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Abbas Bukhari D, Bibi Z, Ullah A, Rehman A. Isolation, characterization, and cloning of thermostable pullulanase from Geobacillus stearothermophilus ADM-11. Saudi J Biol Sci 2024; 31:103901. [PMID: 38234990 PMCID: PMC10792974 DOI: 10.1016/j.sjbs.2023.103901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 12/04/2023] [Accepted: 12/08/2023] [Indexed: 01/19/2024] Open
Abstract
This study aimed to identify thermo-stable pullulanase-producing bacteria in soil samples of potato fields and food-producing companies. Pullulan agar medium was used to screen 17 bacterial strains, which were incubated at 65 °C. The isolate with the maximum activity (375U/ml) was selected and recognized as Geobacillus stearothermophilus ADM-11 by morphological, biochemical characterization, and 16S rRNA gene sequencing. The pullulanase production required optimum pH of 7 and temperature of 75 °C, respectively. The electrophoresis of purified pullulanase on SDS-polyacrylamide gel revealed 83 kDa of a molecular weight that is active at 70 °C and pH 7.0. It was also stable at 90 °C but its activity was decreased by 10 % at 100 °C. The action of pullulanase was increased and stabilized by Ca+2 among the metal ions. Beta and gamma-cyclodextrins inhibited enzyme activity while ethylenediaminetetraacetate (EDTA) and phenylmethylsulfonyl fluoride (PMSF) have no significant effect on pullulanase activity. A full-length pullulanase gene was amplified from G. stearothermophilus ADM-11 using genomic DNA 2.1 kb of PCR product which was then purified and ligated in the cloning vector pTZ57R using the TA cloning technique. Colony PCR confirmed cloning on the positive clones after the pullulanase gene had been ligated and subjected to restriction digestion. It revealed 74 % similarity with the reported pullulanase gene from Geobacillus sp. 44C. The thermostability of pullulanase and its ability to degrade raw pullulan may therefore have wide-scale applications in starch processing, the detergent business, and new biotechnological applications.
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Affiliation(s)
| | - Zuhra Bibi
- Department of Zoology, Government College University, Lahore, Pakistan
| | - Arif Ullah
- Department of Zoology, Government College University, Lahore, Pakistan
| | - Abdul Rehman
- Institute of Microbiology and Molecular Genetics, University of the Punjab, Lahore, Pakistan
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Jomrit J, Suhardi S, Summpunn P. Effects of Signal Peptide and Chaperone Co-Expression on Heterologous Protein Production in Escherichia coli. Molecules 2023; 28:5594. [PMID: 37513466 PMCID: PMC10384211 DOI: 10.3390/molecules28145594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 07/17/2023] [Accepted: 07/21/2023] [Indexed: 07/30/2023] Open
Abstract
Various host systems have been employed to increase the yield of recombinant proteins. However, some recombinant proteins were successfully produced at high yields but with no functional activities. To achieve both high protein yield and high activities, molecular biological strategies have been continuously developed. This work describes the effect of signal peptide (SP) and co-expression of molecular chaperones on the production of active recombinant protein in Escherichia coli. Extracellular enzymes from Bacillus subtilis, including β-1,4-xylanase, β-1,4-glucanase, and β-mannanase constructed with and without their signal peptides and intracellular enzymes from Pseudomonas stutzeri ST201, including benzoylformate decarboxylase (BFDC), benzaldehyde dehydrogenase (BADH), and d-phenylglycine aminotransferase (d-PhgAT) were cloned and overexpressed in E. coli BL21(DE3). Co-expression of molecular chaperones with all enzymes studied was also investigated. Yields of β-1,4-xylanase (Xyn), β-1,4-glucanase (Cel), and β-mannanase (Man), when constructed without their N-terminal signal peptides, increased 1112.61-, 1.75-, and 1.12-fold, respectively, compared to those of spXyn, spCel, and spMan, when constructed with their signal peptides. For the natural intracellular enzymes, the chaperones, GroEL-GroES complex, increased yields of active BFDC, BADH, and d-PhgAT, up to 1.31-, 4.94- and 37.93-fold, respectively, and also increased yields of Man and Xyn up to 1.53- and 3.46-fold, respectively, while other chaperones including DnaK-DnaJ-GrpE and Trigger factor (Tf) showed variable effects with these enzymes. This study successfully cloned and overexpressed extracellular and intracellular enzymes in E. coli BL21(DE3). When the signal peptide regions of the secretory enzymes were removed, yields of active enzymes were higher than those with intact signal peptides. In addition, a higher yield of active enzymes was obtained, in general, when these enzymes were co-expressed with appropriate chaperones. Therefore, E. coli can produce cytoplasmic and secretory enzymes effectively if only the enzyme coding sequence without its signal peptide is used and appropriate chaperones are co-expressed to assist in correct folding.
