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Zhang Y, Cao X, Liu Q, Chen Y, Wang Y, Cong H, Li C, Li Y, Wang Y, Jiang J, Li L. Multi-omics analysis of Streptomyces djakartensis strain MEPS155 reveal a molecular response strategy combating Ceratocystis fimbriata causing sweet potato black rot. Food Microbiol 2024; 122:104557. [PMID: 38839221 DOI: 10.1016/j.fm.2024.104557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 04/19/2024] [Accepted: 04/28/2024] [Indexed: 06/07/2024]
Abstract
To investigate the potential antifungal mechanisms of rhizosphere Actinobacteria against Ceratocystis fimbriata in sweet potato, a comprehensive approach combining biochemical analyses and multi-omics techniques was employed in this study. A total of 163 bacterial strains were isolated from the rhizosphere soil of sweet potato. Among them, strain MEPS155, identified as Streptomyces djakartensis, exhibited robust and consistent inhibition of C. fimbriata mycelial growth in in vitro dual culture assays, attributed to both cell-free supernatant and volatile organic compounds. Moreover, strain MEPS155 demonstrated diverse plant growth-promoting attributes, including the production of indole-3-acetic acid, 1-aminocyclopropane-1-carboxylate deaminase, phosphorus solubilization, nitrogen fixation, and enzymatic activities such as cellulase, chitinase, and protease. Notably, strain MEPS155 exhibited efficacy against various sweet potato pathogenic fungi. Following the inoculation of strain MEPS155, a significant reduction (P < 0.05) in malondialdehyde content was observed in sweet potato slices, indicating a potential protective effect. The whole genome of MEPS155 was characterized by a size of 8,030,375 bp, encompassing 7234 coding DNA sequences and 32 secondary metabolite biosynthetic gene clusters. Transcriptomic analysis revealed 1869 differentially expressed genes in the treated group that cultured with C. fimbriata, notably influencing pathways associated with porphyrin metabolism, fatty acid biosynthesis, and biosynthesis of type II polyketide products. These alterations in gene expression are hypothesized to be linked to the production of secondary metabolites contributing to the inhibition of C. fimbriata. Metabolomic analysis identified 1469 potential differently accumulated metabolites (PDAMs) when comparing MEPS155 and the control group. The up-regulated PDAMs were predominantly associated with the biosynthesis of various secondary metabolites, including vanillin, myristic acid, and protocatechuic acid, suggesting potential inhibitory effects on plant pathogenic fungi. Our study underscores the ability of strain S. djakartensis MEPS155 to inhibit C. fimbriata growth through the production of secretory enzymes or secondary metabolites. The findings contribute to a theoretical foundation for future investigations into the role of MEPS155 in postharvest black rot prevention in sweet potato.
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Affiliation(s)
- Yongjing Zhang
- The Key Laboratory of Biotechnology for Medicinal and Edible Plant Resources of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu Province, 221116, China
| | - Xiaoying Cao
- The Key Laboratory of Biotechnology for Medicinal and Edible Plant Resources of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu Province, 221116, China
| | - Qiao Liu
- The Key Laboratory of Biotechnology for Medicinal and Edible Plant Resources of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu Province, 221116, China
| | - Yujie Chen
- The Key Laboratory of Biotechnology for Medicinal and Edible Plant Resources of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu Province, 221116, China
| | - Yiming Wang
- The Key Laboratory of Biotechnology for Medicinal and Edible Plant Resources of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu Province, 221116, China
| | - Hao Cong
- The Key Laboratory of Biotechnology for Medicinal and Edible Plant Resources of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu Province, 221116, China
| | - Changgen Li
- The Key Laboratory of Biotechnology for Medicinal and Edible Plant Resources of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu Province, 221116, China
| | - Yanting Li
- The Key Laboratory of Biotechnology for Medicinal and Edible Plant Resources of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu Province, 221116, China
| | - Yixuan Wang
- The Key Laboratory of Biotechnology for Medicinal and Edible Plant Resources of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu Province, 221116, China
| | - Jihong Jiang
- The Key Laboratory of Biotechnology for Medicinal and Edible Plant Resources of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu Province, 221116, China.
| | - Ludan Li
- The Key Laboratory of Biotechnology for Medicinal and Edible Plant Resources of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu Province, 221116, China.
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Vanderstraeten J, da Fonseca MJM, De Groote P, Grimon D, Gerstmans H, Kahn A, Moraïs S, Bayer EA, Briers Y. Combinatorial assembly and optimisation of designer cellulosomes: a galactomannan case study. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:60. [PMID: 35637485 PMCID: PMC9153192 DOI: 10.1186/s13068-022-02158-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 05/14/2022] [Indexed: 11/10/2022]
Abstract
BACKGROUND Designer cellulosomes are self-assembled chimeric enzyme complexes that can be used to improve lignocellulosic biomass degradation. They are composed of a synthetic multimodular backbone protein, termed the scaffoldin, and a range of different chimeric docking enzymes that degrade polysaccharides. Over the years, several functional designer cellulosomes have been constructed. Since many parameters influence the efficiency of these multi-enzyme complexes, there is a need to optimise designer cellulosome architecture by testing combinatorial arrangements of docking enzyme and scaffoldin variants. However, the modular cloning procedures are tedious and cumbersome. RESULTS VersaTile is a combinatorial DNA assembly method, allowing the rapid construction and thus comparison of a range of modular proteins. Here, we present the extension of the VersaTile platform to facilitate the construction of designer cellulosomes. We have constructed a tile repository, composed of dockerins, cohesins, linkers, tags and enzymatically active modules. The developed toolbox allows us to efficiently create and optimise designer cellulosomes at an unprecedented speed. As a proof of concept, a trivalent designer cellulosome able to degrade the specific hemicellulose substrate, galactomannan, was constructed and optimised. The main factors influencing cellulosome efficiency were found to be the selected dockerins and linkers and the docking enzyme ratio on the scaffoldin. The optimised designer cellulosome was able to hydrolyse the galactomannan polysaccharide and release mannose and galactose monomers. CONCLUSION We have eliminated one of the main technical hurdles in the designer cellulosome field and anticipate the VersaTile platform to be a starting point in the development of more elaborate multi-enzyme complexes.
