.pone.0146454] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 12/17/2015] [Indexed: 12/20/2022] Open
Abstract
With the ultimate goal of identifying robust cellulases for industrial biocatalytic conversions, we have isolated and characterized a new thermostable and very halotolerant GH5 cellulase. This new enzyme, termed CelDZ1, was identified by bioinformatic analysis from the genome of a polysaccharide-enrichment culture isolate, initiated from material collected from an Icelandic hot spring. Biochemical characterization of CelDZ1 revealed that it is a glycoside hydrolase with optimal activity at 70°C and pH 5.0 that exhibits good thermostability, high halotolerance at near-saturating salt concentrations, and resistance towards metal ions and other denaturing agents. X-ray crystallography of the new enzyme showed that CelDZ1 is the first reported cellulase structure that lacks the defined sugar-binding 2 subsite and revealed structural features which provide potential explanations of its biochemical characteristics.
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Affiliation(s)
- Dimitra Zarafeta
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece
- Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Dimitrios Kissas
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece
- Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Christopher Sayer
- Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | | | - Efthymios Ladoukakis
- Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Michail N. Isupov
- Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Aristotelis Chatziioannou
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Xu Peng
- Danish Archaea Centre, Department of Biology, Copenhagen University, Copenhagen, Denmark
| | - Jennifer A. Littlechild
- Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Georgios Skretas
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Fragiskos N. Kolisis
- Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
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91
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Sindhu R, Binod P, Pandey A. Biological pretreatment of lignocellulosic biomass--An overview. BIORESOURCE TECHNOLOGY 2016; 199:76-82. [PMID: 26320388 DOI: 10.1016/j.biortech.2015.08.030] [Citation(s) in RCA: 378] [Impact Index Per Article: 47.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 08/10/2015] [Accepted: 08/11/2015] [Indexed: 05/06/2023]
Abstract
Pretreatment is an important step involved in the production of bioethanol from lignocelluosic biomass. Though several pretreatment regimes are available, biological pretreatment seems to be promising being an eco-friendly process and there is no inhibitor generation during the process. In the current scenario there are few limitations in using this strategy for pilot scale process. The first and foremost one is the long incubation time for effective delignification. This can be minimized to an extent by using suitable microbial consortium. There is an urgent need for research and development activities and fine tuning of the process for the development of an economically viable process. This review presents an overview of various aspects of biological pretreatment, enzymes involved in the process, parameters affecting biological pretreatment as well as future perspectives.
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Affiliation(s)
- Raveendran Sindhu
- Biotechnology Division, National Institute for Interdisciplinary Science and Technology, CSIR, Trivandrum 695 019, India.
| | - Parameswaran Binod
- Biotechnology Division, National Institute for Interdisciplinary Science and Technology, CSIR, Trivandrum 695 019, India
| | - Ashok Pandey
- Biotechnology Division, National Institute for Interdisciplinary Science and Technology, CSIR, Trivandrum 695 019, India
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92
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Kameshwar AKS, Qin W. Recent Developments in Using Advanced Sequencing Technologies for the Genomic Studies of Lignin and Cellulose Degrading Microorganisms. Int J Biol Sci 2016; 12:156-71. [PMID: 26884714 PMCID: PMC4737673 DOI: 10.7150/ijbs.13537] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 11/03/2015] [Indexed: 01/23/2023] Open
Abstract
Lignin is a complex polyphenyl aromatic compound which exists in tight associations with cellulose and hemicellulose to form plant primary and secondary cell wall. Lignocellulose is an abundant renewable biomaterial present on the earth. It has gained much attention in the scientific community in recent years because of its potential applications in bio-based industries. Microbial degradation of lignocellulose polymers was well studied in wood decaying fungi. Based on the plant materials they degrade these fungi were classified as white rot, brown rot and soft rot. However, some groups of bacteria belonging to the actinomycetes, α-proteobacteria and β-proteobacteria were also found to be efficient in degrading lignocellulosic biomass but not well understood unlike the fungi. In this review we focus on recent advancements deployed for finding and understanding the lignocellulose degradation by microorganisms. Conventional molecular methods like sequencing 16s rRNA and Inter Transcribed Spacer (ITS) regions were used for identification and classification of microbes. Recent progression in genomics mainly next generation sequencing technologies made the whole genome sequencing of microbes possible in a great ease. The whole genome sequence studies reveals high quality information about genes and canonical pathways involved in the lignin and other cell wall components degradation.
