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Akkaya A, Ensari Y, Ozseker EE, Batur OO, Buyuran G, Evran S. Recombinant Production and Biochemical Characterization of Thermostable Arabinofuranosidase from Acidothermophilic Alicyclobacillus Acidocaldarius. Protein J 2023:10.1007/s10930-023-10117-5. [PMID: 37119380 DOI: 10.1007/s10930-023-10117-5] [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] [Accepted: 04/17/2023] [Indexed: 05/01/2023]
Abstract
The complete enzymatic degradation of lignocellulosic biomass requires the cooperative action of cellulosic, hemicellulosic, and lignolytic enzymes such as cellulase, xylanase, laccase, galactosidase, and arabinofuranosidase. Arabinofuranosidases (E.C 3.2.1.55), which belong to the glycoside hydrolase family of enzymes, hydrolyze the 1,3- and 1,5-α-arabinosyl bonds in L-arabinose- containing molecules. L-arabinoses are present in hemicellulosic part of lignocellulosic biomass. Arabinofuranosidases also play an important role in the complete hydrolysis of arabinoxylans. Analysis of the genome project and CAZY database revealed two putative arabinofuranosidase genes in the A. acidocaldarius genome. The aim of the study was cloning, heterologous expression, purification and biochemical characterization of the arabinofuranosidase enzyme encoded in A. acidocaldarius genome. For this purpose, the AbfA gene of the arabinofuranosidase protein was cloned into the pQE-40 vector, heterologously expressed in E. coli BL21 GOLD (DE3) and successfully purified using His-Tag. Biochemical characterization of the purified enzyme revealed that A. acidocaldarius arabinofuranosidase exhibited activity over a wide pH and temperature range with optimum activity at 45 ºC and pH 6.5 in phosphate buffer towards 4-nitrophenyl-α-L-arabinofuranoside as the substrate. In addition, the enzyme is highly stable over wide range of temperature and maintaining 60% of its activity after 90 min of incubation at 80 ºC. Through the bioinformatics studies, the homology model of A. acidocaldarius arabinofuranosidase was generated and the substrate binding site and residues located in this site were identified. Further molecular docking analysis revealed that the substrate located in the catalytically active pose and, residues N174, E175, and E294 have direct interaction with 4-nitrophenyl-α-L-arabinofuranoside. Moreover, based on phylogenetic analysis, A. acidocaldarius arabinofuranosidase exists in the sub-group of intracellular arabinofuranosidases, and G. stearothermophilus and B.subtilis arabinofuranosidases are close relatives of A. acidocaldarius arabinofuranosidase. This is the first study to report the gene cloning, recombinant expression and biochemical and bioinformatic characterization of an auxiliary GH51 arabinofuranosidase from an acidothermophilic bacterium A. acidocaldarius.
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Affiliation(s)
- Alper Akkaya
- Faculty of Science, Biochemistry Department, Ege University, Bornova, Izmir, 35100, Turkey
| | - Yunus Ensari
- Faculty of Engineering and Architecture, Bioengineering Department, Kafkas University, Kars, 36000, Turkey.
| | - Emine Erdogan Ozseker
- Faculty of Science, Biochemistry Department, Ege University, Bornova, Izmir, 35100, Turkey
| | - Ozge Ozsen Batur
- Faculty of Science, Department of Chemistry, Eskişehir Osmangazi University, Eskişehir, 26480, Turkey
| | - Gozde Buyuran
- Vocational School of Health Services, Kırşehir Ahi Evran University, Kırşehir, 40100, Turkey
| | - Serap Evran
- Faculty of Science, Biochemistry Department, Ege University, Bornova, Izmir, 35100, Turkey
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Botero J, Sombolestani AS, Cnockaert M, Peeters C, Borremans W, De Vuyst L, Vereecken NJ, Michez D, Smagghe G, Bonilla-Rosso G, Engel P, Vandamme P. A phylogenomic and comparative genomic analysis of Commensalibacter, a versatile insect symbiont. Anim Microbiome 2023; 5:25. [PMID: 37120592 PMCID: PMC10149009 DOI: 10.1186/s42523-023-00248-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 04/21/2023] [Indexed: 05/01/2023] Open
Abstract
BACKGROUND To understand mechanisms of adaptation and plasticity of pollinators and other insects a better understanding of diversity and function of their key symbionts is required. Commensalibacter is a genus of acetic acid bacterial symbionts in the gut of honey bees and other insect species, yet little information is available on the diversity and function of Commensalibacter bacteria. In the present study, whole-genome sequences of 12 Commensalibacter isolates from bumble bees, butterflies, Asian hornets and rowan berries were determined, and publicly available genome assemblies of 14 Commensalibacter strains were used in a phylogenomic and comparative genomic analysis. RESULTS The phylogenomic analysis revealed that the 26 Commensalibacter isolates represented four species, i.e. Commensalibacter intestini and three novel species for which we propose the names Commensalibacter melissae sp. nov., Commensalibacter communis sp. nov. and Commensalibacter papalotli sp. nov. Comparative genomic analysis revealed that the four Commensalibacter species had similar genetic pathways for central metabolism characterized by a complete tricarboxylic acid cycle and pentose phosphate pathway, but their genomes differed in size, G + C content, amino acid metabolism and carbohydrate-utilizing enzymes. The reduced genome size, the large number of species-specific gene clusters, and the small number of gene clusters shared between C. melissae and other Commensalibacter species suggested a unique evolutionary process in C. melissae, the Western honey bee symbiont. CONCLUSION The genus Commensalibacter is a widely distributed insect symbiont that consists of multiple species, each contributing in a species specific manner to the physiology of the holobiont host.
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Affiliation(s)
- Juliana Botero
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000, Ghent, Belgium
| | - Atena Sadat Sombolestani
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000, Ghent, Belgium
| | - Margo Cnockaert
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000, Ghent, Belgium
| | - Charlotte Peeters
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000, Ghent, Belgium
| | - Wim Borremans
- Research Group of Industrial Microbiology and Food Biotechnology, Department of Bioengineering Sciences, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Luc De Vuyst
- Research Group of Industrial Microbiology and Food Biotechnology, Department of Bioengineering Sciences, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Nicolas J Vereecken
- Agroecology Lab, Université libre de Bruxelles, Boulevard du Triomphe CP 264/02, 1050, Brussels, Belgium
| | - Denis Michez
- Laboratory of Zoology, Research Institute for Biosciences, University of Mons, Place du parc 20, 7000, Mons, Belgium
| | - Guy Smagghe
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - German Bonilla-Rosso
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Philipp Engel
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000, Ghent, Belgium.
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Valorisation of multiple components from residual biomass for food and biofuel applications: A virtual biorefinery evaluation. FOOD AND BIOPRODUCTS PROCESSING 2023. [DOI: 10.1016/j.fbp.2023.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
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Liu Y, Angelov A, Feiler W, Baudrexl M, Zverlov V, Liebl W, Vanderhaeghen S. Arabinan saccharification by biogas reactor metagenome-derived arabinosyl hydrolases. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:121. [PMID: 36371193 PMCID: PMC9655821 DOI: 10.1186/s13068-022-02216-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 10/19/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Plant cell walls represent the most plentiful renewable organic resource on earth, but due to their heterogeneity, complex structure and partial recalcitrance, their use as biotechnological feedstock is still limited. RESULTS In order to identify efficient enzymes for polysaccharide breakdown, we have carried out functional screening of metagenomic fosmid libraries from biogas fermenter microbial communities grown on sugar beet pulp, an arabinan-rich agricultural residue, or other sources containing microbes that efficiently depolymerize polysaccharides, using CPH (chromogenic polysaccharide hydrogel) or ICB (insoluble chromogenic biomass) labeled polysaccharide substrates. Seventy-one depolymerase-encoding genes were identified from 55 active fosmid clones by using Illumina and Sanger sequencing and dbCAN CAZyme (carbohydrate-active enzyme) annotation. An around 56 kb assembled DNA fragment putatively originating from Xylanivirga thermophila strain or a close relative was analyzed in detail. It contained 48 ORFs (open reading frames), of which 31 were assigned to sugar metabolism. Interestingly, a large number of genes for enzymes putatively involved in degradation and utilization of arabinose-containing carbohydrates were found. Seven putative arabinosyl hydrolases from this DNA fragment belonging to glycoside hydrolase (GH) families GH51 and GH43 were biochemically characterized, revealing two with endo-arabinanase activity and four with exo-α-L-arabinofuranosidase activity but with complementary cleavage properties. These enzymes were found to act synergistically and can completely hydrolyze SBA (sugar beet arabinan) and DA (debranched arabinan). CONCLUSIONS We screened 32,776 fosmid clones from several metagenomic libraries with chromogenic lignocellulosic substrates for functional enzymes to advance the understanding about the saccharification of recalcitrant lignocellulose. Seven putative X. thermophila arabinosyl hydrolases were characterized for pectic substrate degradation. The arabinosyl hydrolases displayed maximum activity and significant long-term stability around 50 °C. The enzyme cocktails composed in this study fully degraded the arabinan substrates and thus could serve for arabinose production in food and biofuel industries.
