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Leadbeater DR, Bruce NC. Functional characterisation of a new halotolerant seawater active glycoside hydrolase family 6 cellobiohydrolase from a salt marsh. Sci Rep 2024; 14:3205. [PMID: 38332324 PMCID: PMC10853513 DOI: 10.1038/s41598-024-53886-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 02/06/2024] [Indexed: 02/10/2024] Open
Abstract
Realising a fully circular bioeconomy requires the valorisation of lignocellulosic biomass. Cellulose is the most attractive component of lignocellulose but depolymerisation is inefficient, expensive and resource intensive requiring substantial volumes of potable water. Seawater is an attractive prospective replacement, however seawater tolerant enzymes are required for the development of seawater-based biorefineries. Here, we report a halophilic cellobiohydrolase SMECel6A, identified and isolated from a salt marsh meta-exo-proteome dataset with high sequence divergence to previously characterised cellobiohydrolases. SMECel6A contains a glycoside hydrolase family 6 (GH6) domain and a carbohydrate binding module family 2 (CBM2) domain. Characterisation of recombinant SMECel6A revealed SMECel6A to be active upon crystalline and amorphous cellulose. Mono- and oligosaccharide product profiles revealed cellobiose as the major hydrolysis product confirming SMECel6A as a cellobiohydrolase. We show SMECel6A to be halophilic with optimal activity achieved in 0.5X seawater displaying 80.6 ± 6.93% activity in 1 × seawater. Structural predictions revealed similarity to a characterised halophilic cellobiohydrolase despite sharing only 57% sequence identity. Sequential thermocycling revealed SMECel6A had the ability to partially reversibly denature exclusively in seawater retaining significant activity. Our study confirms that salt marsh ecosystems harbour enzymes with attractive traits with biotechnological potential for implementation in ionic solution based bioprocessing systems.
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Affiliation(s)
- Daniel R Leadbeater
- Centre for Novel Agricultural Products, Department of Biology, University of York, Heslington, York, YO10 5DD, UK.
| | - Neil C Bruce
- Centre for Novel Agricultural Products, Department of Biology, University of York, Heslington, York, YO10 5DD, UK.
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2
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Huang Z, Ni G, Dai L, Zhang W, Feng S, Wang F. Biochemical Characterization of Novel GH6 Endoglucanase from Myxococcus sp. B6-1 and Its Effects on Agricultural Straws Saccharification. Foods 2023; 12:2517. [PMID: 37444255 DOI: 10.3390/foods12132517] [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: 05/25/2023] [Revised: 06/21/2023] [Accepted: 06/25/2023] [Indexed: 07/15/2023] Open
Abstract
Cellulase has been widely used in many industrial fields, such as feed and food industry, because it can hydrolyze cellulose to oligosaccharides with a lower degree of polymerization. Endo-β-1,4-glucanase is a critical speed-limiting cellulase in the saccharification process. In this study, endo-β-1,4-glucanase gene (CelA257) from Myxococcus sp. B6-1 was cloned and expressed in Escherichia coli. CelA257 contained carbohydrate-binding module (CBM) 4-9 and glycosyl hydrolase (GH) family 6 domain that shares 54.7% identity with endoglucanase from Streptomyces halstedii. The recombinant enzyme exhibited optimal activity at pH 6.5 and 50 °C and was stable over a broad pH (6-9.5) range and temperature < 50 °C. CelA257 exhibited broad substrate specificity to barley β-glucan, lichenin, CMC, chitosan, laminarin, avicel, and phosphoric acid swollen cellulose (PASC). CelA257 degraded both cellotetrose (G4) and cellppentaose (G5) to cellobiose (G2) and cellotriose (G3). Adding CelA257 increased the release of reducing sugars in crop straw powers, including wheat straw (0.18 mg/mL), rape straw (0.42 mg/mL), rice straw (0.16 mg/mL), peanut straw (0.16 mg/mL), and corn straw (0.61 mg/mL). This study provides a potential additive in biomass saccharification applications.