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Affiliation(s)
- Julie Vanderstraeten
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Valentin Vaerwyckweg 1, 9000, Ghent, Belgium
| | - Maria João Maurício da Fonseca
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Valentin Vaerwyckweg 1, 9000, Ghent, Belgium
| | - Philippe De Groote
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Valentin Vaerwyckweg 1, 9000, Ghent, Belgium
| | - Dennis Grimon
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Valentin Vaerwyckweg 1, 9000, Ghent, Belgium
| | - Hans Gerstmans
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Valentin Vaerwyckweg 1, 9000, Ghent, Belgium.,Laboratory for Biomolecular Discovery and Engineering, Department of Biology, VIB-KU Leuven Center for Microbiology, Kasteelpark Arenberg 31, 3001, Louvain, Belgium
| | - Amaranta Kahn
- Department of Biomolecular Sciences, The Weizmann Institute of Science, 7610001, Rehovot, Israel.,Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Avenida General Norton de Matos, s/n, 4450-208, Matosinhos, Portugal
| | - Sarah Moraïs
- Department of Biomolecular Sciences, The Weizmann Institute of Science, 7610001, Rehovot, Israel.,Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, 8499000, Beer-Sheva, Israel
| | - Edward A Bayer
- Department of Biomolecular Sciences, The Weizmann Institute of Science, 7610001, Rehovot, Israel.,Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, 8499000, Beer-Sheva, Israel
| | - Yves Briers
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Valentin Vaerwyckweg 1, 9000, Ghent, Belgium.
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Manno-Oligosaccharide Production from Biomass Hydrolysis by Using Endo-1,4-β-Mannanase (ManNj6-379) from Nonomuraea jabiensis ID06-379. Processes (Basel) 2022. [DOI: 10.3390/pr10020269] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
A novel endo-β-1,4-mannanase gene was cloned from a novel actinomycetes, Nonomuraea jabiensis ID06-379, isolated from soil, overexpressed as an extracellular protein (47.8 kDa) in Streptomyces lividans 1326. This new endo-1,4-β-mannanase gene (manNj6-379) is encoded by 445-amino acids. The ManNj6-379 consists of a 28-residue signal peptide and a carbohydrate-binding module of family 2 belonging to the glycoside hydrolase (GH) family 5, with 59–77% identity to GH5 mannan endo-1,4-β-mannanase. The recombinant ManNj6-379 displayed an optimal pH of 6.5 with pH stability ranging between 5.5 and 7.0 and was stable for 120 min at 50 °C and lower temperatures. The optimal temperature for activity was 70 °C. An enzymatic hydrolysis assay revealed that ManNj6-379 could hydrolyze commercial β-mannan and biomass containing mannan.
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Erkan SB, Ozcan A, Yilmazer C, Gurler HN, Karahalil E, Germec M, Yatmaz E, Kucukcetin A, Turhan I. The effects of mannanase activity on viscosity in different gums. J FOOD PROCESS PRES 2021. [DOI: 10.1111/jfpp.14820] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Selime Benemir Erkan
- Faculty of Engineering Department of Food Engineering Akdeniz University Antalya Turkey
| | - Ali Ozcan
- Faculty of Engineering Department of Food Engineering Akdeniz University Antalya Turkey
| | - Cansu Yilmazer
- Faculty of Engineering Department of Food Engineering Akdeniz University Antalya Turkey
| | - Hilal Nur Gurler
- Faculty of Engineering Department of Food Engineering Akdeniz University Antalya Turkey
| | - Ercan Karahalil
- Faculty of Engineering Department of Food Engineering Akdeniz University Antalya Turkey
| | - Mustafa Germec
- Faculty of Engineering Department of Food Engineering Akdeniz University Antalya Turkey
| | - Ercan Yatmaz
- Faculty of Engineering Department of Food Engineering Akdeniz University Antalya Turkey
- Göynük Culinary Arts Vocational School Akdeniz University Antalya Turkey
| | - Ahmet Kucukcetin
- Faculty of Engineering Department of Food Engineering Akdeniz University Antalya Turkey
| | - Irfan Turhan
- Faculty of Engineering Department of Food Engineering Akdeniz University Antalya Turkey
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Role of extremophiles and their extremozymes in biorefinery process of lignocellulose degradation. Extremophiles 2021; 25:203-219. [PMID: 33768388 DOI: 10.1007/s00792-021-01225-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 03/10/2021] [Indexed: 12/20/2022]
Abstract
Technological advances in the field of life sciences have led to discovery of organisms that live in harsh environmental conditions referred to as extremophiles. These organisms have adapted themselves to thrive in extreme habitat giving these organisms an advantage over conventional mesophilic organisms in various industrial applications. Extremozymes produced by these extremophiles have high tolerance to inhospitable environmental conditions making them an ideal enzyme system for various industrial processes. A notable application of these extremophiles and extremozymes is their use in the degradation of recalcitrant lignocellulosic biomass and application in biorefineries. For maximum utilization of the trapped carbon source from this obstinate biomass, pretreatment is a necessary step that requires various physiochemical and enzymatic treatments. From search for novel extremophiles and extremozymes to development of various genetic and protein engineering techniques, investigation on extremozymes with enhanced stability and efficiency is been done. Since extremozymes are easily calibrated to work under such conditions, they have become an emerging topic in the research field of biofuel production. The review discusses the various extremozymes that play an important role in lignocellulose degradation along with recent studies on their molecular and genetic evolution for industrial application and production of biofuels and various value-added products.