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Affiliation(s)
- Juntratip Jomrit
- School of Pharmacy, Walailak University, Nakhon Si Thammarat 80160, Thailand
| | - Suhardi Suhardi
- Department of Animal Science, Faculty of Agriculture, Mulawarman University, Samarinda 75123, Indonesia
| | - Pijug Summpunn
- Food Technology and Innovation Research Center of Excellence, School of Agricultural Technology and Food industry, Walailak University, Nakhon Si Thammarat 80160, Thailand
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Bharwad K, Shekh S, Singh NK, Patel A, Joshi C. Heterologous expression and biochemical characterization of novel multifunctional thermostable α-amylase from hot-spring metagenome. Int J Biol Macromol 2023; 242:124810. [PMID: 37182622 DOI: 10.1016/j.ijbiomac.2023.124810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/24/2023] [Accepted: 05/07/2023] [Indexed: 05/16/2023]
Abstract
Hot-springs are regarded as the best source of industrially significant biocules and one of the unique locations for extremophiles. The α-amylase is one of the most important enzymes used in starch consuming industries, where the need of thermostability is paramount. In this study, the full metagenome sequences obtained from the soil of Tuwa hot-spring (Gujarat, India) were examined for the presence of several thermostable enzymes using bioinformatic techniques. The whole gene sequence for α-amylase was found from the metagenome. The α-amylase gene was amplified, cloned, and expressed in Escherichia coli and further characterized in vitro. The rm-α-amylase was found optimally active at 60 °C and at pH 6.0 and showed significantly high activity in 0.1 mM Co2+ as well as in other heavy metal ions without any effect on its thermostability. Apart from α-amylase activity the purified rm-α-amylase was also shown to hydrolyse agar, xylan, pectin, alginate and cellulose. To our knowledge, this is the first report of a new, multifunctional, thermostable amylase that was discovered from the hot-spring metagenomes. Owing to their multifunctionality, resilience towards high temperature and heavy metal ions, stability with solvents, additives and inhibitors, rm-α-amylase can be exploited for a variety of biotechnological applications.
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Affiliation(s)
- Krishna Bharwad
- Gujarat Biotechnology Research Centre, Gandhinagar 382011, India
| | - Satyamitra Shekh
- Gujarat Biotechnology Research Centre, Gandhinagar 382011, India
| | | | - Amrutlal Patel
- Gujarat Biotechnology Research Centre, Gandhinagar 382011, India
| | - Chaitanya Joshi
- Gujarat Biotechnology Research Centre, Gandhinagar 382011, India.
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Patel VK, Das A, Kumari R, Kajla S. In silico Analysis of Diverse Endo-β-1,4-glucanases Reveals Their Molecular Evolution. J EVOL BIOCHEM PHYS+ 2023. [DOI: 10.1134/s0022093023010088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
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Gu X, Fu L, Pan A, Gui Y, Zhang Q, Li J. Multifunctional alkalophilic α-amylase with diverse raw seaweed degrading activities. AMB Express 2021; 11:139. [PMID: 34669086 PMCID: PMC8528909 DOI: 10.1186/s13568-021-01300-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 10/12/2021] [Indexed: 12/15/2022] Open
Abstract
Uncultured microbes are an important resource for the discovery of novel enzymes. In this study, an amylase gene (amy2587) that codes a protein with 587 amino acids (Amy2587) was obtained from the metagenomic library of macroalgae-associated bacteria. Recombinant Amy2587 was expressed in Escherichia coli BL21 (DE3) and was found to simultaneously possess α-amylase, agarase, carrageenase, cellulase, and alginate lyase activities. Moreover, recombinant Amy2587 showed high thermostability and alkali resistance which are important characteristics for industrial application. To investigate the multifunctional mechanism of Amy2587, three motifs (functional domains) in the Amy2587 sequence were deleted to generate three truncated Amy2587 variants. The results showed that, even though these functional domains affected the multiple substrates degrading activity of Amy2587, they did not wholly explain its multifunctional characteristics. To apply the multifunctional activity of Amy2587, three seaweed substrates (Grateloupia filicina, Chondrus ocellatus, and Scagassum) were digested using Amy2587. After 2 h, 6 h, and 24 h of digestion, 121.2 ± 4 µg/ml, 134.8 ± 6 µg/ml, and 70.3 ± 3.5 µg/ml of reducing sugars were released, respectively. These results show that Amy2587 directly and effectively degraded three kinds of raw seaweeds. This finding provides a theoretical basis for one-step enzymatic digestion of raw seaweeds to obtain seaweed oligosaccharides.