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Affiliation(s)
- Zhen Huang
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China
| | - Guorong Ni
- College of Land Resources and Environment, Jiangxi Agriculture University, Nanchang 330045, China
| | - Longhua Dai
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China
| | - Weiqi Zhang
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China
| | - Siting Feng
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China
| | - Fei Wang
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China
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Junghare M, Manavalan T, Fredriksen L, Leiros I, Altermark B, Eijsink VGH, Vaaje-Kolstad G. Biochemical and structural characterisation of a family GH5 cellulase from endosymbiont of shipworm P. megotara. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:61. [PMID: 37016457 PMCID: PMC10071621 DOI: 10.1186/s13068-023-02307-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 03/24/2023] [Indexed: 04/06/2023]
Abstract
BACKGROUND Cellulases play a key role in the enzymatic conversion of plant cell-wall polysaccharides into simple and economically relevant sugars. Thus, the discovery of novel cellulases from exotic biological niches is of great interest as they may present properties that are valuable in the biorefining of lignocellulosic biomass. RESULTS We have characterized a glycoside hydrolase 5 (GH5) domain of a bi-catalytic GH5-GH6 multi-domain enzyme from the unusual gill endosymbiont Teredinibacter waterburyi of the wood-digesting shipworm Psiloteredo megotara. The catalytic GH5 domain, was cloned and recombinantly produced with or without a C-terminal family 10 carbohydrate-binding module (CBM). Both variants showed hydrolytic endo-activity on soluble substrates such as β-glucan, carboxymethylcellulose and konjac glucomannan, respectively. However, low activity was observed towards the crystalline form of cellulose. Interestingly, when co-incubated with a cellulose-active LPMO, a clear synergy was observed that boosted the overall hydrolysis of crystalline cellulose. The crystal structure of the GH5 catalytic domain was solved to 1.0 Å resolution and revealed a substrate binding cleft extension containing a putative + 3 subsite, which is uncommon in this enzyme family. The enzyme was active in a wide range of pH, temperatures and showed high tolerance for NaCl. CONCLUSIONS This study provides significant knowledge in the discovery of new enzymes from shipworm gill endosymbionts and sheds new light on biochemical and structural characterization of cellulolytic cellulase. Study demonstrated a boost in the hydrolytic activity of cellulase on crystalline cellulose when co-incubated with cellulose-active LPMO. These findings will be relevant for the development of future enzyme cocktails that may be useful for the biotechnological conversion of lignocellulose.
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Affiliation(s)
- Madan Junghare
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1432, Ås, Norway.
| | - Tamilvendan Manavalan
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1432, Ås, Norway
| | - Lasse Fredriksen
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1432, Ås, Norway
| | - Ingar Leiros
- The Norwegian Structural Biology Centre, Department of Chemistry, The Arctic University of Norway, 9037, Tromsø, Norway
| | - Bjørn Altermark
- The Norwegian Structural Biology Centre, Department of Chemistry, The Arctic University of Norway, 9037, Tromsø, Norway
| | - Vincent G H Eijsink
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1432, Ås, Norway
| | - Gustav Vaaje-Kolstad
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1432, Ås, Norway.
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Takenaka S, Takada A, Kimura Y, Watanabe M, Kuntiya A. Improvement of the halotolerance of a Bacillus serine protease by protein surface engineering. J Basic Microbiol 2021; 62:174-184. [PMID: 34811778 DOI: 10.1002/jobm.202100335] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 10/24/2021] [Accepted: 11/06/2021] [Indexed: 11/07/2022]
Abstract
A moderately halotolerant serine protease was previously isolated from Bacillus subtilis from salted, fermented food. Eight mutation sites on the protein surface were selected for protein engineering based on sequence and structural comparisons with moderately halotolerant proteases and homologous non-halotolerant proteases. The newly constructed multiple mutants with substituted Asp and Arg residues were compared with the recombinant wild type (rApr) and the previously constructed mAla-8 substituted with Ala to analyze the contribution of protein surface charge to the salt adaptation of the protease. The three mutants showed >1.2-fold greater halotolerance than rApr. In addition, the mutants showed a broader range of pH stability than rApr, retaining >80% of their maximum activity in the pH range 5.0-11. The mutants also retained >75% of their activity after incubation for 1 h at pH 8.0 and 55°C or at pH 11.5 and 25°C. The Asp and Arg residues exchanged by multiple substitution probably played a role in increasing protein surface hydration and solubility in high salt conditions. This study illustrated that increasing a high proportion of the negative or positive charge on the surface of the Bacillus serine protease stably improved the protein's salt adaptation.
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Affiliation(s)
- Shinji Takenaka
- Department of Agrobioscience, Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Airi Takada
- Department of Agrobioscience, Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Yukihiro Kimura
- Department of Agrobioscience, Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Masanori Watanabe
- Department of Food, Life, and Environmental Science, Faculty of Agriculture, Yamagata University, Yamagata, Japan
| | - Ampin Kuntiya
- Bioprocess Research Cluster, School of Agro-Industry, Faculty of Agro-Industry, Chiang Mai University, Chiang Mai, Thailand
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Dadwal A, Sharma S, Satyanarayana T. Recombinant cellobiohydrolase of Myceliophthora thermophila: characterization and applicability in cellulose saccharification. AMB Express 2021; 11:148. [PMID: 34735642 PMCID: PMC8568750 DOI: 10.1186/s13568-021-01311-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 10/29/2021] [Indexed: 12/31/2022] Open
Abstract
A codon optimized cellobiohydrolase (CBH) encoding synthetic gene of 1188 bp from a thermophilic mold Myceliophthora thermophila (MtCel6A) was cloned and heterologously expressed in Escherichia coli for the first time. In silico analysis suggested that MtCel6A is a GH6 CBH and belongs to CBHII family, which is structurally similar to Cel6A of Humicola insolens. The recombinant MtCel6A is expressed as active inclusion bodies, and the molecular mass of the purified enzyme is ~ 45 kDa. The rMtCel6A is active in a wide range of pH (4-12) and temperatures (40-100 °C) with optima at pH 10.0 and 60 °C. It exhibits T1/2 of 6.0 and 1.0 h at 60 and 90 °C, respectively. The rMtCel6A is an extremozyme with organic solvent, salt and alkali tolerance. The Km, Vmax, kcat and kcat/Km values of the enzyme are 3.2 mg mL-1, 222.2 μmol mg-1 min-1, 2492 s-1 and 778.7 s-1 mg-1 mL-1, respectively. The product analysis of rMtCel6A confirmed that it is an exoenzyme that acts from the non-reducing end of cellulose. The addition of rMtCel6A to the commercial cellulase mix (Cellic CTec2) led to 1.9-fold increase in saccharification of the pre-treated sugarcane bagasse. The rMtCel6A is a potential CBH that finds utility in industrial processes such as in bioethanol, paper pulp and textile industries.