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Affiliation(s)
- Yajing Liu
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Straβe 4, 85354 Freising-Weihenstephan, Germany
- Present Address: Chair of Chemistry of Biogenic Resources, Technical University of Munich, Schulgasse 16, 94315 Straubing, Germany
| | - Angel Angelov
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Straβe 4, 85354 Freising-Weihenstephan, Germany
- Present Address: NGS Competence Center Tübingen, Universitätsklinikum Tübingen, Calwerstraße 7, 72076 Tübingen, Germany
| | - Werner Feiler
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Straβe 4, 85354 Freising-Weihenstephan, Germany
| | - Melanie Baudrexl
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Straβe 4, 85354 Freising-Weihenstephan, Germany
| | - Vladimir Zverlov
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Straβe 4, 85354 Freising-Weihenstephan, Germany
| | - Wolfgang Liebl
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Straβe 4, 85354 Freising-Weihenstephan, Germany
| | - Sonja Vanderhaeghen
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Straβe 4, 85354 Freising-Weihenstephan, Germany
- Present Address: IMGM Laboratories, Lochhamer Straße 29a, 82152 Planegg, Germany
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Xu H, Zhang L, Feng X, Yang Q, Zheng K, Duan S, Cheng L. Metagenomic and proteomic analysis of bacterial retting community and proteome profile in the degumming process of kenaf bast. BMC PLANT BIOLOGY 2022; 22:516. [PMID: 36333799 PMCID: PMC9636830 DOI: 10.1186/s12870-022-03890-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 10/19/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Data on the microbial community and functional proteins associated with degumming in kenaf remains scant. Here, we analyzed the microbial communities associated with kenaf (Hibiscus cannabinus) bast fibers during retting to identify potential candidate degumming bacteria. Retting liquids were collected and analyzed at 0 days, 10 days, and 34 days and then evaluated the yield and quality of kenaf fiber at the different retting times. Besides, the microbial communities were characterized using metagenomic and proteomic analysis by LC-MS/MS technology. RESULTS The data showed that increase in the retting time significantly improves the softness, dispersion, and fiber whiteness of the kenaf fiber. The relative abundance of Acinetobacter increased from 2.88% at the baseline to 6.64% at the 34th retting. On the other hand, some members of Clostridium were reduced from 3% at the baseline to 2% at the 34th retting. Analysis of carbohydrate active enzymes showed constant changes in the utilization of carbohydrates. Besides, benzoquinone reductase, cellobiose dehydrogenase, glucose 1-oxidase, aryl alcohol oxidase and alcohol oxidase were the top five most abundant enzymes in the retting liquids. This present results demonstrated that the expressions of B7GYR8, Q6RYW5 and Q6FFK2 proteins were suppressed in Acinetobacter with the retting time. On the contrary, P05149 was upregulated with the retting time. In Clostridium, P37698, P52040 and P54937 proteins were upregulated with the retting time. CONCLUSION In addition, bacteria Acinetobacter and Clostridium might be playing important roles in the kenaf degumming process. Similarly, up-regulation of P37698, P52040 and P54937 proteins is an important manifestation and mediates important roles in the degumming process.
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Affiliation(s)
- Huan Xu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Science, 348 West XianJiahu Road, Changsha, China
| | - Lixia Zhang
- Xinyang City Academy of Agricultural Sciences, 20 Minquan South Street, Shihe District, Xinyang, Henan, China
| | - Xiangyuan Feng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Science, 348 West XianJiahu Road, Changsha, China
| | - Qi Yang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Science, 348 West XianJiahu Road, Changsha, China
| | - Ke Zheng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Science, 348 West XianJiahu Road, Changsha, China
| | - Shengwen Duan
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Science, 348 West XianJiahu Road, Changsha, China.
| | - Lifeng Cheng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Science, 348 West XianJiahu Road, Changsha, China.
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Zeng C, Ji X, Shi Y, Mu S, Huang Y, Zhong M, Han Y, Duan C, Li X, Li D. Specific and efficient hydrolysis of all outer glucosyls in protopanaxadiol type and protopanaxatriol type ginsenosides by a β-glucosidase from Thermoclostridium stercorarium. Enzyme Microb Technol 2022; 162:110152. [DOI: 10.1016/j.enzmictec.2022.110152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/11/2022] [Accepted: 10/31/2022] [Indexed: 11/05/2022]
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Optimization, purification, and characterization of xylanase production by a newly isolated Trichoderma harzianum strain by a two-step statistical experimental design strategy. Sci Rep 2022; 12:17791. [PMID: 36273028 PMCID: PMC9588001 DOI: 10.1038/s41598-022-22723-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 10/18/2022] [Indexed: 01/19/2023] Open
Abstract
Xylanases are hydrolytic enzymes with a wide range of applications in several industries such as biofuels, paper and pulp, food, and feed. The objective of this study was to optimize the culture conditions and medium components for maximal xylanase production from a newly isolated Trichoderma harzianum strain using the Plackett-Burman Design (PBD) and Box Behnken Design (BBD) experimental strategies. Xylanase production was enhanced 4.16-fold to 153.80 U/ml by BBD compared to a preliminary one-factor-at-a-time (OFAT) activity of 37.01 U/ml and 2.24-fold compared to the PBD (68.70 U/ml). The optimal conditions for xylanase production were: 6 days of fermentation, incubation temperature of 70 °C, pH 5.0, agitation of 160 rpm, and 1.2% wheat bran and ammonium sulphate. The experimental design effectively provided conditions for the production of an acidic-thermostable enzyme with exciting potential for application in animal feed improvement. The acidic-thermostable xylanase was purified from the submerged culture and SDS-PAGE analysis revealed a molecular weight of 72 kDa. This protein had maximum xylanolytic activity at pH 6.0 and 65 °C and was stable for 4 h retaining > 70% activity and exhibited substrate specificity for beechwood xylan with a Km of 5.56 mg/ml and Vmax of 1052.63 µmol/min/mg. Enzyme activity was enhanced by Fe2+, Mg2+, and Zn2+. There was an absence of strong inhibitors of xylanase activity. Overall, these characteristics indicate the potential for at least two industrial applications.