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Ma L, Aizhan R, Wang X, Yi Y, Shan Y, Liu B, Zhou Y, Lü X. Cloning and characterization of low-temperature adapted GH5-CBM3 endo-cellulase from Bacillus subtilis 1AJ3 and their application in the saccharification of switchgrass and coffee grounds. AMB Express 2020; 10:42. [PMID: 32140794 PMCID: PMC7058755 DOI: 10.1186/s13568-020-00975-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 02/21/2020] [Indexed: 01/27/2023] Open
Abstract
Endocellulase is a key cellulase for cellulosic material pretreatment in the industry by hydrolyzing long cellulose chains into short chains. To investigate the endocellulase characteristics from Bacillus subtilis 1AJ3, and increase its production yield, this paper cloned an endocellulase gene denoted CEL-5A from strain 1AJ3 and expressed in E. coli BL21 (DE3). The CEL-5A gene was sequenced with a full-length of 1500 bp, encoding a totally of 500 amino acids, and containing two domains: the GH5 family catalytic domain (CD) and the CBM3 family cellulose-binding domain (CBD). Recombinant endocellulase Cel-5A with a His-tag was purified of the Ni-NTA column, and SDS-PAGE results demonstrated that Cel-5A exhibited a molecular weight of 56.4 kDa. The maximum enzyme activity of Cel-5A was observed at pH 4.5 and 50 °C. Moreover, it was active over the broad temperature region of 30–60 °C, and stable within the pH range of 4.5–10.0. In addition, Co2+ was able to increase enzyme activity, while the majority of metal ions demonstrated stable enzyme activity under low- concentration. The substrate specificity of Cel-5A exhibited a high specific activity on the β-1,3-1,4 glucan linkage from barley. The Michaelis–Menten constant and the maximum velocity of the recombinant Cel-5A for CMC-Na were determined as 14.87 mg/mL and 19.19 μmol/min/mg, respectively. When Cel-5A was applied to the switchgrass and coffee grounds, its color became lighter and the biomass was observed to loosen following hydrolyzation. The saccharification rate reached 12% of the total weight of switchgrass in 20 h. These properties highlight the potential application of Cel-5A as an endocellulase in the pretreatment of biomass, for example, in the coffee grounds/waste, and related industries.
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Li J, Gu X, Pan A. Multifunctional α-amylase Amy19 possesses agarase, carrageenase, and cellulase activities. Int J Biol Macromol 2019; 126:585-594. [DOI: 10.1016/j.ijbiomac.2018.12.217] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 11/29/2018] [Accepted: 12/22/2018] [Indexed: 11/28/2022]
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Singh G, Patel AK, Gupta A, Gupta D, Mishra VK. Current Advancements in Recombinant Technology for Industrial Production of Cellulases: Part-II. Fungal Biol 2019. [DOI: 10.1007/978-3-030-14726-6_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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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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Siu-Rodas Y, Calixto-Romo MDLA, Guillén-Navarro K, Sánchez JE, Zamora-Briseño JA, Amaya-Delgado L. Bacillus subtilis with endocellulase and exocellulase activities isolated in the thermophilic phase from composting with coffee residues. Rev Argent Microbiol 2017; 50:234-243. [PMID: 29289440 DOI: 10.1016/j.ram.2017.08.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 06/24/2017] [Accepted: 08/03/2017] [Indexed: 11/28/2022] Open
Abstract
The goal of this study was to isolate, select and characterize bacteria with cellulolytic activity from two different coffee residue composting piles, one of which had an internal temperature of 57°C and pH 5.5 and the other, a temperature of 61°C, and pH 9.3. Culture media were manipulated with carboxymethylcellulose and crystalline cellulose as sole carbon sources. The enzyme activity was assessed by hydrolysis halo formation, reducing sugar production and zymograms. Three out of twenty isolated strains showed higher enzymatic activity and were identified as Bacillus subtilis according to their morphological, physiological, biochemical characteristics and based on the sequence analysis of 16S rDNA regions. The enzymatic extracts of the three selected strains showed exocellulase and endocellulase maximum activity of 0.254 and 0.519 U/ml, respectively; the activity of these enzymes was maintained even in acid pH (4.8) and basic (9.3) and at temperatures of up to 60°C. The enzymatic activities observed in this study are within the highest reported for cellulose produced by bacteria of the genus Bacillus. Endocellulase activity was shown in the zymograms from 24h until 144h of incubation. Furthermore, the pH effect on the endocellulase activity is reported for the first time by zymograms. The findings in this study entail the possibility to use these enzymes in the procurement of fermentable substrates for the production of energy from the large amount of residues generated by the coffee agroindustry.