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Affiliation(s)
- Anica Dadwal
- Department of Biological Sciences & Engineering, Netaji Subhas Institute of Technology (University of Delhi), Azad Hind Fauj Marg, Sector-3 Dwarka, New Delhi, 110078, India
| | - Shilpa Sharma
- Department of Biological Sciences & Engineering, Netaji Subhas Institute of Technology (University of Delhi), Azad Hind Fauj Marg, Sector-3 Dwarka, New Delhi, 110078, India
- Department of Biological Sciences & Engineering, Netaji Subhas University of Technology, Azad Hind Fauj Marg, Sector-3 Dwarka, New Delhi, 110078, India
| | - Tulasi Satyanarayana
- Department of Biological Sciences & Engineering, Netaji Subhas Institute of Technology (University of Delhi), Azad Hind Fauj Marg, Sector-3 Dwarka, New Delhi, 110078, India.
- Department of Biological Sciences & Engineering, Netaji Subhas University of Technology, Azad Hind Fauj Marg, Sector-3 Dwarka, New Delhi, 110078, India.
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Identification and characterization of a novel endo-β-1,4-glucanase from a soil metagenomic library. Carbohydr Res 2021; 510:108460. [PMID: 34700218 DOI: 10.1016/j.carres.2021.108460] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 10/08/2021] [Accepted: 10/17/2021] [Indexed: 11/23/2022]
Abstract
A cosmid clone cZFYN1413 with CMCase activity was identified from a soil metagenomic library. The sequence analysis of a subclone of cZFYN1413 revealed an endo-β-1,4-glucanase gene ZFYN1413 belonging to glycoside hydrolase family 6 and a transmembrane region in the N-terminal of ZFYN1413. Expression of ZFYN1413 in Escherichia coli BL21 (DE3) resulted in ZFYN1413-87, which was a truncated protein cleaved in transmembrane region of ZFYN1413. ZFYN1413-87 was expressed and its enzyme properties were studied. ZFYN1413-87 possessed strong endo-β-1,4-glucanase activity, and 52% of the activity could be retained after the protein was treated in buffer of pH 3.0 for 2 h. The study provided a special example of endo-β-1,4-glucanase in GH6 family.
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Joshi N, Kaushal G, Singh SP. Biochemical characterization of a novel thermo-halo-tolerant GH5 endoglucanase from a thermal spring metagenome. Biotechnol Bioeng 2021; 118:1531-1544. [PMID: 33410140 DOI: 10.1002/bit.27668] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 01/01/2021] [Accepted: 01/03/2021] [Indexed: 12/31/2022]
Abstract
A novel endoglucanase gene, celM , was cloned from a thermal spring metagenome. The gene was expressed in Escherichia coli, and the protein was extracted and purified. The protein catalyzed the hydrolysis of amorphous cellulose in a wide range of temperatures, 30-95°C, with optimal activity at 80°C. It was able to tolerate high temperature (80°C) with a half-life of 8 h. Its activity was eminent in a wide pH range of 3.0-11.0, with the highest activity at pH 6.0. The enzyme was tested for halostability. Any significant loss was not recorded in the activity of CelM after the exposure to salinity (3 M NaCl) for 30 days. Furthermore, CelM displayed a substantial resistance toward metal ions, denaturant, reducing agent, organic solvent, and non-ionic surfactants. The amorphous cellulose, treated with CelM , was randomly cleaved, generating cello-oligosaccharides of 2-5 degree of polymerization. Furthermore, CelM was demonstrated to catalyze the hydrolysis of cellulose fraction in the delignified biomass samples, for example, sweet sorghum bagasse, rice straw, and corncob, into cello-oligosaccharides. Given that CelM is a thermo-halo-tolerant GH5 endoglucanase, with resistance to detergents and organic solvent, the biocatalyst could be of potential usefulness for a variety of industrial applications.