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Affiliation(s)
| | - Wensheng Qin
- Department of Biology, Lakehead University, 955 Oliver Road, Thunder Bay, Ontario, P7B 5E1, Canada
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93
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Visualization of microbe-dietary remnant interactions in digesta from pigs, by fluorescence in situ hybridization and staining methods; effects of a dietary arabinoxylan-rich wheat fraction. Food Hydrocoll 2016. [DOI: 10.1016/j.foodhyd.2015.09.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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94
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Zhang X, Wang S, Wu X, Liu S, Li D, Xu H, Gao P, Chen G, Wang L. Subsite-specific contributions of different aromatic residues in the active site architecture of glycoside hydrolase family 12. Sci Rep 2015; 5:18357. [PMID: 26670009 PMCID: PMC4680936 DOI: 10.1038/srep18357] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 11/16/2015] [Indexed: 01/22/2023] Open
Abstract
The active site architecture of glycoside hydrolase (GH) is a contiguous subregion of the enzyme constituted by residues clustered in the three-dimensional space, recognizing the monomeric unit of ligand through hydrogen bonds and hydrophobic interactions. Mutations of the key residues in the active site architecture of the GH12 family exerted different impacts on catalytic efficiency. Binding affinities between the aromatic amino acids and carbohydrate rings were quantitatively determined by isothermal titration calorimetry (ITC) and the quantum mechanical (QM) method, showing that the binding capacity order of Tyr>Trp>His (and Phe) was determined by their side-chain properties. The results also revealed that the binding constant of a certain residue remained unchanged when altering its location, while the catalytic efficiency changed dramatically. Increased binding affinity at a relatively distant subsite, such as the mutant of W7Y at the -4 subsite, resulted in a marked increase in the intermediate product of cellotetraose and enhanced the reactivity of endoglucanase by 144%; while tighter binding near the catalytic center, i.e. W22Y at the -2 subsite, enabled the enzyme to bind and hydrolyze smaller oligosaccharides. Clarification of the specific roles of the aromatics at different subsites may pave the way for a more rational design of GHs.
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Affiliation(s)
- Xiaomei Zhang
- The State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, P.R. China
| | - Shuai Wang
- The State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, P.R. China
| | - Xiuyun Wu
- The State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, P.R. China
| | - Shijia Liu
- The State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, P.R. China
| | - Dandan Li
- The State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, P.R. China
| | - Hao Xu
- Key Laboratory of Colloid and Interface Chemistry, Ministry of Education, Institute of Theoretical Chemistry, Shandong University, Jinan, 250100, P.R. China
| | - Peiji Gao
- The State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, P.R. China
| | - Guanjun Chen
- The State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, P.R. China
| | - Lushan Wang
- The State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, P.R. China
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95
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Chatzifragkou A, Kosik O, Prabhakumari PC, Lovegrove A, Frazier RA, Shewry PR, Charalampopoulos D. Biorefinery strategies for upgrading Distillers’ Dried Grains with Solubles (DDGS). Process Biochem 2015. [DOI: 10.1016/j.procbio.2015.09.005] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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96
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Champasri C, Champasri T, Woranam K. Purification, Biochemical Characterization of a Macrotermes gilvus Cellulase and Zymogram Analysis. ACTA ACUST UNITED AC 2015. [DOI: 10.3923/ajb.2015.190.204] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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97
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Saini JK, Saini R, Tewari L. Lignocellulosic agriculture wastes as biomass feedstocks for second-generation bioethanol production: concepts and recent developments. 3 Biotech 2015; 5:337-353. [PMID: 28324547 PMCID: PMC4522714 DOI: 10.1007/s13205-014-0246-5] [Citation(s) in RCA: 272] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 08/05/2014] [Indexed: 12/02/2022] Open
Abstract
Production of liquid biofuels, such as bioethanol, has been advocated as a sustainable option to tackle the problems associated with rising crude oil prices, global warming and diminishing petroleum reserves. Second-generation bioethanol is produced from lignocellulosic feedstock by its saccharification, followed by microbial fermentation and product recovery. Agricultural residues generated as wastes during or after processing of agricultural crops are one of such renewable and lignocellulose-rich biomass resources available in huge amounts for bioethanol production. These agricultural residues are converted to bioethanol in several steps which are described here. This review enlightens various steps involved in production of the second-generation bioethanol. Mechanisms and recent advances in pretreatment, cellulases production and second-generation ethanol production processes are described here.