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6
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Characterization of a thermotolerant and acidophilic mannanase producing Microbacterium sp. CIAB417 for mannooligosachharide production from agro-residues and dye decolorization. Int J Biol Macromol 2020; 163:1154-1161. [PMID: 32673718 DOI: 10.1016/j.ijbiomac.2020.07.114] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 07/10/2020] [Accepted: 07/10/2020] [Indexed: 11/20/2022]
Abstract
Mannanases are ubiquitous enzymes and are being explored for diverse industrial applications. In this study, a novel bacterial strain Microbacterium sp. CIAB417 was identified and characterized for extracellular production of mannanase. Microbacterium sp. CIAB417 was found to produce maximum mannanase after 36 h of incubation at 37 °C. Mannanase produced by the isolate was observed for maximum activity at optimum pH of 6 and optimum temperature of 50 °C. Crude mannanase was found to be capable of producing mannooligosachharides (MOS) by hydrolyzing hemicellulose from locust bean gum and Aloe vera. The produced MOS was characterized and found to be mixture of mannobiose to mannohexose units. Mannanase was also explored for decolorization of dyes. Bromophenol blue and coomassie blue R-250 were observed to be decolorized to the extent of 45.40 and 42.75%, respectively. Hence, the identified bacterial strain producing mannanase could be of great significance for applications in food and textile industry.
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7
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Berini F, Marinelli F, Binda E. Streptomycetes: Attractive Hosts for Recombinant Protein Production. Front Microbiol 2020; 11:1958. [PMID: 32973711 PMCID: PMC7468451 DOI: 10.3389/fmicb.2020.01958] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 07/24/2020] [Indexed: 01/28/2023] Open
Abstract
Enzymes are increasingly applied as biocatalysts for fulfilling industrial needs in a variety of applications and there is a bursting of interest for novel therapeutic proteins. Consequently, developing appropriate expression platforms for efficiently producing such recombinant proteins represents a crucial challenge. It is nowadays widely accepted that an ideal ‘universal microbial host’ for heterologous protein expression does not exist. Indeed, the first-choice microbes, as Escherichia coli or yeasts, possess known intrinsic limitations that inevitably restrict their applications. In this scenario, bacteria belonging to the Streptomyces genus need to be considered with more attention as promising, alternative, and versatile platforms for recombinant protein production. This is due to their peculiar features, first-of-all their natural attitude to secrete proteins in the extracellular milieu. Additionally, streptomycetes are considered robust and scalable industrial strains and a wide range of tools for their genetic manipulation is nowadays available. This mini-review includes an overview of recombinant protein production in streptomycetes, covering nearly 100 cases of heterologous proteins expressed in these Gram-positives from the 1980s to December 2019. We investigated homologous sources, heterologous hosts, and molecular tools (promoters/vectors/signal peptides) used for the expression of these recombinant proteins. We reported on their final cellular localization and yield. Thus, this analysis might represent a useful source of information, showing pros and cons of using streptomycetes as platform for recombinant protein production and paving the way for their more extensive use in future as alternative heterologous hosts.
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Affiliation(s)
- Francesca Berini
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Flavia Marinelli
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Elisa Binda
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
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8
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Xie J, He Z, Wang Z, Wang B, Pan L. Efficient expression of a novel thermophilic fungal β-mannosidase from Lichtheimia ramosa with broad-range pH stability and its synergistic hydrolysis of locust bean gum. J Biosci Bioeng 2019; 128:416-423. [PMID: 31130335 DOI: 10.1016/j.jbiosc.2019.04.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 03/28/2019] [Accepted: 04/10/2019] [Indexed: 10/26/2022]
Abstract
β-Mannosidase (EC 3.2.1.25) is an exoglycosidase specific for the hydrolysis of terminal β-1,4-glycosidic linkage in mannan which can be applied in the food manufacture, animal feed, bioethanol making and coffee extraction industries. A novel β-mannosidase gene (Lrman5A) from Lichtheimia ramosa was synthesized and recombinantly expressed in Pichia pastoris X33. Lrman5A encodes 444 amino acids with a calculated molecular mass of 51.0 kDa which shares the highest identity (73%) with the β-mannosidase from Rhizomucor miehei. Purified recombinant Lrman5A showed the maximal activity at pH 6.0 and 65°C, had broad-range pH stability (retaining >65% activity after incubation at pH 3.0-8.5 at 37°C for 24 h), and was highly thermostable (retaining >80% activity after incubation at 65°C for 10 min). The specific activity, and Km of Lrman5A was 17.5 U/mg and 1.377 mM, respectively. Lrman5A and GH5 β-mannanase displayed significant synergistic effects on the degradation of locust bean gum (LBG) and released more mannose (up to 2.89 folds) by simultaneous or sequential addition. Due to its hydrolytic properties, Lrman5A may have potential applications in the area of bioenergy, feed and food processing.
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Affiliation(s)
- Jianhua Xie
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, People's Republic of China; AsiaPac (Dongguan) Bio-Technology Co., Ltd., Songshan Lake National Hi-tech Industrial Development Zone, No. 3, North Industrial Road, Dongguan City, Guangdong 523808, People's Republic of China
| | - Zhimei He
- AsiaPac (Dongguan) Bio-Technology Co., Ltd., Songshan Lake National Hi-tech Industrial Development Zone, No. 3, North Industrial Road, Dongguan City, Guangdong 523808, People's Republic of China
| | - Zheng Wang
- AsiaPac (Dongguan) Bio-Technology Co., Ltd., Songshan Lake National Hi-tech Industrial Development Zone, No. 3, North Industrial Road, Dongguan City, Guangdong 523808, People's Republic of China
| | - Bin Wang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, People's Republic of China; Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, Guangzhou, Guangdong 510006, People's Republic of China.