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Affiliation(s)
- Namrata Joshi
- Center of Innovative and Applied Bioprocessing (DBT-CIAB), Mohali, Punjab, India
| | - Girija Kaushal
- Center of Innovative and Applied Bioprocessing (DBT-CIAB), Mohali, Punjab, India
| | - Sudhir P Singh
- Center of Innovative and Applied Bioprocessing (DBT-CIAB), Mohali, Punjab, India
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A novel high performance in-silico screened metagenome-derived alkali-thermostable endo-β-1,4-glucanase for lignocellulosic biomass hydrolysis in the harsh conditions. BMC Biotechnol 2020; 20:56. [PMID: 33076889 PMCID: PMC7574624 DOI: 10.1186/s12896-020-00647-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 09/21/2020] [Indexed: 01/09/2023] Open
Abstract
Background Lignocellulosic biomass, is a great resource for the production of bio-energy and bio-based material since it is largely abundant, inexpensive and renewable. The requirement of new energy sources has led to a wide search for novel effective enzymes to improve the exploitation of lignocellulose, among which the importance of thermostable and halotolerant cellulase enzymes with high pH performance is significant. Results The primary aim of this study was to discover a novel alkali-thermostable endo-β-1,4-glucanase from the sheep rumen metagenome. At first, the multi-step in-silico screening approach was utilized to find primary candidate enzymes with superior properties. Among the computationally selected candidates, PersiCel4 was found and subjected to cloning, expression, and purification followed by functional and structural characterization. The enzymes’ kinetic parameters, including Vmax, Km, and specific activity, were calculated. The PersiCel4 demonstrated its optimum activity at pH 8.5 and a temperature of 85 °C and was able to retain more than 70% of its activity after 150 h of storage at 85 °C. Furthermore, this enzyme was able to maintain its catalytic activity in the presence of different concentrations of NaCl and several metal ions contains Mg2+, Mn2+, Cu2+, Fe2+ and Ca2+. Our results showed that treatment with MnCl2 could enhance the enzyme’s activity by 78%. PersiCel4 was ultimately used for enzymatic hydrolysis of autoclave pretreated rice straw, the most abundant agricultural waste with rich cellulose content. In autoclave treated rice straw, enzymatic hydrolysis with the PersiCel4 increased the release of reducing sugar up to 260% after 72 h in the harsh condition (T = 85 °C, pH = 8.5). Conclusion Considering the urgent demand for stable cellulases that are operational on extreme temperature and pH conditions and due to several proposed distinctive characteristics of PersiCel4, it can be used in the harsh condition for bioconversion of lignocellulosic biomass.
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Li F, Dong J, Lv X, Wen Y, Chen S. Recombinant expression and characterization of two glycoside hydrolases from extreme alklinphilic bacterium Cellulomonas bogoriensis 69B4 T. AMB Express 2020; 10:44. [PMID: 32157462 PMCID: PMC7064699 DOI: 10.1186/s13568-020-00979-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 02/26/2020] [Indexed: 01/05/2023] Open
Abstract
Two novel glycoside hydrolases were cloned from the genomic DNA of alklinphilic bacterium Cellulomonas bogoriensis 69B4T and functionally expressed in Escherichia coli. The two enzymes shared less than 73% of identities with other known glycosidases and belonged to glycoside hydrolase families 5 and 9. Recombinant Cel5A exhibited optimum activity at pH 5.0 and at a temperature of 70 °C, and Cel9A showed optimum activity at pH 7.0 and at a temperature of 60 °C. The two enzymes exhibited activity at alkaline pH 11 and were stable over a wide range of pH. The maximum activities of Cel5A and Cel9A were observed in 0.5 M NaCl and 1 M KCl, respectively. In addition, these two enzymes exhibited excellent halostability with residual activities of more than 70% after pre-incubation for 6 days in 5 M NaCl or 4 M KCl. Substrate specificity analysis revealed that Cel5A and Cel9A specifically cleaved the β-1,4-glycosidic linkage in cellulose with the highest activity on carboxymethyl cellulose sodium (78.3 and 145.3 U/mg, respectively). Cel5A is an endoglucanase, whereas Cel9A exhibits endo and exo activities. As alkali-activated, thermo-tolerant, and salt-tolerant cellulases, Cel5A and Cel9A are promising candidates for further research and industrial applications.