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Affiliation(s)
- Yadira Siu-Rodas
- El Colegio de la Frontera Sur (ECOSUR), Carretera Antiguo Aeropuerto Km. 2.5, col. Centro, C.P. 30700 Tapachula, Chiapas, Mexico
| | | | - Karina Guillén-Navarro
- El Colegio de la Frontera Sur (ECOSUR), Carretera Antiguo Aeropuerto Km. 2.5, col. Centro, C.P. 30700 Tapachula, Chiapas, Mexico
| | - José E Sánchez
- El Colegio de la Frontera Sur (ECOSUR), Carretera Antiguo Aeropuerto Km. 2.5, col. Centro, C.P. 30700 Tapachula, Chiapas, Mexico
| | - Jesús Alejandro Zamora-Briseño
- El Colegio de la Frontera Sur (ECOSUR), Carretera Antiguo Aeropuerto Km. 2.5, col. Centro, C.P. 30700 Tapachula, Chiapas, Mexico
| | - Lorena Amaya-Delgado
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco (CIATEJ), Camino del Arenero 1227, El Bajío del Arenal, C.P. 45019 Zapopan, Jalisco, Mexico
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Hatefi A, Makhdoumi A, Asoodeh A, Mirshamsi O. Characterization of a bi-functional cellulase produced by a gut bacterial resident of Rosaceae branch borer beetle, Osphranteria coerulescens (Coleoptera: Cerambycidae). Int J Biol Macromol 2017; 103:158-164. [DOI: 10.1016/j.ijbiomac.2017.05.042] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 04/12/2017] [Accepted: 05/09/2017] [Indexed: 10/19/2022]
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Park T, Seo S, Shin T, Cho BW, Cho S, Kim B, Lee S, Ha JK, Seo J. Molecular cloning, purification, expression, and characterization of β-1, 4-endoglucanase gene ( Cel5A) from Eubacterium cellulosolvens sp. isolated from Holstein steers' rumen. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2017; 31:607-615. [PMID: 28920412 PMCID: PMC5838334 DOI: 10.5713/ajas.17.0552] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 08/25/2017] [Accepted: 09/04/2017] [Indexed: 11/27/2022]
Abstract
Objective This study was conducted to isolate the cellulolytic microorganism from the rumen of Holstein steers and characterize endoglucanase gene (Cel5A) from the isolated microorganism. Methods To isolate anaerobic microbes having endoglucanase, rumen fluid was obtained from Holstein steers fed roughage diet. The isolated anaerobic bacteria had 98% similarity with Eubacterium cellulosolvens (E. cellulosolvens) Ce2 (Accession number: AB163733). The Cel5A from isolated E. cellulolsovens sp. was cloned using the published genome sequence and expressed through the Escherichia coli BL21. Results The maximum activity of recombinant Cel5A (rCel5A) was observed at 50°C and pH 4.0. The enzyme was constant at the temperature range of 20°C to 40°C but also, at the pH range of 3 to 9. The metal ions including Ca2+, K+, Ni2+, Mg2+, and Fe2+ increased the endoglucanase activity but the addition of Mn2+, Cu2+, and Zn2+ decreased. The Km and Vmax value of rCel5A were 14.05 mg/mL and 45.66 μmol/min/mg. Turnover number, Kcat and catalytic efficiency, Kcat/Km values of rCel5A was 96.69 (s−1) and 6.88 (mL/mg/s), respectively. Conclusion Our results indicated that rCel5A of E. cellulosolvens isolated from Holstein steers had a broad pH range with high stability under various conditions, which might be one of the beneficial characteristics of this enzyme for possible industrial application.
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Affiliation(s)
- Tansol Park
- Department of Agricultural Biotechnology, College of Agriculture and Life Science, Seoul National University, Seoul 08826, Korea.,Department of Animal Sciences, The Ohio State University, Columbus, OH 43210, USA
| | - Seongwon Seo
- Department of Animal Biosystem Sciences, Chungnam National University, Daejeon 34134, Korea
| | - Teaksoon Shin
- Life and Industry Convergence Research Institute, Department of Animal Science, Pusan National University, Miryang 50463, Korea
| | - Byung-Wook Cho
- Life and Industry Convergence Research Institute, Department of Animal Science, Pusan National University, Miryang 50463, Korea
| | - Seongkeun Cho
- Life and Industry Convergence Research Institute, Department of Animal Science, Pusan National University, Miryang 50463, Korea
| | - Byeongwoo Kim
- Life and Industry Convergence Research Institute, Department of Animal Science, Pusan National University, Miryang 50463, Korea
| | - Seyoung Lee
- Division of Animal Husbandry, Yonam College, Cheonan, 31005, Korea
| | - Jong K Ha
- Department of Agricultural Biotechnology, College of Agriculture and Life Science, Seoul National University, Seoul 08826, Korea
| | - Jakyeom Seo
- Life and Industry Convergence Research Institute, Department of Animal Science, Pusan National University, Miryang 50463, Korea
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Garg R, Srivastava R, Brahma V, Verma L, Karthikeyan S, Sahni G. Biochemical and structural characterization of a novel halotolerant cellulase from soil metagenome. Sci Rep 2016; 6:39634. [PMID: 28008971 PMCID: PMC5180356 DOI: 10.1038/srep39634] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 11/25/2016] [Indexed: 12/20/2022] Open
Abstract
Cellulase catalyzes the hydrolysis of β-1,4-linkages of cellulose to produce industrially relevant monomeric subunits. Cellulases find their applications in pulp and paper, laundry, food and feed, textile, brewing industry and in biofuel production. These industries always have great demand for cellulases that can work efficiently even in harsh conditions such as high salt, heat, and acidic environments. While, cellulases with high thermal and acidic stability are already in use, existence of a high halotolerant cellulase is still elusive. Here, we report a novel cellulase Cel5R, obtained from soil metagenome that shows high halotolerance and thermal stability. The biochemical and functional characterization of Cel5R revealed its endoglucanase activity and high halostability. In addition, the crystal structure of Cel5R determined at 2.2 Å resolution reveals a large number of acidic residues on the surface of the protein that contribute to the halophilic nature of this enzyme. Moreover, we demonstrate that the four free and non-conserved cysteine residues (C65, C90, C231 and C273) contributes to the thermal stability of Cel5R by alanine scanning experiments. Thus, the newly identified endoglucanase Cel5R is a promising candidate for various industrial applications.