| | - Li Pan
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, People's Republic of China; Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, Guangzhou, Guangdong 510006, People's Republic of China
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9
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Cloning, expression, and characterization of novel GH5 endoglucanases from Thermobifida alba AHK119. J Biosci Bioeng 2019; 127:554-562. [DOI: 10.1016/j.jbiosc.2018.10.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 10/13/2018] [Accepted: 10/16/2018] [Indexed: 01/01/2023]
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10
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Aulitto M, Fusco S, Limauro D, Fiorentino G, Bartolucci S, Contursi P. Galactomannan degradation by thermophilic enzymes: a hot topic for biotechnological applications. World J Microbiol Biotechnol 2019; 35:32. [DOI: 10.1007/s11274-019-2591-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 01/10/2019] [Indexed: 01/06/2023]
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11
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Costa DAL, Filho EXF. Microbial β-mannosidases and their industrial applications. Appl Microbiol Biotechnol 2018; 103:535-547. [PMID: 30426153 DOI: 10.1007/s00253-018-9500-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 10/30/2018] [Accepted: 10/31/2018] [Indexed: 12/18/2022]
Abstract
Heteropolymers of mannan are polysaccharide components of the plant cell wall of gymnosperms and some angiosperms, including palm trees (Arecales and Monocot). Degradation of the complex structure of these polysaccharides requires the synergistic action of enzymes that disrupt the internal carbon skeleton of mannan and accessory enzymes that remove side chain substituents. However, complete degradation of these polysaccharides is carried out by an exo-hydrolase termed β-mannosidase. Microbial β-mannosidases belong to families 1, 2, and 5 of glycosyl hydrolases, and catalyze the hydrolysis of non-reducing ends of mannose oligomers. Besides, these enzymes are also involved in transglycosylation reactions. Because of their activity at different temperatures and pH values, these enzymes are used in a variety of industrial applications and the pharmaceutical, food, and biofuel industries.
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12
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Fu Y, Yeom SJ, Kwon KK, Hwang J, Kim H, Woo EJ, Lee DH, Lee SG. Structural and functional analyses of the cellulase transcription regulator CelR. FEBS Lett 2018; 592:2776-2785. [PMID: 30062758 DOI: 10.1002/1873-3468.13206] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 07/05/2018] [Accepted: 07/19/2018] [Indexed: 11/10/2022]
Abstract
CelR is a transcriptional regulator that controls the expression of cellulases catalyzing cellulose hydrolysis. However, the structural mechanism of its regulation has remained unclear. Here, we report the first structure of CelR, in this case with cellobiose bound. CelR consists of a DNA-binding domain (DBD) and a regulatory domain (RD), and homodimerizes with each monomer bound to cellobiose. A hinge region (HR) in CelR connects the DBD with the RD, and Leu59 in the HR acts as a 'leucine lever' that transduces a transcriptional activation signal. Furthermore, an α4 helix mediates the ligand-binding signal for transcriptional activation. Tyr84 and Gln301 can potentially alter the ligand specificity of CelR. This study provides a pivotal step toward understanding transcription of the cellulases.
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Affiliation(s)
- Yaoyao Fu
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea.,The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, Jiangsu Normal University, China
| | - Soo-Jin Yeom
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea
| | - Kil Koang Kwon
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea
| | - Jungwon Hwang
- Infection and Immunity Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea
| | - Haseong Kim
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea.,Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, Korea
| | - Eui-Jeon Woo
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea.,Department of Bio-Analytical Science, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon, Korea
| | - Dae-Hee Lee
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea.,Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, Korea
| | - Seung-Goo Lee
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea.,Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, Korea
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13
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Ladevèze S, Laville E, Despres J, Mosoni P, Potocki-Véronèse G. Mannoside recognition and degradation by bacteria. Biol Rev Camb Philos Soc 2016; 92:1969-1990. [PMID: 27995767 DOI: 10.1111/brv.12316] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 11/01/2016] [Accepted: 11/11/2016] [Indexed: 11/29/2022]
Abstract
Mannosides constitute a vast group of glycans widely distributed in nature. Produced by almost all organisms, these carbohydrates are involved in numerous cellular processes, such as cell structuration, protein maturation and signalling, mediation of protein-protein interactions and cell recognition. The ubiquitous presence of mannosides in the environment means they are a reliable source of carbon and energy for bacteria, which have developed complex strategies to harvest them. This review focuses on the various mannosides that can be found in nature and details their structure. It underlines their involvement in cellular interactions and finally describes the latest discoveries regarding the catalytic machinery and metabolic pathways that bacteria have developed to metabolize them.
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Affiliation(s)
- Simon Ladevèze
- LISBP, Université de Toulouse, CNRS, INRA, INSA, 31077, Toulouse, France
| | - Elisabeth Laville
- LISBP, Université de Toulouse, CNRS, INRA, INSA, 31077, Toulouse, France
| | - Jordane Despres
- INRA, UR454 Microbiologie, F-63122, Saint-Genès Champanelle, France
| | - Pascale Mosoni
- INRA, UR454 Microbiologie, F-63122, Saint-Genès Champanelle, France
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14
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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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Affiliation(s)
- Prakram Singh Chauhan
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, SAS Nagar, Mohali, India and
| | - Naveen Gupta
- Department of Microbiology, Panjab University, Chandigarh, India
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Li YX, Liu Y, Yan QJ, Yang SQ, Jiang ZQ. Characterization of a novel glycoside hydrolase family 5 β-mannosidase from Absidia corymbifera with high transglycosylation activity. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.molcatb.2015.09.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Chen CY, Huang YC, Yang TY, Jian JY, Chen WL, Yang CH. Degradation of konjac glucomannan by Thermobifida fusca thermostable β-mannanase from yeast transformant. Int J Biol Macromol 2015; 82:1-6. [PMID: 26476245 DOI: 10.1016/j.ijbiomac.2015.10.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 10/01/2015] [Accepted: 10/03/2015] [Indexed: 11/19/2022]
Abstract
Native konjac glucomannan was used as the substrate for thermophilic actinomycetes, Thermobifida fusca BCRC19214, to produce β-mannanase. The β-mannanase was purified and five internal amino acid sequences were determined by LC-MS/MS. These sequences had high homology with the β-mannanase from T. fusca YX. The tfm gene which encoded the β-mannanase was cloned, sequenced and heterologous expressed in Yarrowia lipolytica P01 g expression system. Recombinant heterologous expression resulted in extracellular β-mannanase production at levels as high as 3.16 U/ml in the culture broth within 48 h cultivation. The recombinant β-mannanase from Y. lipolytica transformant had superior thermal property. The optimal temperature of the recombinant β-mannanase from Y. lipolytica transformant (pYLSC1-tfm) was 80°C. When native konjac glucomannan was incubated with the recombinant β-mannanase from Y. lipolytica transformant (pYLSC1-tfm) at 50°C, there was a fast decrease of viscosity happen during the initial phase of reaction. This viscosity reduction was accompanied by an increase of reducing sugars. The surface of konjac glucomannan film became smooth. After 24h of treatment, the DPw of native konjac glucomannan decreased from 6,435,139 to 3089.