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Yin YR, Sang P, Xian WD, Li X, Jiao JY, Liu L, Hozzein WN, Xiao M, Li WJ. Expression and Characteristics of Two Glucose-Tolerant GH1 β-glucosidases From Actinomadura amylolytica YIM 77502 T for Promoting Cellulose Degradation. Front Microbiol 2018; 9:3149. [PMID: 30619214 PMCID: PMC6305311 DOI: 10.3389/fmicb.2018.03149] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 12/04/2018] [Indexed: 01/25/2023] Open
Abstract
The bioconversion of lignocellulose in various industrial processes, such as biofuel production, requires the degradation of cellulose. Actinomadura amylolytica YIM 77502T is an aerobic, Gram-positive actinomycete that can efficiently degrade crystalline cellulose by extracellular cellulases. Genomic analysis of A. amylolytica identified 9 cellulase and 11 β-glucosidase genes that could potentially encode proteins that digest cellulose. Extracellular proteome characterization of A. amylolytica cell-free culture supernatant by liquid chromatography tandem mass spectrometry analysis revealed that 4 of these cellulases and 2 of these β-glucosidases functioned during cellulose hydrolysis. Thin-layer chromatography analysis revealed extracellular β-glucosidases play a major role in carboxyl methyl cellulose (CMC) degradation of products in culture supernatants. In this study, 2 of the identified secreted β-glucosidases, AaBGL1 and AaBGL2, were functionally expressed in Escherichia coli and found to have β-glucosidase activity with wide substrate specificities, including for p-nitrophenyl β-D-glucopyranoside (pNPG), p-nitrophenyl-beta-D-cellobioside (pNPC), and cellobiose. Moreover, AaBGL1 and AaBGL2 had high tolerances for glucose. After adding these β-glucosidases to commercial cellulases, the degradation rates of CMC, Avicel, birch sawdust, and corncob powder increased by 37, 42, 33, and 9%, respectively. Overall, this work identifies an alternative potential source of β-glucosidases with potential applications in commercial cellulose utilization and the bioenergy industry.
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Affiliation(s)
- Yi-Rui Yin
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Peng Sang
- College of Agriculture and Biological Science, Dali University, Dali, China
| | - Wen-Dong Xian
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xin Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jian-Yu Jiao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Lan Liu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Wael N Hozzein
- Bioproducts Research Chair, Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia.,Department of Botany and Microbiology, Faculty of Science, Beni-Suef University, Beni-Suef, Egypt
| | - Min Xiao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi, China
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Expression and characterisation of a pH and salt tolerant, thermostable and xylose tolerant recombinant GH43 β-xylosidase from Thermobifida halotolerans YIM 90462 T for promoting hemicellulose degradation. Antonie van Leeuwenhoek 2018; 112:339-350. [PMID: 30225545 DOI: 10.1007/s10482-018-1161-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Accepted: 09/03/2018] [Indexed: 10/28/2022]
Abstract
A gene encoding a β-xylosidase (designated as Thxyl43A) was cloned from strain Thermobifida halotolerans YIM 90462T. The open reading frame of this gene encodes 550 amino acid residues. The gene was over-expressed in Escherichia coli and the recombinant protein was purified. The monomeric Thxyl43A protein presented a molecular mass of 61.5 kDa. When p-nitrophenyl-β-d-xylopyranoside was used as the substrate, recombinant Thxyl43A exhibited optimal activity at 55 °C and pH 4.0 to 7.0, being thermostable by maintaining 47% of its activity after 30 h incubation at 55 °C. The recombinant enzyme retained more than 80% residual activity after incubation at pH range of 4.0 to 12.0 for 24 h, respectively, which indicated notable thermostability and pH stability of Thxyl43A. Moreover, Thxyl43A displayed high catalytic activity (> 60%) in presence of 5-35% NaCl (w/v) or 1-20% ionic liquid (w/v) or 1-50 mM xylose. These properties suggest that Thxyl43A has potential for promoting hemicellulose degradation and other industrial applications.
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Escuder-Rodríguez JJ, DeCastro ME, Cerdán ME, Rodríguez-Belmonte E, Becerra M, González-Siso MI. Cellulases from Thermophiles Found by Metagenomics. Microorganisms 2018; 6:microorganisms6030066. [PMID: 29996513 PMCID: PMC6165527 DOI: 10.3390/microorganisms6030066] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 07/04/2018] [Accepted: 07/05/2018] [Indexed: 01/05/2023] Open
Abstract
Cellulases are a heterogeneous group of enzymes that synergistically catalyze the hydrolysis of cellulose, the major component of plant biomass. Such reaction has biotechnological applications in a broad spectrum of industries, where they can provide a more sustainable model of production. As a prerequisite for their implementation, these enzymes need to be able to operate in the conditions the industrial process requires. Thus, cellulases retrieved from extremophiles, and more specifically those of thermophiles, are likely to be more appropriate for industrial needs in which high temperatures are involved. Metagenomics, the study of genes and gene products from the whole community genomic DNA present in an environmental sample, is a powerful tool for bioprospecting in search of novel enzymes. In this review, we describe the cellulolytic systems, we summarize their biotechnological applications, and we discuss the strategies adopted in the field of metagenomics for the discovery of new cellulases, focusing on those of thermophilic microorganisms.
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Affiliation(s)
- Juan-José Escuder-Rodríguez
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía, Facultade de Ciencias, Universidade da Coruña, 15071 A Corunna, Spain.
| | - María-Eugenia DeCastro
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía, Facultade de Ciencias, Universidade da Coruña, 15071 A Corunna, Spain.
| | - María-Esperanza Cerdán
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía, Facultade de Ciencias, Universidade da Coruña, 15071 A Corunna, Spain.
| | - Esther Rodríguez-Belmonte
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía, Facultade de Ciencias, Universidade da Coruña, 15071 A Corunna, Spain.
| | - Manuel Becerra
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía, Facultade de Ciencias, Universidade da Coruña, 15071 A Corunna, Spain.
| | - María-Isabel González-Siso
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía, Facultade de Ciencias, Universidade da Coruña, 15071 A Corunna, Spain.