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Pisa JH, Hero JS, Romero HG, Martínez MA. A genome-proteome-based approach for xylan degradation by Cohnella sp. AR92. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:755-765. [PMID: 35940859 DOI: 10.1111/1758-2229.13113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
Several members of Cohnella genus have been reported as xylanolytic bacteria with significant capacity as carbohydrate-active enzyme producers (CAZymes), whose mechanisms involving xylan degradation are a key goal for suitable applications in bio-based industries. Using Cohnella sp. AR92 bacterium, we ensembled a genomic-proteomic approach to assess plant biomass conversion targeting its xylanolytic set of enzymes. Also, the genomic traits of the strain AR92 were compared to other Cohnella spp., showing a significant variability in terms of genome sizes and content of genes that code CAZymes. The AR92 strain genome harbours 209 CAZymes encoding sequences active on different polysaccharides, particularly directed towards xylans. Concurrent proteomic data recovered from cultures containing three kinds of lignocellulosic-derived substrates showed a broad set of xylan-degrading enzymes. The most abundant CAZymes expressed in the different conditions assayed were endo-β-1,4-xylanases belonging to the GH11 and GH10 families, enzymes that were previously proved to be useful in the biotransformation of lignocellulosic biomass derived from sugarcane as well as onto xylan-enriched substrates. Therefore, considering the large reserve of CAZymes of Cohnella sp. AR92, a xylan processing model for AR92 strain is proposed.
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Affiliation(s)
- José Horacio Pisa
- PROIMI - CONICET (National Scientific and Technical Research Council), Tucumán, Argentina
| | - Johan Sebastian Hero
- PROIMI - CONICET (National Scientific and Technical Research Council), Tucumán, Argentina
| | - Héctor Gabriel Romero
- Department of Ecology and Evolution, Faculty of Sciences/CURE, University of the Republic, Montevideo, Uruguay
| | - María Alejandra Martínez
- PROIMI - CONICET (National Scientific and Technical Research Council), Tucumán, Argentina
- Faculty of Exact Sciences and Technology, National University of Tucuman, Tucumán, Argentina
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Kim IJ, Jeong D, Kim SR. Upstream processes of citrus fruit waste biorefinery for complete valorization. BIORESOURCE TECHNOLOGY 2022; 362:127776. [PMID: 35970501 DOI: 10.1016/j.biortech.2022.127776] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/08/2022] [Accepted: 08/09/2022] [Indexed: 06/15/2023]
Abstract
Citrus fruit waste (CW) is a useful biomass and its valorization into fuels and biochemicals has received much attention. For economic feasibility, increased efficiency of the preceding extraction and enzyme saccharification processes is necessary. However, at present, there is a lack of systematic reviews addressing these two integral upstream processes in concert for CW biorefinery. Here, the state-of-the-art advancements in enzyme extraction and saccharification processes-using which relevant essential oils, flavonoids, and sugars can be obtained-are reviewed. Specifically, the extraction options for two commercially available CW-derived products, essential oils and pectin, are discussed. With respect to enzyme saccharification, the use of an undefined commercial mixture routinely results in suboptimal sugar production. In this respect, applicable strategies for enzyme mixture customization are suggested for maximizing the hydrolytic efficiency of CW. The enzyme degradation system for CW-derived carbohydrates and its extensive application for sugar production are also discussed.
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Affiliation(s)
- In Jung Kim
- Department of Applied Biosciences, Graduate School, Kyungpook National University, Daegu 41566, Korea
| | - Deokyeol Jeong
- School of Food Science and Biotechnology, Kyungpook National University, Daegu 41566, Korea
| | - Soo Rin Kim
- School of Food Science and Biotechnology, Kyungpook National University, Daegu 41566, Korea; Research Institute of Tailored Food Technology, Kyungpook National University, Daegu 41566, Korea.
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Pagar RR, Musale SR, Pawar G, Kulkarni D, Giram PS. Comprehensive Review on the Degradation Chemistry and Toxicity Studies of Functional Materials. ACS Biomater Sci Eng 2022; 8:2161-2195. [PMID: 35522605 DOI: 10.1021/acsbiomaterials.1c01304] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
In recent decades there has been growing interest of material chemists in the successful development of functional materials for drug delivery, tissue engineering, imaging, diagnosis, theranostic, and other biomedical applications with advanced nanotechnology tools. The efficacy and safety of functional materials are determined by their pharmacological, toxicological, and immunogenic effects. It is essential to consider all degradation pathways of functional materials and to assess plausible intermediates and final products for quality control. This review provides a brief insight into chemical degradation mechanisms of functional materials like oxidation, photodegradation, and physical and enzymatic degradation. The intermediates and products of degradation were confirmed with analytical methods such as proton nuclear magnetic resonance (1H NMR), gel permeation chromatography (GPC), UV-vis spectroscopy (UV-vis), infrared spectroscopy (IR), differential scanning calorimetry (DSC), mass spectroscopy, and other sophisticated analytical methods. These analytical methods are also used for regulatory, quality control, and stability purposes in industry. The assessment of degradation is important to predetermine the behavior of functional materials in specific storage conditions and can be relevant to their behavior during in vivo applications. Another important aspect is the evaluation of the toxicity of functional materials. Toxicity can be accessed with various methods using in vitro, in vivo, ex vivo, and in silico models. In vitro cell culture methods are used to determine mitochondrial damage, reactive oxygen species, stress responses, and cellular toxicity. In vitro cellular toxicity can be measured by MTT assay, LDH leakage assay, and hemolysis. In vivo studies are performed using various animal models involving zebrafish, rodents (mice and rats), and nonhuman primates. Ex vivo studies are also used for efficacy and toxicity determinations of functional materials like ex vivo potency assay and precision-cut liver slice (PCLS) models. The in silico tools with computational simulations like quantitative structure-activity relationships (QSAR), pharmacokinetics (PK) and pharmacodynamics (PD), dose and time response, and quantitative cationic-activity relationships ((Q)CARs) are used for prediction of the toxicity of functional materials. In this review, we studied the principle methods used for degradation studies, different degradation pathways, and mechanisms of functional material degradation with prototype examples. We discuss toxicity assessments with different toxicity approaches used for estimation of the safety and efficacy of functional materials.
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Affiliation(s)
- Roshani R Pagar
- Department of Pharmaceutics, Dr. D.Y. Patil Institute of Pharmaceutical Sciences and Research, Pimpri, Pune, Maharashtra 411018, India
| | - Shubham R Musale
- Department of Pharmaceutics, Dr. D.Y. Patil Institute of Pharmaceutical Sciences and Research, Pimpri, Pune, Maharashtra 411018, India
| | - Ganesh Pawar
- Department of Pharmacology, Dr. D.Y. Patil Institute of Pharmaceutical Sciences and Research, Pimpri, Pune, Maharashtra 411018, India
| | - Deepak Kulkarni
- Srinath College of Pharmacy, Bajajnagar, Aurangabad, Maharashtra 431136, India
| | - Prabhanjan S Giram
- Department of Pharmaceutics, Dr. D.Y. Patil Institute of Pharmaceutical Sciences and Research, Pimpri, Pune, Maharashtra 411018, India.,Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
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Jayasekara S, Dissanayake L, Jayakody LN. Opportunities in the microbial valorization of sugar industrial organic waste to biodegradable smart food packaging materials. Int J Food Microbiol 2022; 377:109785. [PMID: 35752069 DOI: 10.1016/j.ijfoodmicro.2022.109785] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 05/12/2022] [Accepted: 06/07/2022] [Indexed: 12/20/2022]
Abstract
Many petroleum-derived plastics, including food packaging materials are non-biodegradable and designed for single-use applications. Annually, around 175 Mt. of plastic enters the land and ocean ecosystems due to mismanagement and lack of techno economically feasible plastic waste recycling technologies. Renewable sourced, biodegradable polymer-based food packaging materials can reduce this environmental pollution. Sugar production from sugarcane or sugar beet generates organic waste streams that contain fermentable substrates, including sugars, acids, and aromatics. Microbial metabolism can be leveraged to funnel those molecules to platform chemicals or biopolymers to generate biodegradable food packaging materials that have active or sensing molecules embedded in biopolymer matrices. The smart package can real-time monitor food quality, assure health safety, and provide economic and environmental benefits. Active packaging materials display functional properties such as antimicrobial, antioxidant, and light or gas barrier. This article provides an overview of potential biodegradable smart/active polymer packages for food applications by valorizing sugar industry-generated organic waste. We highlight the potential microbial pathways and metabolic engineering strategies to biofunnel the waste carbon efficiently into the targeted platform chemicals such as lactic, succinate, muconate, and biopolymers, including polyhydroxyalkanoates, and bacterial cellulose. The obtained platform chemicals can be used to produce biodegradable polymers such as poly (butylene adipate-co-terephthalate) (PBAT) that could replace incumbent polyethylene and polypropylene food packaging materials. When nanomaterials are added, these polymers can be active/smart. The process can remarkably lower the greenhouse gas emission and energy used to produce food-packaging material via sugar industrial waste carbon relative to the petroleum-based production. The proposed green routes enable the valorization of sugar processing organic waste into biodegradable materials and enable the circular economy.