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Affiliation(s)
- Cheng-Yu Chen
- Department of Cosmetic Science, Providence University, Taichung 43301, Taiwan; Graduate Institute of Biotechnology, National Chung Hsing University, Taichung 40227, Taiwan
| | - Yu-Chun Huang
- Department of Cosmetic Science, Providence University, Taichung 43301, Taiwan
| | - Ting-Ya Yang
- Department of Cosmetic Science, Providence University, Taichung 43301, Taiwan
| | - Jhen-Yi Jian
- Department of Cosmetic Science, Providence University, Taichung 43301, Taiwan
| | - Wei-Lin Chen
- Department of Cosmetic Science, Providence University, Taichung 43301, Taiwan; Department of Applied Chemistry, Providence University, Taichung 43301, Taiwan
| | - Chao-Hsun Yang
- Department of Cosmetic Science, Providence University, Taichung 43301, Taiwan; Department of Applied Chemistry, Providence University, Taichung 43301, Taiwan.
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Shivlata L, Satyanarayana T. Thermophilic and alkaliphilic Actinobacteria: biology and potential applications. Front Microbiol 2015; 6:1014. [PMID: 26441937 PMCID: PMC4585250 DOI: 10.3389/fmicb.2015.01014] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 09/07/2015] [Indexed: 11/13/2022] Open
Abstract
Microbes belonging to the phylum Actinobacteria are prolific sources of antibiotics, clinically useful bioactive compounds and industrially important enzymes. The focus of the current review is on the diversity and potential applications of thermophilic and alkaliphilic actinobacteria, which are highly diverse in their taxonomy and morphology with a variety of adaptations for surviving and thriving in hostile environments. The specific metabolic pathways in these actinobacteria are activated for elaborating pharmaceutically, agriculturally, and biotechnologically relevant biomolecules/bioactive compounds, which find multifarious applications.
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Bai X, Hu H, Chen H, Wei Q, Yang Z, Huang Q. Expression of a β-mannosidase from Paenibacillus polymyxa A-8 in Escherichia coli and characterization of the recombinant enzyme. PLoS One 2014; 9:e111622. [PMID: 25423086 PMCID: PMC4244029 DOI: 10.1371/journal.pone.0111622] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 10/06/2014] [Indexed: 11/19/2022] Open
Abstract
Paenibacillus polymyxa A-8, which secretes β-mannosidase, was isolated from the soil sample under a pine tree located in the "Laoban" mountain region of Sichuan, China. The β-mannosidase gene (MANB) was isolated from P. polymyxa A-8, using primers according to the complete genome. The MANB (2,550 bp) encoding 849 amino acid residues was expressed in Escherichia coli. The specific activities of β-mannosidase produced by P. polymyxa A-8 and E. coli pET30a-MANB were 12 nkat/mg and 635 nkat/mg respectively. SDS-PAGE analysis indicated that the molecular mass of the recombinant MANB was approximately 96 kDa. The recombinant MANB was active between pH 7.0-8.5 with the maximum activity at pH 7.0. It had good pH stability and adaptability. The MANB had the optimal temperature of 35°C and was relatively stable at 35-40°C. In addition, the MANB activity was enhanced by K+, Ca2+, Mn2+, and Mg2+ and inhibited by Zn2+, Cu2+, and Hg2+.
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Affiliation(s)
- Xi Bai
- College of Science, Sichuan Agricultural University, Yaan, Sichuan 625000, P. R. China
| | - Hong Hu
- College of Science, Sichuan Agricultural University, Yaan, Sichuan 625000, P. R. China
- College of Animal Science, Anhui Science and Technology University, Fengyang, Anhui 233100, P. R. China
| | - Huaping Chen
- College of Science, Sichuan Agricultural University, Yaan, Sichuan 625000, P. R. China
| | - Quanbin Wei
- College of Science, Sichuan Agricultural University, Yaan, Sichuan 625000, P. R. China
| | - Zeshen Yang
- Liang Shan Zhong Ze New Technology Development Co., Ltd, Xichang, Sichuan 615000, P. R. China
| | - Qianming Huang
- College of Science, Sichuan Agricultural University, Yaan, Sichuan 625000, P. R. China
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Blumer-Schuette SE, Brown SD, Sander KB, Bayer EA, Kataeva I, Zurawski JV, Conway JM, Adams MWW, Kelly RM. Thermophilic lignocellulose deconstruction. FEMS Microbiol Rev 2014; 38:393-448. [DOI: 10.1111/1574-6976.12044] [Citation(s) in RCA: 128] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Revised: 08/20/2013] [Accepted: 08/28/2013] [Indexed: 11/28/2022] Open
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Shi H, Huang Y, Zhang Y, Li W, Li X, Wang F. High-level expression of a novel thermostable and mannose-tolerant β-mannosidase from Thermotoga thermarum DSM 5069 in Escherichia coli. BMC Biotechnol 2013; 13:83. [PMID: 24099409 PMCID: PMC3852774 DOI: 10.1186/1472-6750-13-83] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Accepted: 10/04/2013] [Indexed: 11/10/2022] Open
Abstract
Background Mannan is one of the primary polysaccharides in hemicellulose and is widely distributed in plants. β-Mannosidase is an important constituent of the mannan-degrading enzyme system and it plays an important role in many industrial applications, such as food, feed and pulp/paper industries as well as the production of second generation bio-fuel. Therefore, the mannose-tolerant β-mannosidase with high catalytic efficiency for bioconversion of mannan has a great potential in the fields as above. Results A β-mannosidase gene (Tth man5) of 1,827 bp was cloned from the extremely thermophilic bacterium Thermotoga thermarum DSM 5069 that encodes a protein containing 608 amino acid residues, and was over-expressed in Escherichia coli BL21 (DE3). The results of phylogenetic analysis, amino acid alignment and biochemical properties indicate that the Tth Man5 is a novel β-mannosidase of glycoside hydrolase family 5. The optimal activity of the Tth Man5 β-mannosidase was obtained at pH 5.5 and 85°C and was stable over a pH range of 5.0 to 8.5 and exhibited 2 h half-life at 90°C. The kinetic parameters Km and Vmax values for p-nitrophenyl-β-D-mannopyranoside and 1,4-β-D-mannan were 4.36±0.5 mM and 227.27±1.59 μmol min-1 mg-1, 58.34±1.75 mg mL-1 and 285.71±10.86 μmol min-1 mg-1, respectively. The kcat/Km values for p-nitrophenyl-β-D-mannopyranoside and 1,4-β-D-mannan were 441.35±0.04 mM-1 s-1 and 41.47±1.58 s-1 mg-1 mL, respectively. It displayed high tolerance to mannose, with a Ki value of approximately 900 mM. Conclusions This work provides a novel and useful β-mannosidase with high mannose tolerance, thermostability and catalytic efficiency, and these characteristics constitute a powerful tool for improving the enzymatic conversion of mannan through synergetic action with other mannan-degrading enzymes.