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13
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The unique GH5 cellulase member in the extreme halotolerant fungus Aspergillus glaucus CCHA is an endoglucanase with multiple tolerance to salt, alkali and heat: prospects for straw degradation applications. Extremophiles 2018; 22:675-685. [DOI: 10.1007/s00792-018-1028-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Accepted: 04/13/2018] [Indexed: 12/14/2022]
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14
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Takenaka S, Yoshinami J, Kuntiya A, Techapun C, Leksawasdi N, Seesuriyachan P, Chaiyaso T, Watanabe M, Tanaka K, Yoshida KI. Characterization and mutation analysis of a halotolerant serine protease from a new isolate of Bacillus subtilis. Biotechnol Lett 2017; 40:189-196. [PMID: 29038928 DOI: 10.1007/s10529-017-2459-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 10/12/2017] [Indexed: 11/29/2022]
Abstract
OBJECTIVES A bacterial halotolerant enzyme was characterized to understand the molecular mechanism of salt adaptation and to explore its protein engineering potential. RESULTS Halotolerant serine protease (Apr_No16) from a newly isolated Bacillus subtilis strain no. 16 was characterized. Multiple alignments with previously reported non-halotolerant proteases, including subtilisin Carlsberg, indicated that Apr_No16 has eight acidic or polar amino acid residues that are replaced by nonpolar amino acids in non-halotolerant proteases. Those residues were hypothesized to be one of the primary contributors to salt adaptation. An eightfold mutant substituted with Ala residues exhibited 1.2- and 1.8-fold greater halotolerance at 12.5% (w/v) NaCl than Apr_No16 and Carlsberg, respectively. Amino acid substitution notably shifted the theoretical pI of the eightfold mutant, from 6.33 to 9.23, compared with Apr_No16. The resulting protein better tolerated high salt conditions. CONCLUSIONS Changing the pI of a bacterial serine protease may be an effective strategy to improve the enzyme's halotolerance.
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Affiliation(s)
- Shinji Takenaka
- Department of Agrobioscience, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe, 657-8501, Japan.
| | - Jyun Yoshinami
- Department of Agrobioscience, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe, 657-8501, Japan
| | - Ampin Kuntiya
- Bioprocess Research Cluster, The School of Agro-Industry, Faculty of Agro-Industry, Chiang Mai University, Chiang Mai, Thailand
| | - Charin Techapun
- Bioprocess Research Cluster, The School of Agro-Industry, Faculty of Agro-Industry, Chiang Mai University, Chiang Mai, Thailand
| | - Noppol Leksawasdi
- Bioprocess Research Cluster, The School of Agro-Industry, Faculty of Agro-Industry, Chiang Mai University, Chiang Mai, Thailand
| | - Phisit Seesuriyachan
- Bioprocess Research Cluster, The School of Agro-Industry, Faculty of Agro-Industry, Chiang Mai University, Chiang Mai, Thailand
| | - Thanongsak Chaiyaso
- Bioprocess Research Cluster, The School of Agro-Industry, Faculty of Agro-Industry, Chiang Mai University, Chiang Mai, Thailand
| | - Masanori Watanabe
- Department of Food, Life, and Environmental Science, Faculty of Agriculture, Yamagata University, Yamagata, Japan
| | - Kosei Tanaka
- Organization of Advanced Science and Technology, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo, 657-8501, Japan
| | - Ken-Ichi Yoshida
- Department of Agrobioscience, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe, 657-8501, Japan.,Department of Science, Technology and Innovation, Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo, 657-8501, Japan
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15
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Yin YR, Meng ZH, Hu QW, Jiang Z, Xian WD, Li LH, Hu W, Zhang F, Zhou EM, Zhi XY, Li WJ. The Hybrid Strategy of Thermoactinospora rubra YIM 77501 T for Utilizing Cellulose as a Carbon Source at Different Temperatures. Front Microbiol 2017; 8:942. [PMID: 28611745 PMCID: PMC5447088 DOI: 10.3389/fmicb.2017.00942] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 05/10/2017] [Indexed: 01/02/2023] Open
Abstract
Thermoactinospora rubra YIM 77501T is an aerobic, Gram-positive, spore-forming and cellulose degrading thermophilic actinomycete isolated from a sandy soil sample of a volcano. Its growth temperature range is 28–60°C. The genomic sequence of this strain revealed that there are 27 cellulase genes belonging to six glycoside hydrolase families. To understand the strategy that this strain uses to utilize carbon sources such as cellulose at different temperatures, comparative transcriptomics analysis of T. rubra YIM 77501T was performed by growing it with cellulose (CMC) and without cellulose (replaced with glucose) at 30, 40, and 50°C, respectively. Transcriptomic analyses showed four cellulase genes (TrBG2, TrBG3, TrBG4, and ThrCel6B) were up-regulated at 30, 40, and 50°C. The rate of gene expression of TrBG2, TrBG3, TrBG4, and ThrCel6B were 50°C > 30°C > 40°C. One cellulase gene (TrBG1) and two cellulase genes (TrBG5 and ThrCel6A) were up-regulated only at 30 and 50°C, respectively. These up-regulated cellulase genes were cloned and expressed in Escherichia coli. The enzymatic properties of up-regulated cellulases showed a variety of responses to temperature. Special up-regulated cellulases TrBG1 and ThrCel6A displayed temperature acclimation for each growth condition. These expression patterns revealed that a hybrid strategy was used by T. rubra to utilize carbon sources at different temperatures. This study provides genomic, transcriptomics, and experimental data useful for understanding how microorganisms respond to environmental changes and their application in enhancing cellulose hydrolysis for animal feed and bioenergy production.