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Affiliation(s)
- Sandhya Jayasekara
- School of Biological Science, Southern Illinois University Carbondale, Carbondale, IL, USA
| | - Lakshika Dissanayake
- School of Biological Science, Southern Illinois University Carbondale, Carbondale, IL, USA
| | - Lahiru N Jayakody
- School of Biological Science, Southern Illinois University Carbondale, Carbondale, IL, USA; Fermentation Science Institute, Southern Illinois University Carbondale, Carbondale, IL, USA.
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Comparative analysis of genome-based CAZyme cassette in Antarctic Microbacterium sp. PAMC28756 with 31 other Microbacterium species. Genes Genomics 2022; 44:733-746. [PMID: 35486322 DOI: 10.1007/s13258-022-01254-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 03/31/2022] [Indexed: 11/04/2022]
Abstract
BACKGROUND The genus Microbacterium belongs to the family Microbacteriaceae and phylum Actinobacteria. A detailed study on the complete genome and systematic comparative analysis of carbohydrate-active enzyme (CAZyme) among the Microbacterium species would add knowledge on metabolic and environmental adaptation. Here we present the comparative genomic analysis of CAZyme using the complete genome of Antarctic Microbacterium sp. PAMC28756 with other complete genomes of 31 Microbacterium species available. OBJECTIVE The genomic and CAZyme comparison of Microbacterium species and to rule out the specific features of CAZyme for the environmental and metabolic adaptation. METHODS Bacterial source were collected from NCBI database, CAZyme annotation of Microbacterium species was analyzed using dbCAN2 Meta server. Cluster of orthologous groups (COGs) analysis was performed using the eggNOG4.5 database. Whereas, KEGG database was used to compare and obtained the functional genome annotation information in carbohydrate metabolism and glyoxylate cycle. RESULTS Out of 32 complete genomes of Microbacterium species, strain No. 7 isolated from Activated Sludge showed the largest genomic size at 4.83 Mb. The genomic size of PAMC28756 isolated from Antarctic lichen species Stereocaulons was 3.54 Mb, the G + C content was 70.4% with 3,407 predicted genes, of which 3.36% were predicted CAZyme. In addition, while comparing the Glyoxylate cycle among 32 bacteria, except 10 strains, all other, including our strain have Glyoxylate pathway. PAMC28756 contained the genes that degrade cellulose, hemicellulose, amylase, pectinase, chitins and other exo-and endo glycosidases. Utilizing these polysaccharides can provides source of energy in an extreme environment. In addition, PAMC28756 assigned the (10.15%) genes in the carbohydrate transport and metabolism functional group closely related to the CAZyme for polysaccharides degradation. CONCLUSIONS The genomic content and CAZymes distribution was varied in Microbacterium species. There was the presence of more than 10% genes in the carbohydrate transport and metabolism functional group closely related to the CAZyme for polysaccharides degradation. In addition, occurrence of glyoxylate cycle for alternative utilization of carbon sources suggest the adaptation of PAMC28756 in the harsh microenvironment.
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Synergy of Cellulase Systems between Acetivibrio thermocellus and Thermoclostridium stercorarium in Consolidated-Bioprocessing for Cellulosic Ethanol. Microorganisms 2022; 10:microorganisms10030502. [PMID: 35336078 PMCID: PMC8951355 DOI: 10.3390/microorganisms10030502] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 02/21/2022] [Accepted: 02/21/2022] [Indexed: 11/18/2022] Open
Abstract
Anaerobes harbor some of the most efficient biological machinery for cellulose degradation, especially thermophilic bacteria, such as Acetivibrio thermocellus and Thermoclostridium stercorarium, which play a fundamental role in transferring lignocellulose into ethanol through consolidated bioprocessing (CBP). In this study, we compared activities of two cellulase systems under varying kinds of hemicellulose and cellulose. A. thermocellus was identified to contribute specifically to cellulose hydrolysis, whereas T. stercorarium contributes to hemicellulose hydrolysis. The two systems were assayed in various combinations to assess their synergistic effects using cellulose and corn stover as the substrates. Their maximum synergy degrees on cellulose and corn stover were, respectively, 1.26 and 1.87 at the ratio of 3:2. Furthermore, co-culture of these anaerobes on the mixture of cellulose and xylan increased ethanol concentration from 21.0 to 40.4 mM with a high cellulose/xylan-to-ethanol conversion rate of up to 20.7%, while the conversion rates of T. stercorarium and A. thermocellus monocultures were 19.3% and 15.2%. The reason is that A. thermocellus had the ability to rapidly degrade cellulose while T. stercorarium co-utilized both pentose and hexose, the metabolites of cellulose degradation, to produce ethanol. The synergistic effect of cellulase systems and metabolic pathways in A. thermocellus and T. stercorarium provides a novel strategy for the design, selection, and optimization of ethanol production from cellulosic biomass through CBP.
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Guo H, He T, Lee DJ. Contemporary proteomic research on lignocellulosic enzymes and enzymolysis: A review. BIORESOURCE TECHNOLOGY 2022; 344:126263. [PMID: 34728359 DOI: 10.1016/j.biortech.2021.126263] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 10/26/2021] [Accepted: 10/27/2021] [Indexed: 06/13/2023]
Abstract
This review overviewed the current researches on the isolation of novel strains, the development of novel identification protocols, the key enzymes and their synergistic interactions with other functional enzyme systems, and the strategies for enhancing enzymolysis efficiencies. The main obstacle for realizing biorefinery of lignocellulosic biomass to biofuels or biochemicals is the high cost of enzymolysis stage. Therefore, research prospects to reduce the costs for lignocellulose hydrolysis were outlined.
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Affiliation(s)
- Hongliang Guo
- College of Forestry, Northeast Forestry University, Harbin 150040, China; College of Food Engineering, Harbin University of Commerce, Harbin 150076, China
| | - Tongyuan He
- College of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Duu-Jong Lee
- Department of Chemical Engineering, National Taiwan University, Taipei 10617, Taiwan; Department of Mechanical Engineering, City University of Hong Kong, Kowloon Tang, Hong Kong.
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15
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Saini S, Sharma KK. Fungal lignocellulolytic enzymes and lignocellulose: A critical review on their contribution to multiproduct biorefinery and global biofuel research. Int J Biol Macromol 2021; 193:2304-2319. [PMID: 34800524 DOI: 10.1016/j.ijbiomac.2021.11.063] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 10/27/2021] [Accepted: 11/10/2021] [Indexed: 01/15/2023]
Abstract
The continuous increase in the global energy demand has diminished fossil fuel reserves and elevated the risk of environmental deterioration and human health. Biorefinery processes involved in producing bio-based energy-enriched chemicals have paved way to meet the energy demands. Compared to the thermochemical processes, fungal system biorefinery processes seems to be a promising approach for lignocellulose conversion. It also offers an eco-friendly and energy-efficient route for biofuel generation. Essentially, ligninolytic white-rot fungi and their enzyme arsenals degrade the plant biomass into structural constituents with minimal by-products generation. Hemi- or cellulolytic enzymes from certain soft and brown-rot fungi are always favoured to hydrolyze complex polysaccharides into fermentable sugars and other value-added products. However, the cost of saccharifying enzymes remains the major limitation, which hinders their application in lignocellulosic biorefinery. In the past, research has been focused on the role of lignocellulolytic fungi in biofuel production; however, a cumulative study comprising the contribution of the lignocellulolytic enzymes in biorefinery technologies is still lagging. Therefore, the overarching goal of this review article is to discuss the major contribution of lignocellulolytic fungi and their enzyme arsenal in global biofuel research and multiproduct biorefinery.