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Affiliation(s)
- Hao Shi
- College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China.
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Draft Genome Sequence of the Lignocellulose Decomposer Thermobifida fusca Strain TM51. GENOME ANNOUNCEMENTS 2013; 1:1/4/e00482-13. [PMID: 23846276 PMCID: PMC3709153 DOI: 10.1128/genomea.00482-13] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Here, we present the complete genome sequence of Thermobifida fusca strain TM51, which was isolated from the hot upper layer of a compost pile in Hungary. T. fusca TM51 is a thermotolerant, aerobic actinomycete with outstanding lignocellulose-decomposing activity.
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Gomez del Pulgar EM, Saadeddin A. The cellulolytic system ofThermobifida fusca. Crit Rev Microbiol 2013; 40:236-47. [DOI: 10.3109/1040841x.2013.776512] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Fliedrová B, Gerstorferová D, Křen V, Weignerová L. Production of Aspergillus niger β-mannosidase in Pichia pastoris. Protein Expr Purif 2012; 85:159-64. [PMID: 22884703 DOI: 10.1016/j.pep.2012.07.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Revised: 07/23/2012] [Accepted: 07/25/2012] [Indexed: 12/19/2022]
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25
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Fekete CA, Kiss L. Purification and Characterization of a Recombinant β-d-xylosidase from Thermobifida fusca TM51. Protein J 2012; 31:641-50. [DOI: 10.1007/s10930-012-9440-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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26
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Peng F, Peng P, Xu F, Sun RC. Fractional purification and bioconversion of hemicelluloses. Biotechnol Adv 2012; 30:879-903. [PMID: 22306329 DOI: 10.1016/j.biotechadv.2012.01.018] [Citation(s) in RCA: 185] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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27
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Zahura UA, Rahman MM, Inoue A, Ojima T. Characterization of a β-D-mannosidase from a marine gastropod, Aplysia kurodai. Comp Biochem Physiol B Biochem Mol Biol 2012; 162:24-33. [DOI: 10.1016/j.cbpb.2012.02.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2011] [Revised: 02/10/2012] [Accepted: 02/13/2012] [Indexed: 10/28/2022]
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Shi P, Yao G, Cao Y, Yang P, Yuan T, Huang H, Bai Y, Yao B. Cloning and characterization of a new β-mannosidase from Streptomyces sp. S27. Enzyme Microb Technol 2011; 49:277-83. [DOI: 10.1016/j.enzmictec.2011.06.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2010] [Revised: 06/01/2011] [Accepted: 06/04/2011] [Indexed: 10/18/2022]
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29
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Sinsereekul N, Wangkam T, Thamchaipenet A, Srikhirin T, Eurwilaichitr L, Champreda V. Recombinant expression of BTA hydrolase in Streptomyces rimosus and catalytic analysis on polyesters by surface plasmon resonance. Appl Microbiol Biotechnol 2010; 86:1775-84. [PMID: 20174792 DOI: 10.1007/s00253-010-2465-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2009] [Revised: 01/20/2010] [Accepted: 01/21/2010] [Indexed: 11/28/2022]
Abstract
A recombinant polyester-degrading hydrolase from Thermobifida sp. BCC23166 targeting on aliphatic-aromatic copolyester (rTfH) was produced in Streptomyces rimosus R7. rTfH was expressed by induction with thiostrepton as a C-terminal His(6) fusion from the native gene sequence under the control of tipA promoter and purified from the culture supernatant to high homogeneity by a single step affinity purification on Ni-Sepharose matrix. The enzyme worked optimally at 50-55 degrees C and showed esterase activity on C3-C16 p-nitrophenyl alkanoates with a specific activity of 76.5 U/mg on p-nitrophenyl palmitate. Study of rTfH catalysis on surface degradation of polyester films using surface plasmon resonance analysis revealed that the degradation rates were in the order of poly-epsilon-caprolactone > Ecoflex > polyhydroxybutyrate. Efficient hydrolysis of Ecoflex by rTfH was observed in mild alkaline conditions, with the highest activity at pH 8.0 and ionic strength at 250 mM sodium chloride, with the maximal specific activity of 0.79 mg(-1)min(-1)mg(-1) protein. Under the optimal conditions, rTfH showed a remarkable 110-time higher specific activity on Ecoflex in comparison to a lipase from Thermomyces lanuginosus, while less difference in degradation efficiency of the two enzymes was observed on the aliphatic polyesters, suggesting greater specificities of rTfH to the aliphatic-aromatic copolyester. This study demonstrated the use of streptomycetes as an alternative expression system for production of the multi-polyester-degrading enzyme of actinomycete origin and provided insights on its catalytic properties on surface degradation contributing to further biotechnological application of this enzyme.