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Affiliation(s)
- Roma Garg
- CSIR-Institute Of Microbial Technology, Council Of Scientific and Industrial Research (CSIR), Sector 39 A, Chandigarh 160036, India
| | - Ritika Srivastava
- CSIR-Institute Of Microbial Technology, Council Of Scientific and Industrial Research (CSIR), Sector 39 A, Chandigarh 160036, India
| | - Vijaya Brahma
- CSIR-Institute Of Microbial Technology, Council Of Scientific and Industrial Research (CSIR), Sector 39 A, Chandigarh 160036, India
| | - Lata Verma
- CSIR-Institute Of Microbial Technology, Council Of Scientific and Industrial Research (CSIR), Sector 39 A, Chandigarh 160036, India
| | - Subramanian Karthikeyan
- CSIR-Institute Of Microbial Technology, Council Of Scientific and Industrial Research (CSIR), Sector 39 A, Chandigarh 160036, India
| | - Girish Sahni
- CSIR-Institute Of Microbial Technology, Council Of Scientific and Industrial Research (CSIR), Sector 39 A, Chandigarh 160036, India
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Extending the linker region increases the activity of the Bacillus subtilis cellulase CelI15. Biotechnol Lett 2016; 38:1587-93. [PMID: 27271520 DOI: 10.1007/s10529-016-2136-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 05/26/2016] [Indexed: 12/15/2022]
Abstract
OBJECTIVES To investigate the effect of the linker region (LR) on the enzymatic activity, stability, and flexibility of Bacillus subtilis cellulase CelI15, six mutants were constructed that contained increasing numbers of the LR. RESULTS The CelI15 mutant with three copies of the LR (approx. 57 amino acids) showed the highest activity, which was almost 20 % greater than that of wild type CelI15. The stability of the mutant enzymes increased as the copy number of the LR decreased. However, the substrate affinity of the mutant enzymes increased as the LR copy number increased, and the mutant with four copies of the LR exhibited the highest substrate affinity. Additionally, the flexibility of the CelI15 mutants increased as the LR copy number increased from zero to four copies, although it decreased sharply for the mutant with five copies of the LR. CONCLUSION The activity of CelI15 was increased by increasing the LR copy number, which could be a potential way to improve its enzymatic properties.
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Chang CJ, Lee CC, Chan YT, Trudeau DL, Wu MH, Tsai CH, Yu SM, Ho THD, Wang AHJ, Hsiao CD, Arnold FH, Chao YC. Exploring the Mechanism Responsible for Cellulase Thermostability by Structure-Guided Recombination. PLoS One 2016; 11:e0147485. [PMID: 26986867 PMCID: PMC4795783 DOI: 10.1371/journal.pone.0147485] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 01/05/2016] [Indexed: 12/29/2022] Open
Abstract
Cellulases from Bacillus and Geobacillus bacteria are potentially useful in the biofuel and animal feed industries. One of the unique characteristics of these enzymes is that they are usually quite thermostable. We previously identified a cellulase, GsCelA, from thermophilic Geobacillus sp. 70PC53, which is much more thermostable than its Bacillus homolog, BsCel5A. Thus, these two cellulases provide a pair of structures ideal for investigating the mechanism regarding how these cellulases can retain activity at high temperature. In the present study, we applied the SCHEMA non-contiguous recombination algorithm as a novel tool, which assigns protein sequences into blocks for domain swapping in a way that lessens structural disruption, to generate a set of chimeric proteins derived from the recombination of GsCelA and BsCel5A. Analyzing the activity and thermostability of this designed library set, which requires only a limited number of chimeras by SCHEMA calculations, revealed that one of the blocks may contribute to the higher thermostability of GsCelA. When tested against swollen Avicel, the highly thermostable chimeric cellulase C10 containing this block showed significantly higher activity (22%-43%) and higher thermostability compared to the parental enzymes. With further structural determinations and mutagenesis analyses, a 310 helix was identified as being responsible for the improved thermostability of this block. Furthermore, in the presence of ionic calcium and crown ether (CR), the chimeric C10 was found to retain 40% residual activity even after heat treatment at 90°C. Combining crystal structure determinations and structure-guided SCHEMA recombination, we have determined the mechanism responsible for the high thermostability of GsCelA, and generated a novel recombinant enzyme with significantly higher activity.