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Affiliation(s)
- Sonu Saini
- Laboratory of Enzymology and Recombinant DNA Technology, Department of Microbiology, Maharshi Dayanand University, Rohtak 124001, Haryana, India
| | - Krishna Kant Sharma
- Laboratory of Enzymology and Recombinant DNA Technology, Department of Microbiology, Maharshi Dayanand University, Rohtak 124001, Haryana, India.
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16
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Liu Y, Vanderhaeghen S, Feiler W, Angelov A, Baudrexl M, Zverlov V, Liebl W. Characterization of Two α-l-Arabinofuranosidases from Acetivibrio mesophilus and Their Synergistic Effect in Degradation of Arabinose-Containing Substrates. Microorganisms 2021; 9:microorganisms9071467. [PMID: 34361903 PMCID: PMC8307384 DOI: 10.3390/microorganisms9071467] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/05/2021] [Accepted: 07/06/2021] [Indexed: 11/16/2022] Open
Abstract
Arabinofuranosidases are important accessory enzymes involved in the degradation of arabinose-containing poly- and oligosaccharides. Two arabinofuranosidases from the recently described novel anaerobic cellulolytic bacterium Acetivibrio mesophilus, designated AmAraf51 and AmAraf43, were heterologously expressed in Escherichia coli and biochemically characterized. AmAraf51 not only removed arabinose moieties at O-3, O-2 and terminal O-5 positions of arabinose-containing oligosaccharides, but also exhibited exo-β-xylosidase side activity. In comparison, AmAraf43 preferably cleaved 1,3-linkages from arabinosyl disubstitutions. AmAraf51 and AmAraf43 demonstrated maximum activity at 70 °C and 57 °C, respectively. Judging from the genetic context and substrate specificity, AmAraf51 may decompose internalized arabino/xylo-oligosaccharides. The embedding of the AmAraf43 gene between genes for several putative xylanolytic enzymes, along with its enzymatic properties suggests that AmAraf43 cleaves arabinose decorations from heteroxylans extracellularly. The enzymes revealed completely converse activity profiles towards arabinan/arabinoxylan: AmAraf51 displayed strong activity on arabinan, while AmAraf43 prefers arabinoxylan. AmAraf51 dramatically stimulated the saccharification level of wheat arabinoxylan (WAX-RS) and sugar beet arabinan when administered along with xylanase M_Xyn10 or arabinanase PpAbn43, respectively. For WAX-RS degradation, the yield of arabinose and xylose was boosted 13.77-fold and 4.96-fold, respectively. The bifunctional activity, thermostability and high catalytic efficiency make AmAraf51 an interesting candidate for industrial applications.
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17
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Xie W, Yu Q, Zhang R, Liu Y, Cao R, Wang S, Zhan R, Liu Z, Wang K, Wang C. Insights into the Catalytic Mechanism of a Novel XynA and Structure-Based Engineering for Improving Bifunctional Activities. Biochemistry 2021; 60:2071-2083. [PMID: 34156819 DOI: 10.1021/acs.biochem.1c00134] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Xylan and cellulose are the two major constituents of numerous types of lignocellulose. The bifunctional enzyme that exhibits xylanase/cellulase activity has attracted a great deal of attention in biofuel production. Previously, a thermostable GH10 family enzyme (XynA) from Bacillus sp. KW1 was found to degrade both xylan and cellulose. To improve bifunctional activity on the basis of structure, we first determined the crystal structure of XynA at 2.3 Å. Via molecular docking and activity assays, we revealed that Gln250 and His252 were indispensable to bifunctionality, because they could interact with two conserved catalytic residues, Glu182 and Glu280, while bringing the substrate close to the activity pocket. Then we used a structure-based engineering strategy to improve xylanase/cellulase activity. Although no mutants with increased bifunctional activity were obtained after much screening, we found the answer in the N-terminal 36-amino acid truncation of XynA. The activities of XynA_ΔN36 toward beechwood xylan, wheat arabinoxylan, filter paper, and barley β-glucan were significantly increased by 0.47-, 0.53-, 2.46-, and 1.04-fold, respectively. Furthermore, upon application, this truncation released more reducing sugars than the wild type in the degradation of pretreated corn stover and sugar cane bagasse. These results showed the detailed molecular mechanism of the GH10 family bifunctional endoxylanase/cellulase. The basis of these catalytic performances and the screened XynA_ΔN36 provide clues for the further use of XynA in industrial applications.
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Affiliation(s)
- Wei Xie
- Guangdong Key Laboratory for Translational Cancer Research of Chinese Medicine, Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510006, China
| | - Qi Yu
- Guangdong Key Laboratory for Translational Cancer Research of Chinese Medicine, Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510006, China
| | - Ruiqing Zhang
- Research Center of Chinese Herbal Resource Science and Engineering, Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education, Joint Laboratory of National Engineering Research Center for the Pharmaceutics of Traditional Chinese Medicines, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510006, China
| | - Yun Liu
- Research Center of Chinese Herbal Resource Science and Engineering, Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education, Joint Laboratory of National Engineering Research Center for the Pharmaceutics of Traditional Chinese Medicines, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510006, China
| | - Ruoting Cao
- Research Center of Chinese Herbal Resource Science and Engineering, Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education, Joint Laboratory of National Engineering Research Center for the Pharmaceutics of Traditional Chinese Medicines, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510006, China
| | - Sidi Wang
- College of Fundamental Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Ruoting Zhan
- Research Center of Chinese Herbal Resource Science and Engineering, Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education, Joint Laboratory of National Engineering Research Center for the Pharmaceutics of Traditional Chinese Medicines, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510006, China
| | - Zhongqiu Liu
- Guangdong Key Laboratory for Translational Cancer Research of Chinese Medicine, Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510006, China
| | - Kui Wang
- Research Center of Chinese Herbal Resource Science and Engineering, Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education, Joint Laboratory of National Engineering Research Center for the Pharmaceutics of Traditional Chinese Medicines, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510006, China
| | - Caiyan Wang
- Guangdong Key Laboratory for Translational Cancer Research of Chinese Medicine, Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510006, China
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18
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Curci N, Strazzulli A, Iacono R, De Lise F, Maurelli L, Di Fenza M, Cobucci-Ponzano B, Moracci M. Xyloglucan Oligosaccharides Hydrolysis by Exo-Acting Glycoside Hydrolases from Hyperthermophilic Microorganism Saccharolobus solfataricus. Int J Mol Sci 2021; 22:3325. [PMID: 33805072 PMCID: PMC8037949 DOI: 10.3390/ijms22073325] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 03/19/2021] [Accepted: 03/22/2021] [Indexed: 12/16/2022] Open
Abstract
In the field of biocatalysis and the development of a bio-based economy, hemicellulases have attracted great interest for various applications in industrial processes. However, the study of the catalytic activity of the lignocellulose-degrading enzymes needs to be improved to achieve the efficient hydrolysis of plant biomasses. In this framework, hemicellulases from hyperthermophilic archaea show interesting features as biocatalysts and provide many advantages in industrial applications thanks to their stability in the harsh conditions encountered during the pretreatment process. However, the hemicellulases from archaea are less studied compared to their bacterial counterpart, and the activity of most of them has been barely tested on natural substrates. Here, we investigated the hydrolysis of xyloglucan oligosaccharides from two different plants by using, both synergistically and individually, three glycoside hydrolases from Saccharolobus solfataricus: a GH1 β-gluco-/β-galactosidase, a α-fucosidase belonging to GH29, and a α-xylosidase from GH31. The results showed that the three enzymes were able to release monosaccharides from xyloglucan oligosaccharides after incubation at 65 °C. The concerted actions of β-gluco-/β-galactosidase and the α-xylosidase on both xyloglucan oligosaccharides have been observed, while the α-fucosidase was capable of releasing all α-linked fucose units from xyloglucan from apple pomace, representing the first GH29 enzyme belonging to subfamily A that is active on xyloglucan.