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Affiliation(s)
- Nitat Sinsereekul
- Department of Genetics, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
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Development and application of a PCR-targeted gene disruption method for studying CelR function in Thermobifida fusca. Appl Environ Microbiol 2010; 76:2098-106. [PMID: 20097808 DOI: 10.1128/aem.02626-09] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Thermobifida fusca is a high-G+C-content, thermophilic, Gram-positive soil actinobacterium with high cellulolytic activity. In T. fusca, CelR is thought to act as the primary regulator of cellulase gene expression by binding to a 14-bp inverted repeat [5'-(T)GGGAGCGCTCCC(A)] that is upstream of many known cellulase genes. Previously, the ability to study the roles and regulation of cellulase genes in T. fusca has been limited largely by a lack of established genetic engineering methods for T. fusca. In this study, we developed an efficient procedure for creating precise chromosomal gene disruptions and demonstrated this procedure by generating a celR deletion strain. The celR deletion strain was then characterized using measurements for growth behavior, cellulase activity, and gene expression. The celR deletion strain of T. fusca exhibited a severely crippled growth phenotype with a prolonged lag phase and decreased cell yields for growth on both glucose and cellobiose. While the maximum endoglucanase activity and cellulase activity were not significantly changed, the endoglucanase activity and cellulase activity per cell were highly elevated. Measurements of mRNA transcript levels in both the celR deletion strain and the wild-type strain indicated that the CelR protein potentially acts as a repressor for some genes and as an activator for other genes. Overall, we established and demonstrated a method for manipulating chromosomal DNA in T. fusca that can be used to study the cellulolytic capabilities of this organism. Components of this method may be useful in developing genetic engineering methods for other currently intractable organisms.
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Production of Ethanol and Feed by High Dry Matter Hydrolysis and Fermentation of Palm Kernel Press Cake. Appl Biochem Biotechnol 2009; 161:318-32. [DOI: 10.1007/s12010-009-8814-6] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2009] [Accepted: 10/06/2009] [Indexed: 11/25/2022]
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32
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Biochemical characterization of a recombinant thermostable β-mannosidase from Thermotoga maritima with transglycosidase activity. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.molcatb.2009.04.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Influence of culture aeration on the cellulase activity of Thermobifida fusca. Appl Microbiol Biotechnol 2009; 85:965-74. [PMID: 19697023 DOI: 10.1007/s00253-009-2155-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2009] [Revised: 07/10/2009] [Accepted: 07/15/2009] [Indexed: 10/20/2022]
Abstract
Currently, one of the hurdles hindering efficient production of cellulosic biofuel is the recalcitrant nature of cellulose to hydrolysis. A wide variety of cellulase enzymes are found natively in microorganisms that can potentially be used to effectively hydrolyze cellulose to fermentable sugars. In this study, phenomenological and mechanistic parameters affecting cellulase activity were studied using the moderately thermophilic, aerobic, and cellulolytic microorganism Thermobifida fusca. Two major sets of experiments were conducted to (1) study the mechanistic differences in growth in a flask compared to a bioreactor and (2) study the cell culture parameters influencing cellulase activity using a series of bioreactor experiments. Specific cellulase and specific endoglucanase activities were found to be higher in the bioreactor as compared to flask growth. Measurements of messenger RNA transcript levels of 18 cellulase-related genes and intracellular ATP levels indicated that measured enzyme activity was likely more influenced by post-transcriptional energetics rather than transcriptional regulation. By delineating the effects of culture aeration and stir speed using a bioreactor, it was found that cellulase activity increased with increasing aeration and increasing stir speeds (highest K(l)a) with a tradeoff of decreased cellular growth at the highest stir speeds tested (400 rpm). Overall, these results allude to a connection between aeration and oxidative respiration that lead to increased ATP allowing for increased cellulase synthesis as the primary constraint on overall cellulase activity.
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Nakasaki K, Tran LTH, Idemoto Y, Abe M, Rollon AP. Comparison of organic matter degradation and microbial community during thermophilic composting of two different types of anaerobic sludge. BIORESOURCE TECHNOLOGY 2009; 100:676-682. [PMID: 18762416 DOI: 10.1016/j.biortech.2008.07.046] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2008] [Revised: 07/23/2008] [Accepted: 07/24/2008] [Indexed: 05/26/2023]
Abstract
Changes in organic matter degradation and microbial communities during thermophilic composting were compared using two different types of anaerobic sludge, one from mesophilic methane fermentation, containing a high concentration of proteins (S-sludge), and the other from thermophilic methane fermentation, containing high concentrations of lipids and fibers (K-sludge). The difference in the organic matter degradation rate corresponded to the difference in the organic matter constituents; the CO(2) evolution rate was greater in the composting of S-sludge than of K-sludge; moreover, the NH(3) evolution resulting from the protein degradation was especially higher in the composting of S-sludge. Then the differences in the microbial communities that contributed to each composting were determined by the PCR-DGGE method. Ureibacillus sp., which is known as a degrader with high organic matter degradation activity, was observed during the composting of S-sludge, whereas Thermobifida fusca, which is a well known thermophilic actinomycete that produces enzymes for lignocellulose degradation, were observed during the composting of K-sludge.
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Affiliation(s)
- Kiyohiko Nakasaki
- Department of Materials Science and Chemical Engineering, Shizuoka University, 3-5-1, Johoku, Naka-ku, Hamamatsu 432-8561, Japan.
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Sasvári Z, Posta K, Hornok L. Expression patterns of cel5A-cel5B, two endoglucanase encoding genes of Thermobifida fusca. Acta Microbiol Immunol Hung 2008; 55:437-46. [PMID: 19130751 DOI: 10.1556/amicr.55.2008.4.8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Expression patterns of cel5A and cel5B, two endoglucanase encoding genes of Thermobifida fusca were compared by quantitative real-time PCR. With Avicel as carbon source the transcript level of cel5A continuously increased until the 10th hour of incubation and then a sharp decrease was observed, whereas cel5B presented a slow constitutive expression on this substrate. When the microcrystalline cellulose powder MN300 was used as the inducing carbon source, the expression patterns of the two genes were similar. A low initial level of expression was followed by a rapid increase at the 5th hour of incubation; a transient repression was then observed at the 10th hour but after this sampling time, the expression levels started to increase again. The relative expression levels of cel5A were always higher than those of cel5B. Differences in transcription patterns of these two genes can be explained with the imperfect structure of the CelR binding regulatory region of cel5B.