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Affiliation(s)
- Jitendra Kumar Saini
- Department of Microbiology, College of Basic Sciences and Humanities, GB Pant University of Agriculture and Technology, Pantnagar, Udham Singh Nagar, 263145, India.
- DBT-IOC Centre for Advanced Bio-Energy Research, Research and Development Centre, Indian Oil Corporation Ltd., Sector-13, Faridabad, 121007, Haryana, India.
| | - Reetu Saini
- Department of Microbiology, M.S. Garg P.G. College, Laksar, Haridwar, 247663, India
- DBT-IOC Centre for Advanced Bio-Energy Research, Research and Development Centre, Indian Oil Corporation Ltd., Sector-13, Faridabad, 121007, Haryana, India
| | - Lakshmi Tewari
- Department of Microbiology, College of Basic Sciences and Humanities, GB Pant University of Agriculture and Technology, Pantnagar, Udham Singh Nagar, 263145, India
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98
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Huy ND, Nguyen CL, Park HS, Loc NH, Choi MS, Kim DH, Seo JW, Park SM. Characterization of a novel manganese dependent endoglucanase belongs in GH family 5 from Phanerochaete chrysosporium. J Biosci Bioeng 2015; 121:154-9. [PMID: 26173955 DOI: 10.1016/j.jbiosc.2015.06.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 05/31/2015] [Accepted: 06/18/2015] [Indexed: 01/22/2023]
Abstract
The cDNA encoding a putative glycoside hydrolase family 5, which has been predicted to be an endoglucanase (PcEg5A), was cloned from Phanerochaete chrysosporium and expressed in Pichia pastoris. PcEg5A contains a carbohydrate-binding domain and two important amino acids, E209 and E319, playing as proton donor and nucleophile in substrate catalytic domain. SDS-PAGE analysis indicated that the recombinant endoglucanase 5A (rPcEg5A) has a molecular size of 43 kDa which corresponds with the theoretical calculation. Optimum pH and temperature were found to be 4.5-6.0, and 50°C-60°C, respectively. Moreover, rPcEg5A exhibited maximal activity in the pH range of 3.0-8.0, whereas over 50% of activity still remained at 20°C and 80°C. rPcEg5A was stable at 60°C for 12 h incubation, indicating that rPcEg5A is a thermostable enzyme. Manganese ion enhanced the enzyme activity by 77%, indicating that rPcEg5A is a metal dependent enzyme. The addition of rPcEg5A to cellobiase (cellobiohydrolase and β-glucosidase) resulted in a 53% increasing saccharification of NaOH-pretreated barley straw, whereas the glucose release was 47% higher than that cellobiase treatment alone. Our study suggested that rPcEg5A is an enzyme with great potential for biomass saccharification.