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Affiliation(s)
- Nicola Curci
- Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, 80126 Naples, Italy; (N.C.); (A.S.); (R.I.); (M.M.)
- Institute of Biosciences and BioResources—National Research Council of Italy, 80131 Naples, Italy; (F.D.L.); (L.M.); (M.D.F.)
| | - Andrea Strazzulli
- Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, 80126 Naples, Italy; (N.C.); (A.S.); (R.I.); (M.M.)
- Task Force on Microbiome Studies, University of Naples Federico II, 80134 Naples, Italy
| | - Roberta Iacono
- Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, 80126 Naples, Italy; (N.C.); (A.S.); (R.I.); (M.M.)
| | - Federica De Lise
- Institute of Biosciences and BioResources—National Research Council of Italy, 80131 Naples, Italy; (F.D.L.); (L.M.); (M.D.F.)
| | - Luisa Maurelli
- Institute of Biosciences and BioResources—National Research Council of Italy, 80131 Naples, Italy; (F.D.L.); (L.M.); (M.D.F.)
| | - Mauro Di Fenza
- Institute of Biosciences and BioResources—National Research Council of Italy, 80131 Naples, Italy; (F.D.L.); (L.M.); (M.D.F.)
| | - Beatrice Cobucci-Ponzano
- Institute of Biosciences and BioResources—National Research Council of Italy, 80131 Naples, Italy; (F.D.L.); (L.M.); (M.D.F.)
| | - Marco Moracci
- Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, 80126 Naples, Italy; (N.C.); (A.S.); (R.I.); (M.M.)
- Task Force on Microbiome Studies, University of Naples Federico II, 80134 Naples, Italy
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19
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Singh N, Mathur AS, Gupta RP, Barrow CJ, Tuli DK, Puri M. Enzyme systems of thermophilic anaerobic bacteria for lignocellulosic biomass conversion. Int J Biol Macromol 2020; 168:572-590. [PMID: 33309672 DOI: 10.1016/j.ijbiomac.2020.12.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 11/30/2020] [Accepted: 12/01/2020] [Indexed: 11/17/2022]
Abstract
Economic production of lignocellulose degrading enzymes for biofuel industries is of considerable interest to the biotechnology community. While these enzymes are widely distributed in fungi, their industrial production from other sources, particularly by thermophilic anaerobic bacteria (growth Topt ≥ 60 °C), is an emerging field. Thermophilic anaerobic bacteria produce a large number of lignocellulolytic enzymes having unique structural features and employ different schemes for biomass degradation, which can be classified into four systems namely; 'free enzyme system', 'cell anchored enzymes', 'complex cellulosome system', and 'multifunctional multimodular enzyme system'. Such enzymes exhibit high specific activity and have a natural ability to withstand harsh bioprocessing conditions. However, achieving a higher production of these thermostable enzymes at current bioprocessing targets is challenging. In this review, the research opportunities for these distinct enzyme systems in the biofuel industry and the associated technological challenges are discussed. The current status of research findings is highlighted along with a detailed description of the categorization of the different enzyme production schemes. It is anticipated that high temperature-based bioprocessing will become an integral part of sustainable bioenergy production in the near future.
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Affiliation(s)
- Nisha Singh
- Centre for Chemistry and Biotechnology, Deakin University, Waurn Ponds, Victoria 3217, Australia; DBT-IOC Centre for Advance Bioenergy Research, Research & Development Centre, Indian Oil Corporation Limited, Sector-13, Faridabad 121007, India
| | - Anshu S Mathur
- DBT-IOC Centre for Advance Bioenergy Research, Research & Development Centre, Indian Oil Corporation Limited, Sector-13, Faridabad 121007, India
| | - Ravi P Gupta
- DBT-IOC Centre for Advance Bioenergy Research, Research & Development Centre, Indian Oil Corporation Limited, Sector-13, Faridabad 121007, India
| | - Colin J Barrow
- Centre for Chemistry and Biotechnology, Deakin University, Waurn Ponds, Victoria 3217, Australia
| | - Deepak K Tuli
- DBT-IOC Centre for Advance Bioenergy Research, Research & Development Centre, Indian Oil Corporation Limited, Sector-13, Faridabad 121007, India
| | - Munish Puri
- Centre for Chemistry and Biotechnology, Deakin University, Waurn Ponds, Victoria 3217, Australia; Medical Biotechnology, Centre for Marine Bioproducts Development, College of Medicine and Public Health, Flinders University, Bedford Park, Adelaide 5042, Australia.
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20
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High-Throughput Generation of Product Profiles for Arabinoxylan-Active Enzymes from Metagenomes. Appl Environ Microbiol 2020; 86:AEM.01505-20. [PMID: 32948521 DOI: 10.1128/aem.01505-20] [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: 06/26/2020] [Accepted: 09/15/2020] [Indexed: 11/20/2022] Open
Abstract
Metagenomics is an exciting alternative to seek carbohydrate-active enzymes from a range of sources. Typically, metagenomics reveals dozens of putative catalysts that require functional characterization for further application in industrial processes. High-throughput screening methods compatible with adequate natural substrates are crucial for an accurate functional elucidation of substrate preferences. Based on DNA sequencer-aided fluorophore-assisted carbohydrate electrophoresis (DSA-FACE) analysis of enzymatic-reaction products, we generated product profiles to consequently infer substrate cleavage positions, resulting in the generation of enzymatic-degradation maps. Product profiles were produced in high throughput for arabinoxylan (AX)-active enzymes belonging to the glycoside hydrolase families GH43 (subfamilies 2 [MG432], 7 [MG437], and 28 [MG4328]) and GH8 (MG8) starting from 12 (arabino)xylo-oligosaccharides. These enzymes were discovered through functional metagenomic studies of feces from the North American beaver (Castor canadensis). This work shows how enzyme loading alters the product profiles of all enzymes studied and gives insight into AX degradation patterns, revealing sequential substrate preferences of AX-active enzymes.IMPORTANCE Arabinoxylan is mainly found in the hemicellulosic fractions of rice straw, corn cobs, and rice husk. Converting arabinoxylan into (arabino)xylo-oligosaccharides as added-value products that can be applied in food, feed, and cosmetics presents a sustainable and economic alternative for the biorefinery industries. Efficient and profitable AX degradation requires a set of enzymes with particular characteristics. Therefore, enzyme discovery and the study of substrate preferences are of utmost importance. Beavers, as consumers of woody biomass, are a promising source of a repertoire of enzymes able to deconstruct hemicelluloses into soluble oligosaccharides. High-throughput analysis of the oligosaccharide profiles produced by these enzymes will assist in the selection of the most appropriate enzymes for the biorefinery.
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Saldarriaga-Hernández S, Velasco-Ayala C, Leal-Isla Flores P, de Jesús Rostro-Alanis M, Parra-Saldivar R, Iqbal HMN, Carrillo-Nieves D. Biotransformation of lignocellulosic biomass into industrially relevant products with the aid of fungi-derived lignocellulolytic enzymes. Int J Biol Macromol 2020; 161:1099-1116. [PMID: 32526298 DOI: 10.1016/j.ijbiomac.2020.06.047] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 06/03/2020] [Accepted: 06/05/2020] [Indexed: 02/08/2023]
Abstract
Lignocellulosic material has drawn significant attention among the scientific community due to its year-round availability as a renewable resource for industrial consumption. Being an economic substrate alternative, various industries are reevaluating processes to incorporate derived compounds from these materials. Varieties of fungi and bacteria have the ability to depolymerize lignocellulosic biomass by synthesizing degrading enzymes. Owing to catalytic activity stability and high yields of conversion, lignocellulolytic enzymes derived from fungi currently have a high spectrum of industrial applications. Moreover, these materials are cost effective, eco-friendly and nontoxic while having a low energy input. Techno-economic analysis for current enzyme production technologies indicates that synthetic production is not commercially viable. Instead, the economic projection of the use of naturally-produced ligninolytic enzymes is promising. This approach may improve the economic feasibility of the process by lowering substrate expenses and increasing lignocellulosic by-product's added value. The present review will discuss the classification and enzymatic degradation pathways of lignocellulolytic biomass as well as the potential and current industrial applications of the involved fungal enzymes.