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Affiliation(s)
- Zita Sasvári
- Agricultural Biotechnology Center, Mycology Group of the Hungarian Academy of Sciences, Institute of Plant Protection, Szent István University, Páter K. u. 1, H-2103 Gödöllo, Hungary
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Chen S, Wilson DB. Proteomic and transcriptomic analysis of extracellular proteins and mRNA levels in Thermobifida fusca grown on cellobiose and glucose. J Bacteriol 2007; 189:6260-5. [PMID: 17601791 PMCID: PMC1951905 DOI: 10.1128/jb.00584-07] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Thermobifida fusca secretes proteins that carry out plant cell wall degradation. Using two-dimensional electrophoresis, the extracellular proteome of T. fusca grown on cellobiose was compared to that of cells grown on glucose. Extracellular proteins, the expression of which is induced by cellobiose, mainly are cellulases and cellulose-binding proteins. Other major extracellular proteins induced by cellobiose include a xylanase (Xyl10A) and two unknown proteins, the C-terminal regions of which are homologous to a lytic transglycosylase goose egg white lysozyme domain and an NLPC_P60 domain (which defines a family of cell wall peptidases), respectively. Transcriptional analysis of genes encoding cellobiose-induced proteins suggests that their expression is controlled at the transcriptional level and that their expression also is induced by cellulose. Some other major extracellular proteins produced by T. fusca grown on both cellobiose and glucose include Lam81A and three unknown proteins that are homologous to aminopeptidases and xylanases or that contain a putative NLPC_P60 domain.
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Affiliation(s)
- Shaolin Chen
- Department of Molecular Biology and Genetics, 458 Biotechnology Building, Cornell University, Ithaca, NY 14853, USA
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Gomes J, Terler K, Kratzer R, Kainz E, Steiner W. Production of thermostable β-mannosidase by a strain of Thermoascus aurantiacus: Isolation, partial purification and characterization of the enzyme. Enzyme Microb Technol 2007. [DOI: 10.1016/j.enzmictec.2006.08.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Ishimizu T, Sasaki A, Okutani S, Maeda M, Yamagishi M, Hase S. Endo-beta-mannosidase, a plant enzyme acting on N-glycan: purification, molecular cloning, and characterization. J Biol Chem 2004; 279:38555-62. [PMID: 15247239 DOI: 10.1074/jbc.m406886200] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Endo-beta-mannosidase is a novel endoglycosidase that hydrolyzes the Manbeta1-4GlcNAc linkage in the trimannosyl core structure of N-glycans. This enzyme was partially purified and characterized in a previous report (Sasaki, A., Yamagishi, M., Mega, T., Norioka, S., Natsuka, S., and Hase, S. (1999) J. Biochem. 125, 363-367). Here we report the purification and molecular cloning of endo-beta-mannosidase. The enzyme purified from lily flowers gave a single band on native-PAGE and three bands on SDS-PAGE with molecular masses of 42, 31, and 28 kDa. Amino acid sequence information from these three polypeptides allowed the cloning of a homologous gene, AtEBM, from Arabidopsis thaliana. AtEBM was engineered for expression in Escherichia coli, and the recombinant protein comprised a single polypeptide chain with a molecular mass of 112 kDa corresponding to the sum of molecular masses of three polypeptides of the lily enzyme. The recombinant protein hydrolyzed pyridylamino derivatives (PA) of Manalpha1-6Manbeta1-4Glc-NAcbeta1-4GlcNAc into Manalpha1-6Man and GlcNAcbeta1-4Glc-NAc-PA, showing that AtEBM is an endo-beta-mannosidase. AtEBM hydrolyzed Man(n)Manalpha1-6Manbeta1-4GlcNAcbeta1-4GlcNAc-PA (n = 0-2) but not PA-sugar chains containing Manalpha1-3Manbeta or Xylosebeta1-2Manbeta as for the lily endo-beta-mannosidase. AtEBM belonged to the clan GH-A of glycosyl hydrolases. Site-directed mutagenesis experiments revealed that two glutamic acid residues (Glu-464 and Glu-549) conserved in this clan were critical for enzyme activity. The amino acid sequence of AtEBM has distinct differences from those of the bacterial, fungal, and animal exo-type beta-mannosidases. Indeed, AtEBM-like genes are only found in plants, indicating that endo-beta-mannosidase is a plant-specific enzyme. The role of this enzyme in the processing and/or degradation of N-glycan will be discussed.
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Affiliation(s)
- Takeshi Ishimizu
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
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Díaz M, Adham SAI, Ramón D, Gil JA, Santamaría RI. Streptomyces lividans and Brevibacterium lactofermentum as heterologous hosts for the production of X22 xylanase from Aspergillus nidulans. Appl Microbiol Biotechnol 2004; 65:401-6. [PMID: 15168093 DOI: 10.1007/s00253-004-1633-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2004] [Revised: 03/31/2004] [Accepted: 04/04/2004] [Indexed: 11/25/2022]
Abstract
The Aspergillus nidulans gene xlnA coding for the fungal xylanase X22 has been cloned and expressed in two heterologous bacterial hosts: Streptomyces lividans and Brevibacterium lactofermentum. Streptomyces strains yielded 10 units/ml of xylanase when the protein was produced with its own signal peptide, and 19 units/ml when its signal peptide was replaced by the one for xylanase Xys1 from Streptomyces halstedii. B. lactofermentum was also able to produce xylanase X22, affording 6 units/ml upon using either the Aspergillus xlnA signal peptide or Streptomyces xysA. These production values are higher than those previously reported for the heterologous expression of the A. nidulans xlnA gene in Saccharomyces cerevisiae (1 unit/ml). Moreover, the X22 enzyme produced by Streptomyces lividans showed oenological properties, indicating that this Streptomyces recombinant strain is a good candidate for the production of this enzyme at the industrial scale.
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Affiliation(s)
- M Díaz
- Instituto de Microbiología Bioquímica/Departamento de Microbiología y Genética, Consejo Superior de Investigaciones Científicas/Universidad de Salamanca, Edificio Departamental, Campus Miguel de Unamuno, 37007, Salamanca, Spain
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