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Affiliation(s)
- Chia-Jung Chang
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, ROC
| | - Cheng-Chung Lee
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan, ROC
- Core Facilities for Protein Structural Analysis, Academia Sinica, Taipei, Taiwan, ROC
| | - Yueh-Te Chan
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan, ROC
- Core Facilities for Protein Structural Analysis, Academia Sinica, Taipei, Taiwan, ROC
| | - Devin L. Trudeau
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Mei-Huey Wu
- Institute of Biotechnology, National Cheng Kung University, Tainan, Taiwan, ROC
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan, ROC
| | - Chih-Hsuan Tsai
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, ROC
| | - Su-May Yu
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, ROC
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Tuan-Hua David Ho
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan, ROC
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Andrew H.-J. Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan, ROC
- Core Facilities for Protein Structural Analysis, Academia Sinica, Taipei, Taiwan, ROC
| | - Chwan-Deng Hsiao
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, ROC
| | - Frances H. Arnold
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Yu-Chan Chao
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, ROC
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan, ROC
- * E-mail:
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16
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Characterization of an acidic cellulase produced by Bacillus subtilis BY-4 isolated from gastrointestinal tract of Tibetan pig. J Taiwan Inst Chem Eng 2015. [DOI: 10.1016/j.jtice.2015.04.025] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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17
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Khare SK, Pandey A, Larroche C. Current perspectives in enzymatic saccharification of lignocellulosic biomass. Biochem Eng J 2015. [DOI: 10.1016/j.bej.2015.02.033] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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18
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RAMDANI MOEIS MAELITA, NATALIA DESSY, WIDYA NINGRUM RAHMA, DWIJAYANTI ARI. Cloning and Expression of Endoglucanase Gene from Thermophilic Bacteria Bacillus sp. RP1. MICROBIOLOGY INDONESIA 2014. [DOI: 10.5454/mi.8.4.4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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19
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Balasubramanian N, Simões N. Bacillus pumilus S124A carboxymethyl cellulase; a thermo stable enzyme with a wide substrate spectrum utility. Int J Biol Macromol 2014; 67:132-9. [DOI: 10.1016/j.ijbiomac.2014.03.014] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Revised: 03/06/2014] [Accepted: 03/07/2014] [Indexed: 11/29/2022]
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20
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Cloning and expression of β-1, 4-endoglucanase gene from Bacillus subtilis isolated from soil long term irrigated with effluents of paper and pulp mill. Microbiol Res 2014; 169:693-8. [PMID: 24636744 DOI: 10.1016/j.micres.2014.02.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Revised: 02/15/2014] [Accepted: 02/16/2014] [Indexed: 11/22/2022]
Abstract
A strain of Bacillus subtilis IARI-SP-1 isolated from soil long term irrigated with effluents of paper and pulp mill showed high β-1, 4-endoglucanase (2.5 IU/ml) but low activity of β-1, 4-exoglucanase (0.8 IU/ml) and β-glucosidase (0.084 IU/ml). The β-1, 4-endoglucanase gene of IARI-SP-1 was amplified using degenerate primers designed based on sequences already available in NCBI GenBank. A full length gene of β-1, 4-endonuclease consisting of 1499 nucleotides was identified through sequence analysis of the amplified product. The ORF encoded for a protein of 500 amino acids with a predicted molecular weight of 55 kDa. The gene was cloned in pET-28a and over expressed in Escherichia coli BL21 (DE3). In comparison to wild strain (B. subtilis), the transformed E. coli exhibited four times increase in cellulase production. Higher enzyme activity was observed in supernatant (8.2 IU/ml) than cell pellet (2.8 IU/ml) suggesting more extracellular production of β-1, 4-endoglucanase. SDS-PAGE and CMC plate assay also confirmed the overproduction by the transformed E. coli. The pH and temperature optima of expressed β-1, 4-endoglucanase enzyme was identical to that of wild strain and was 8 and 50-60 °C, respectively.