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Affiliation(s)
- Yi-Rui Yin
- School of Life Sciences, Yunnan Institute of Microbiology, Yunnan UniversityKunming, China
| | - Zhao-Hui Meng
- Department of Cardiology, The First Affiliated Hospital of Kunming Medical UniversityKunming, China
| | - Qing-Wen Hu
- School of Life Sciences, Yunnan Institute of Microbiology, Yunnan UniversityKunming, China
| | - Zhao Jiang
- School of Life Sciences, Yunnan Institute of Microbiology, Yunnan UniversityKunming, China
| | - Wen-Dong Xian
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen UniversityGuangzhou, China
| | - Lin-Hua Li
- Department of Cardiology, The First Affiliated Hospital of Kunming Medical UniversityKunming, China
| | - Wei Hu
- Department of Cardiology, The First Affiliated Hospital of Kunming Medical UniversityKunming, China
| | - Feng Zhang
- Key Laboratory of Biopesticide and Chemical Biology, School of Life Sciences, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - En-Min Zhou
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen UniversityGuangzhou, China
| | - Xiao-Yang Zhi
- School of Life Sciences, Yunnan Institute of Microbiology, Yunnan UniversityKunming, China
| | - Wen-Jun Li
- School of Life Sciences, Yunnan Institute of Microbiology, Yunnan UniversityKunming, China.,State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen UniversityGuangzhou, China.,Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of SciencesÜrümqi, China
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16
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Gao G, Mao RQ, Xiao Y, Zhou J, Liu YH, Li G. Efficient yeast cell-surface display of an endoglucanase of Aspergillus flavus and functional characterization of the whole-cell enzyme. World J Microbiol Biotechnol 2017; 33:114. [PMID: 28488197 DOI: 10.1007/s11274-016-2182-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 11/21/2016] [Indexed: 11/26/2022]
Abstract
The endoglucanase gene endo753 from Aspergillus flavus NRRL3357 strains was cloned, and the recombinant Endo753 was displayed on the cell surface of Saccharomyces cerevisiae EBY100 strain by the C-terminal fusion using Aga2p protein as anchor attachment tag. The results of indirect immunofluorescence and Western blot confirmed the expression and localization of Endo753 on the yeast cell surface. The hydrolytic activity test of the whole-cell enzyme revealed that Endo753 immobilized on the yeast cell surface had high endoglucanase activity. The functional characterization of the whole-cell enzyme was investigated, and the whole-cell enzyme displayed the maximum activity at pH 8 and 50 °C. The enzyme was stable in a pH range of 7.0-10.0. Furthermore, the whole-cell enzyme displayed high thermostability below 50 °C and moderate stability between 50 and 70 °C. These properties make endo753 a good candidate in bioethanol production from lignocellulosic materials after displaying on the yeast cell surface.
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Affiliation(s)
- Gang Gao
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China
| | - Run-Qian Mao
- Guangdong Entomological Institute, Guangzhou, 510260, People's Republic of China.
| | - Yue Xiao
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China
| | - Jing Zhou
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China
| | - Yu-Huan Liu
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China
| | - Gang Li
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China.