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Affiliation(s)
- Sara Saldarriaga-Hernández
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Campus Monterrey, Ave. Eugenio Garza Sada 2501, Monterrey, Nuevo Leon 64849, Mexico
| | - Carolina Velasco-Ayala
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Campus Monterrey, Ave. Eugenio Garza Sada 2501, Monterrey, Nuevo Leon 64849, Mexico
| | - Paulina Leal-Isla Flores
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Campus Monterrey, Ave. Eugenio Garza Sada 2501, Monterrey, Nuevo Leon 64849, Mexico
| | - Magdalena de Jesús Rostro-Alanis
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Campus Monterrey, Ave. Eugenio Garza Sada 2501, Monterrey, Nuevo Leon 64849, Mexico
| | - Roberto Parra-Saldivar
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Campus Monterrey, Ave. Eugenio Garza Sada 2501, Monterrey, Nuevo Leon 64849, Mexico
| | - Hafiz M N Iqbal
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Campus Monterrey, Ave. Eugenio Garza Sada 2501, Monterrey, Nuevo Leon 64849, Mexico
| | - Danay Carrillo-Nieves
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Av. General Ramón Corona 2514, Nuevo México, Zapopan C.P. 45138, Jalisco, Mexico.
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Liew KJ, Bruce NC, Sani RK, Chong CS, Yaakop AS, Shamsir MS, Goh KM. Global Transcriptomic Responses of Roseithermus sacchariphilus Strain RA in Media Supplemented with Beechwood Xylan. Microorganisms 2020; 8:E976. [PMID: 32610703 PMCID: PMC7409140 DOI: 10.3390/microorganisms8070976] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/23/2020] [Accepted: 06/27/2020] [Indexed: 11/17/2022] Open
Abstract
The majority of the members in order Rhodothermales are underexplored prokaryotic extremophiles. Roseithermus, a new genus within Rhodothermales, was first described in 2019. Roseithermus sacchariphilus is the only species in this genus. The current report aims to evaluate the transcriptomic responses of R. sacchariphilus strain RA when cultivated on beechwood xylan. Strain RA doubled its growth in Marine Broth (MB) containing xylan compared to Marine Broth (MB) alone. Strain RA harbors 54 potential glycosyl hydrolases (GHs) that are affiliated with 30 families, including cellulases (families GH 3, 5, 9, and 44) and hemicellulases (GH 2, 10, 16, 29, 31,43, 51, 53, 67, 78, 92, 106, 113, 130, and 154). The majority of these GHs were upregulated when the cells were grown in MB containing xylan medium and enzymatic activities for xylanase, endoglucanase, β-xylosidase, and β-glucosidase were elevated. Interestingly, with the introduction of xylan, five out of six cellulolytic genes were upregulated. Furthermore, approximately 1122 genes equivalent to one-third of the total genes for strain RA were upregulated. These upregulated genes were mostly involved in transportation, chemotaxis, and membrane components synthesis.
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Affiliation(s)
- Kok Jun Liew
- Faculty of Science, Universiti Teknologi Malaysia, Johor 81310, Malaysia; (K.J.L.); (C.S.C.); (M.S.S.)
| | - Neil C. Bruce
- Centre for Novel Agricultural Products, Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK;
| | - Rajesh Kumar Sani
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA;
| | - Chun Shiong Chong
- Faculty of Science, Universiti Teknologi Malaysia, Johor 81310, Malaysia; (K.J.L.); (C.S.C.); (M.S.S.)
| | - Amira Suriaty Yaakop
- School of Biological Sciences, Universiti Sains Malaysia, Pulau Pinang 11800, Malaysia;
| | - Mohd Shahir Shamsir
- Faculty of Science, Universiti Teknologi Malaysia, Johor 81310, Malaysia; (K.J.L.); (C.S.C.); (M.S.S.)
- Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia, Pagoh Higher Education Hub, Johor 84600, Malaysia
| | - Kian Mau Goh
- Faculty of Science, Universiti Teknologi Malaysia, Johor 81310, Malaysia; (K.J.L.); (C.S.C.); (M.S.S.)
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Zhang F, You S, Huang T, Wang JZ, Zhu LL, Wang B, Ye WS, Herman RA, Luo H, Wang J. Dual promoter strategy enhances co-expression of α-L-rhamnosidase and enhanced fluorescent protein for whole-cell catalysis and bioresource valorization. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 722:137865. [PMID: 32192973 DOI: 10.1016/j.scitotenv.2020.137865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 02/17/2020] [Accepted: 03/10/2020] [Indexed: 06/10/2023]
Abstract
Developing circular economy is the only way to improve the efficiency of resource utilization. Whole-cell catalysis is an effective method to recycle enzymes, improve catalytic efficiency, and reduce production costs. The enzyme, α-L-rhamnosidase has considerable application prospects in the field of biocatalysis as it can hydrolyze a variety of α-L rhamnoses. In the present study, the genes for α-L-rhamnosidase (rhaB1) and enhanced fluorescent protein (EGFP) were co-expressed using a bi-promoter expression vector pRSFDuet1 and their enzymatic properties were evaluated. To our knowledge, this study has established an effective rhamnosidase-fluorescent indicator and whole-cell catalytic system for the first time. Moreover, we analyzed the change in the activity of the crude rhaB1-EGFP as well as its whole-cell during the biocatalysis process using fluorescence intensity. Recombinant rhaB1-EGFP as a product which contains rhaB1 and EGFP showed higher thermal stability, pH stability, and conversion efficiency than rhaB1, and its optimum temperature for rutin catalysis was ideal for industrial applications. Moreover, under the optimal conditions of a rutin concentration of 0.05 g/L, pH of 6.0, temperature of 40 °C, a yield of 92.5% was obtained. Furthermore, we demonstrated the relationship between the fluorescence intensity and enzyme activity. This study established a highly efficient whole-cell catalytic system whose activity can be evaluated by fluorescence intensity, providing a reference for enzyme recycling.
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Affiliation(s)
- Fan Zhang
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212018, PR China
| | - Shuai You
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212018, PR China; Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang 212018, PR China; Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Zhenjiang 212018, PR China; Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, Zhenjiang 212018, PR China
| | - Ting Huang
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212018, PR China
| | - Jin-Zheng Wang
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212018, PR China
| | - Lin-Lin Zhu
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212018, PR China
| | - Bo Wang
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212018, PR China
| | - Wang-Sheng Ye
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212018, PR China
| | - Richard Ansah Herman
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212018, PR China
| | - Heng Luo
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212018, PR China; Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang 212018, PR China; Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Zhenjiang 212018, PR China; Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, Zhenjiang 212018, PR China
| | - Jun Wang
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212018, PR China; Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang 212018, PR China; Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Zhenjiang 212018, PR China; Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, Zhenjiang 212018, PR China.