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21
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Woo MH, Chang YH, Lee HS, Pak PJ, Kim JS, Chung N. First Thermostable Endo-β-1,4-Glucanase from Newly Isolated Xanthomonas sp. EC102. Protein J 2014; 33:110-7. [DOI: 10.1007/s10930-013-9535-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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22
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Cucurachi M, Busconi M, Marudelli M, Soffritti G, Fogher C. Direct amplification of new cellulase genes from woodland soil purified DNA. Mol Biol Rep 2013; 40:4317-25. [PMID: 23645028 DOI: 10.1007/s11033-013-2519-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Accepted: 04/27/2013] [Indexed: 12/12/2022]
Abstract
Eight genes encoding cellulolytic enzymes were obtained by direct PCR amplification of genomic DNA recovered from woodland soil samples. The direct amplifications were carried out by using primers designed from available online cellulase nucleotide sequences. The isolated genes were all different from each other and homologous to endo-β-1,4-glucanases of Bacillus subtilis. The cellulases were functionally expressed in Escherichia coli and tested on soluble substrate at 37 and 60 °C, showing different cellulolytic activities. Among these, the enzyme renamed CelWS6 exhibited good activity at higher temperatures. Further analysis of CelWS6 showed a high performance in acid environments (between pH 4.0 and 6.0) and at elevated temperatures with its maximum activity at pH 5.0 and 50 °C. At the optimum pH, it was very stable since more than 80 % of its original activity was maintained after an incubation of 120 min at 60 °C. Because the cellulases had different cellulolytic activities, but similar amino acid sequences, it was possible to assess the relationship between sequence and protein function.
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Affiliation(s)
- Marco Cucurachi
- Plantechno s.r.l, via Staffolo 60, 26041, Vicomoscano, Cremona, Italy
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23
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Bhalla A, Bansal N, Kumar S, Bischoff KM, Sani RK. Improved lignocellulose conversion to biofuels with thermophilic bacteria and thermostable enzymes. BIORESOURCE TECHNOLOGY 2013; 128:751-9. [PMID: 23246299 DOI: 10.1016/j.biortech.2012.10.145] [Citation(s) in RCA: 174] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2012] [Revised: 09/20/2012] [Accepted: 10/29/2012] [Indexed: 05/07/2023]
Abstract
Second-generation feedstock, especially nonfood lignocellulosic biomass is a potential source for biofuel production. Cost-intensive physical, chemical, biological pretreatment operations and slow enzymatic hydrolysis make the overall process of lignocellulosic conversion into biofuels less economical than available fossil fuels. Lignocellulose conversions carried out at ≤ 50 °C have several limitations. Therefore, this review focuses on the importance of thermophilic bacteria and thermostable enzymes to overcome the limitations of existing lignocellulosic biomass conversion processes. The influence of high temperatures on various existing lignocellulose conversion processes and those that are under development, including separate hydrolysis and fermentation, simultaneous saccharification and fermentation, and extremophilic consolidated bioprocess are also discussed.
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Affiliation(s)
- Aditya Bhalla
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA
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Zhao K, Guo LZ, Lu WD. Extracellular Production of Novel Halotolerant, Thermostable, and Alkali-Stable Carboxymethyl Cellulase by Marine Bacterium Marinimicrobium sp. LS-A18. Appl Biochem Biotechnol 2012; 168:550-67. [DOI: 10.1007/s12010-012-9796-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2012] [Accepted: 07/03/2012] [Indexed: 01/25/2023]
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Zhao XH, Wang W, Wang FQ, Wei DZ. A comparative study of β-1, 4-endoglucanase (possessing β-1, 4-exoglucanase activity) from Bacillus subtilis LH expressed in Pichia pastoris GS115 and Escherichia coli Rosetta (DE3). BIORESOURCE TECHNOLOGY 2012; 110:539-545. [PMID: 22336741 DOI: 10.1016/j.biortech.2011.12.086] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2011] [Revised: 12/15/2011] [Accepted: 12/17/2011] [Indexed: 05/31/2023]
Abstract
β-1, 4-Endoglucanase (EG) from Bacillus subtilis LH was expressed in Escherichia coli Rosetta (DE3) and Pichia pastoris GS115, respectively. The CMCase activity of EG (EGE) from the cell lysate of DE3 reached 20,010U/ml, and that of EG (EGP) from the supernatant of GS115 was only 2008U/ml. EGE and EGP were bifunctional cellulases excluding β-1, 4-glucosidase (BGL). The CMCases of them, optimally active at 65°C and pH 6.8, exhibited more than 80% residual activity at pH 5-10 and 60% activity at 40-70°C and pH 5-9. EGE (EGP) mixed with BGL had more than 1.5-fold higher CMCase and filter paperase activities compared to EGE (EGP). N-glycosylation protected EGP from immobilized-papain attack and accounted for 30kDa and a higher thermostability, whereas EGE was decomposed into a 33kDa active truncated EG (EGT) and two 18kDa fragments. EGE and EGP performed much better than EGT in denim biostoning.