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Affiliation(s)
- Nguyen Duc Huy
- Division of Biotechnology, College of Environmental and Bioresource Sciences, Chonbuk National University, Iksan, Jeonbuk 570-752, Republic of Korea; Institute of Biotechnology, Hue University, Hue 530000, Viet Nam
| | - Cu Le Nguyen
- Division of Biotechnology, College of Environmental and Bioresource Sciences, Chonbuk National University, Iksan, Jeonbuk 570-752, Republic of Korea
| | - Han-Sung Park
- Division of Biotechnology, College of Environmental and Bioresource Sciences, Chonbuk National University, Iksan, Jeonbuk 570-752, Republic of Korea
| | | | - Myoung-Suk Choi
- Institute of Molecular Biology and Genetics, College of Natural Sciences, Chonbuk National University, Jeonju, Jeonbuk 561-756, Republic of Korea
| | - Dae-Hyuk Kim
- Institute of Molecular Biology and Genetics, College of Natural Sciences, Chonbuk National University, Jeonju, Jeonbuk 561-756, Republic of Korea
| | - Jeong-Woo Seo
- Applied Microbiology Research Center, Bio-Materials Research Institute, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, Jeonbuk 580-185, Republic of Korea
| | - Seung-Moon Park
- Division of Biotechnology, College of Environmental and Bioresource Sciences, Chonbuk National University, Iksan, Jeonbuk 570-752, Republic of Korea.
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99
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Szydlowski L, Boschetti C, Crisp A, Barbosa E, Tunnacliffe A. Multiple horizontally acquired genes from fungal and prokaryotic donors encode cellulolytic enzymes in the bdelloid rotifer Adineta ricciae. Gene 2015; 566:125-37. [DOI: 10.1016/j.gene.2015.04.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 04/01/2015] [Accepted: 04/03/2015] [Indexed: 10/23/2022]
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100
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Voronov-Goldman M, Yaniv O, Gul O, Yoffe H, Salama-Alber O, Slutzki M, Levy-Assaraf M, Jindou S, Shimon LJW, Borovok I, Bayer EA, Lamed R, Frolow F. Standalone cohesin as a molecular shuttle in cellulosome assembly. FEBS Lett 2015; 589:1569-76. [PMID: 25896019 DOI: 10.1016/j.febslet.2015.04.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 04/06/2015] [Accepted: 04/08/2015] [Indexed: 11/20/2022]
Abstract
The cellulolytic bacterium Ruminococcus flavefaciens of the herbivore rumen produces an elaborate cellulosome system, anchored to the bacterial cell wall via the covalently bound scaffoldin ScaE. Dockerin-bearing scaffoldins also bind to an autonomous cohesin of unknown function, called cohesin G (CohG). Here, we demonstrate that CohG binds to the scaffoldin-borne dockerin in opposite orientation on a distinct site, relative to that of ScaE. Based on these structural data, we propose that the complexed dockerin is still available to bind ScaE on the cell surface. CohG may thus serve as a molecular shuttle for delivery of scaffoldins to the bacterial cell surface.
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Affiliation(s)
- Milana Voronov-Goldman
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, 69978, Israel; The Daniella Rich Institute for Structural Biology, Tel Aviv University, 69978, Israel
| | - Oren Yaniv
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, 69978, Israel; The Daniella Rich Institute for Structural Biology, Tel Aviv University, 69978, Israel
| | - Ozgur Gul
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Hagar Yoffe
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, 69978, Israel; The Daniella Rich Institute for Structural Biology, Tel Aviv University, 69978, Israel
| | - Orly Salama-Alber
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Michal Slutzki
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Maly Levy-Assaraf
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, 69978, Israel; The Daniella Rich Institute for Structural Biology, Tel Aviv University, 69978, Israel
| | - Sadanari Jindou
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, 69978, Israel; Faculty of Agriculture, Meijo University, Nagoya 468-8502, Japan
| | - Linda J W Shimon
- Department of Chemical Research Support, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ilya Borovok
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, 69978, Israel
| | - Edward A Bayer
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel.
| | - Raphael Lamed
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, 69978, Israel; The Daniella Rich Institute for Structural Biology, Tel Aviv University, 69978, Israel.
| | - Felix Frolow
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, 69978, Israel; The Daniella Rich Institute for Structural Biology, Tel Aviv University, 69978, Israel
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