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17
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Yin YR, Hu QW, Xian WD, Zhang F, Zhou EM, Ming H, Xiao M, Zhi XY, Li WJ. Characterization of a neutral recombinant xylanase from Thermoactinospora rubra YIM 77501T. Antonie van Leeuwenhoek 2016; 110:429-436. [DOI: 10.1007/s10482-016-0798-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Accepted: 11/01/2016] [Indexed: 10/20/2022]
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18
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Tóth Á, Barna T, Szabó E, Elek R, Hubert Á, Nagy I, Nagy I, Kriszt B, Táncsics A, Kukolya J. Cloning, Expression and Biochemical Characterization of Endomannanases from Thermobifida Species Isolated from Different Niches. PLoS One 2016; 11:e0155769. [PMID: 27223892 PMCID: PMC4880297 DOI: 10.1371/journal.pone.0155769] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 05/03/2016] [Indexed: 11/19/2022] Open
Abstract
Thermobifidas are thermotolerant, compost inhabiting actinomycetes which have complex polysaccharide hydrolyzing enzyme systems. The best characterized enzymes of these hydrolases are cellulases from T. fusca, while other important enzymes especially hemicellulases are not deeply explored. To fill this gap we cloned and investigated endomannanases from those reference strains of the Thermobifida genus, which have published data on other hydrolases (T. fusca TM51, T. alba CECT3323, T. cellulosilytica TB100T and T. halotolerans YIM90462T). Our phylogenetic analyses of 16S rDNA and endomannanase sequences revealed that T. alba CECT3323 is miss-classified; it belongs to the T. fusca species. The cloned and investigated endomannanases belong to the family of glycosyl hydrolases 5 (GH5), their size is around 50 kDa and they are modular enzymes. Their catalytic domains are extended by a C-terminal carbohydrate binding module (CBM) of type 2 with a 23–25 residues long interdomain linker region consisting of Pro, Thr and Glu/Asp rich repetitive tetrapeptide motifs. Their polypeptide chains exhibit high homology, interdomain sequence, which don’t show homology to each other, but all of them are built up from 3–6 times repeated tetrapeptide motifs) (PTDP-Tc, TEEP-Tf, DPGT-Th). All of the heterologously expressed Man5A enzymes exhibited activity only on mannan. The pH optima of Man5A enzymes from T. halotolerans, T. cellulosilytica and T. fusca are slightly different (7.0, 7.5 and 8.0, respectively) while their temperature optima span within the range of 70–75°C. The three endomannanases exhibited very similar kinetic performances on LBG-mannan substrate: 0.9–1.7mM of KM and 80–120 1/sec of turnover number. We detected great variability in heat stability at 70°C, which was influenced by the presence of Ca2+. The investigated endomannanases might be important subjects for studying the structure/function relation behind the heat stability and for industrial applications to hemicellulose degradation.
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Affiliation(s)
- Ákos Tóth
- Department of Applied and Environmental Microbiology, National Agricultural Research and Innovation Centre, Budapest, Hungary
| | - Terézia Barna
- Department of Genetics and Applied Microbiology, University of Debrecen, Hungary
| | - Erna Szabó
- Department of Genetics and Applied Microbiology, University of Debrecen, Hungary
| | - Rita Elek
- Department of Genetics and Applied Microbiology, University of Debrecen, Hungary
| | - Ágnes Hubert
- Department of Molecular Structural Biology, Max Planck Institute for Biochemistry, Martinsried, Germany
| | - István Nagy
- Department of Molecular Structural Biology, Max Planck Institute for Biochemistry, Martinsried, Germany
| | - István Nagy
- Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Balázs Kriszt
- Department of Environmental Protection and Environmental Safety, Szent István University, Gödöllő, Hungary
| | - András Táncsics
- Regional University Center of Excellence in Environmental Industry, Szent István University, Gödöllő, Hungary
| | - József Kukolya
- Department of Applied and Environmental Microbiology, National Agricultural Research and Innovation Centre, Budapest, Hungary
- * E-mail:
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19
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Zhang F, Zhang XM, Yin YR, Li WJ. Cloning, expression and characterization of a novel GH5 exo/endoglucanase of Thermobifida halotolerans YIM 90462(T) by genome mining. J Biosci Bioeng 2015; 120:644-9. [PMID: 26026381 DOI: 10.1016/j.jbiosc.2015.04.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 03/30/2015] [Accepted: 04/19/2015] [Indexed: 10/23/2022]
Abstract
The 1389-bp thcel5A gene, which encodes a family 5 of glycoside hydrolases (GH5), was screened from the draft genome of Thermobifida halotolerans YIM 90462(T). ThCel5A was most similar (77% identity) to a GH5 endoglucanase from Thermobifida fusca YX, followed by cellulases from Nocardiopsis dassonvillei subsp. dassonvillei DSM 43111, Nocardiopsis alba ATCC BAA-2165, and Kribbella flavida DSM 17836. The deduced amino acid sequence of ThCel5A, which consisted of 462 amino acid residues, encompassed a family 2 cellulose-binding module and a GH5 catalytic domain. Notably, ThCel5A hydrolysed soluble as well as insoluble cellulose substrates. The enzymatic hydrolysis assay showed that the activity of recombinant ThCel5A was optimized at pH 8.0 and 50°C. Moreover, it retained hydrolytic activity in the presence of various metal ions and >90% activity within the range of pH 8.0-9.0 after 30 min at 50°C. These results suggested that this enzyme has considerable potential in industrial applications.
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Affiliation(s)
- Feng Zhang
- School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, PR China
| | - Xiao-Mei Zhang
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China
| | - Yi-Rui Yin
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China
| | - Wen-Jun Li
- College of Ecology and Evolution, Sun Yat-Sen University, Guangzhou 510275, PR China; Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China.
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