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Affiliation(s)
- Xi-Hua Zhao
- State Key Lab of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
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26
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Cheng YS, Ko TP, Huang JW, Wu TH, Lin CY, Luo W, Li Q, Ma Y, Huang CH, Wang AHJ, Liu JR, Guo RT. Enhanced activity of Thermotoga maritima cellulase 12A by mutating a unique surface loop. Appl Microbiol Biotechnol 2011; 95:661-9. [PMID: 22170108 DOI: 10.1007/s00253-011-3791-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2011] [Revised: 11/20/2011] [Accepted: 11/23/2011] [Indexed: 11/24/2022]
Abstract
Cellulase 12A from Thermotoga maritima (TmCel12A) is a hyperthermostable β-1,4-endoglucanase. We recently determined the crystal structures of TmCel12A and its complexes with oligosaccharides. Here, by using site-directed mutagenesis, the role played by Arg60 and Tyr61 in a unique surface loop of TmCel12A was investigated. The results are consistent with the previously observed hydrogen bonding and stacking interactions between these two residues and the substrate. Interestingly, the mutant Y61G had the highest activity when compared with the wild-type enzyme and the other mutants. It also shows a wider range of working temperatures than does the wild type, along with retention of the hyperthermostability. The k (cat) and K (m) values of Y61G are both higher than those of the wild type. In conjunction with the crystal structure of Y61G-substrate complex, the kinetic data suggest that the higher endoglucanase activity is probably due to facile dissociation of the cleaved sugar moiety at the reducing end. Additional crystallographic analyses indicate that the insertion and deletion mutations at the Tyr61 site did not affect the overall protein structure, but local perturbations might diminish the substrate-binding strength. It is likely that the catalytic efficiency of TmCel12A is a subtle balance between substrate binding and product release. The activity enhancement by the single mutation of Y61G provides a good example of engineered enzyme for industrial application.
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Affiliation(s)
- Ya-Shan Cheng
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan
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Dissecting structure–function–stability relationships of a thermostable GH5-CBM3 cellulase from Bacillus subtilis 168. Biochem J 2011; 441:95-104. [DOI: 10.1042/bj20110869] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Cellulases participate in a number of biological events, such as plant cell wall remodelling, nematode parasitism and microbial carbon uptake. Their ability to depolymerize crystalline cellulose is of great biotechnological interest for environmentally compatible production of fuels from lignocellulosic biomass. However, industrial use of cellulases is somewhat limited by both their low catalytic efficiency and stability. In the present study, we conducted a detailed functional and structural characterization of the thermostable BsCel5A (Bacillus subtilis cellulase 5A), which consists of a GH5 (glycoside hydrolase 5) catalytic domain fused to a CBM3 (family 3 carbohydrate-binding module). NMR structural analysis revealed that the Bacillus CBM3 represents a new subfamily, which lacks the classical calcium-binding motif, and variations in NMR frequencies in the presence of cellopentaose showed the importance of polar residues in the carbohydrate interaction. Together with the catalytic domain, the CBM3 forms a large planar surface for cellulose recognition, which conducts the substrate in a proper conformation to the active site and increases enzymatic efficiency. Notably, the manganese ion was demonstrated to have a hyper-stabilizing effect on BsCel5A, and by using deletion constructs and X-ray crystallography we determined that this effect maps to a negatively charged motif located at the opposite face of the catalytic site.
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Yeoman CJ, Han Y, Dodd D, Schroeder CM, Mackie RI, Cann IKO. Thermostable enzymes as biocatalysts in the biofuel industry. ADVANCES IN APPLIED MICROBIOLOGY 2010; 70:1-55. [PMID: 20359453 DOI: 10.1016/s0065-2164(10)70001-0] [Citation(s) in RCA: 173] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Lignocellulose is the most abundant carbohydrate source in nature and represents an ideal renewable energy source. Thermostable enzymes that hydrolyze lignocellulose to its component sugars have significant advantages for improving the conversion rate of biomass over their mesophilic counterparts. We review here the recent literature on the development and use of thermostable enzymes for the depolymerization of lignocellulosic feedstocks for biofuel production. Furthermore, we discuss the protein structure, mechanisms of thermostability, and specific strategies that can be used to improve the thermal stability of lignocellulosic biocatalysts.
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Affiliation(s)
- Carl J Yeoman
- Institute for Genomic Biology, University of Illinois, Urbana, Illinois, USA
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