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Zhu D, Adebisi WA, Ahmad F, Sethupathy S, Danso B, Sun J. Recent Development of Extremophilic Bacteria and Their Application in Biorefinery. Front Bioeng Biotechnol 2020; 8:483. [PMID: 32596215 PMCID: PMC7303364 DOI: 10.3389/fbioe.2020.00483] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 04/27/2020] [Indexed: 12/22/2022] Open
Abstract
The biorefining technology for biofuels and chemicals from lignocellulosic biomass has made great progress in the world. However, mobilization of laboratory research toward industrial setup needs to meet a series of criteria, including the selection of appropriate pretreatment technology, breakthrough in enzyme screening, pathway optimization, and production technology, etc. Extremophiles play an important role in biorefinery by providing novel metabolic pathways and catalytically stable/robust enzymes that are able to act as biocatalysts under harsh industrial conditions on their own. This review summarizes the potential application of thermophilic, psychrophilic alkaliphilic, acidophilic, and halophilic bacteria and extremozymes in the pretreatment, saccharification, fermentation, and lignin valorization process. Besides, the latest studies on the engineering bacteria of extremophiles using metabolic engineering and synthetic biology technologies for high-efficiency biofuel production are also introduced. Furthermore, this review explores the comprehensive application potential of extremophiles and extremozymes in biorefinery, which is partly due to their specificity and efficiency, and points out the necessity of accelerating the commercialization of extremozymes.
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Affiliation(s)
- Daochen Zhu
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, China
| | - Wasiu Adewale Adebisi
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - Fiaz Ahmad
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - Sivasamy Sethupathy
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - Blessing Danso
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - Jianzhong Sun
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
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25
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Gloster TM. Exploitation of carbohydrate processing enzymes in biocatalysis. Curr Opin Chem Biol 2020; 55:180-188. [PMID: 32203896 DOI: 10.1016/j.cbpa.2020.01.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 01/26/2020] [Accepted: 01/31/2020] [Indexed: 12/14/2022]
Abstract
Exploitation of enzymes in biocatalytic processes provides scope both in the synthesis and degradation of molecules. Enzymes have power not only in their catalytic efficiency, but their chemoselectivity, regioselectivity, and stereoselectivity means the reactions they catalyze are precise and reproducible. Focusing on carbohydrate processing enzymes, this review covers advances in biocatalysis involving carbohydrates over the last 2-3 years. Given the notorious difficulties in the chemical synthesis of carbohydrates, the use of enzymes for synthesis has potential for significant impact in the future. The use of catabolic enzymes in the degradation of biomass, which can be exploited in the production of biofuels to provide a sustainable and greener source of energy, and the synthesis of molecules that have a range of applications including in the pharmaceutical and food industries will be explored.
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Affiliation(s)
- Tracey M Gloster
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, UK.
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26
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Acclimation Improves Methane Production from Molasses Wastewater with High Salinity in an Upflow Anaerobic Filter Reactor: Performance and Microbial Community Dynamics. Appl Biochem Biotechnol 2020; 191:397-411. [DOI: 10.1007/s12010-020-03236-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Accepted: 01/08/2020] [Indexed: 11/26/2022]
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27
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Malgas S, Mafa MS, Mkabayi L, Pletschke BI. A mini review of xylanolytic enzymes with regards to their synergistic interactions during hetero-xylan degradation. World J Microbiol Biotechnol 2019; 35:187. [PMID: 31728656 DOI: 10.1007/s11274-019-2765-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 11/06/2019] [Indexed: 10/25/2022]
Abstract
This review examines the recent models describing the mode of action of various xylanolytic enzymes and how these enzymes can be applied (sequentially or simultaneously) with their distinctive roles in mind to achieve efficient xylan degradation. With respect to homeosynergy, synergism appears to be as a result of β-xylanase and/or oligosaccharide reducing-end β-xylanase liberating xylo-oligomers (XOS) that are preferred substrates of the processive β-xylosidase. With regards to hetero-synergism, two cross relationships appear to exist and seem to be the reason for synergism between the enzymes during xylan degradation. These cross relations are the debranching enzymes such as α-glucuronidase or side-chain cleaving enzymes such as carbohydrate esterases (CE) removing decorations that would have hindered back-bone-cleaving enzymes, while backbone-cleaving-enzymes liberate XOS that are preferred substrates of the debranching and side-chain-cleaving enzymes. This interaction is demonstrated by high yields in co-production of xylan substituents such as arabinose, glucuronic acid and ferulic acid, and XOS. Finally, lytic polysaccharide monooxygenases (LPMO) have also been implicated in boosting whole lignocellulosic biomass or insoluble xylan degradation by glycoside hydrolases (GH) by possibly disrupting entangled xylan residues. Since it has been observed that the same enzyme (same Enzyme Commission, EC, classification) from different GH or CE and/or AA families can display different synergistic interactions with other enzymes due to different substrate specificities and properties, in this review, we propose an approach of enzyme selection (and mode of application thereof) during xylan degradation, as this can improve the economic viability of the degradation of xylan for producing precursors of value added products.
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Affiliation(s)
- Samkelo Malgas
- Enzyme Science Programme (ESP), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, Eastern Cape, 6140, South Africa
| | - Mpho S Mafa
- Enzyme Science Programme (ESP), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, Eastern Cape, 6140, South Africa.,Protein Structure-Function Research Unit (PSFRU), School of Molecular and Cell Biology, Wits University, Johannesburg, Gauteng, 2000, South Africa
| | - Lithalethu Mkabayi
- Enzyme Science Programme (ESP), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, Eastern Cape, 6140, South Africa
| | - Brett I Pletschke
- Enzyme Science Programme (ESP), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, Eastern Cape, 6140, South Africa.
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Biochemical characterisation of four rhamnosidases from thermophilic bacteria of the genera Thermotoga, Caldicellulosiruptor and Thermoclostridium. Sci Rep 2019; 9:15924. [PMID: 31685873 PMCID: PMC6828813 DOI: 10.1038/s41598-019-52251-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 09/23/2019] [Indexed: 01/19/2023] Open
Abstract
Carbohydrate active enzymes are classified in databases based on sequence and structural similarity. However, their function can vary considerably within a similarity-based enzyme family, which makes biochemical characterisation indispensable to unravel their physiological role and to arrive at a meaningful annotation of the corresponding genes. In this study, we biochemically characterised the four related enzymes Tm_Ram106B, Tn_Ram106B, Cb_Ram106B and Ts_Ram106B from the thermophilic bacteria Thermotoga maritima MSB8, Thermotoga neapolitana Z2706-MC24, Caldicellulosiruptor bescii DSM 6725 and Thermoclostridium stercorarium DSM 8532, respectively, as α-l-rhamnosidases. Cobalt, nickel, manganese and magnesium ions stimulated while EDTA and EGTA inhibited all four enzymes. The kinetic parameters such as Km, Vmax and kcat were about average compared to other rhamnosidases. The enzymes were inhibited by rhamnose, with half-maximal inhibitory concentrations (IC50) between 5 mM and 8 mM. The α-l-rhamnosidases removed the terminal rhamnose moiety from the rutinoside in naringin, a natural flavonone glycoside. The Thermotoga sp. enzymes displayed the highest optimum temperatures and thermostabilities of all rhamnosidases reported to date. The four thermophilic and divalent ion-dependent rhamnosidases are the first biochemically characterised orthologous enzymes recently assigned to glycoside hydrolase family 106.
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29
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Bajaj P, Mahajan R. Cellulase and xylanase synergism in industrial biotechnology. Appl Microbiol Biotechnol 2019; 103:8711-8724. [DOI: 10.1007/s00253-019-10146-0] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 09/10/2019] [Accepted: 09/17/2019] [Indexed: 11/29/2022]
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30
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Wang K, Cao R, Wang M, Lin Q, Zhan R, Xu H, Wang S. A novel thermostable GH10 xylanase with activities on a wide variety of cellulosic substrates from a xylanolytic Bacillus strain exhibiting significant synergy with commercial Celluclast 1.5 L in pretreated corn stover hydrolysis. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:48. [PMID: 30899328 PMCID: PMC6408826 DOI: 10.1186/s13068-019-1389-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 02/25/2019] [Indexed: 05/28/2023]
Abstract
BACKGROUND Cellulose and hemicellulose are the two largest components in lignocellulosic biomass. Enzymes with activities towards cellulose and xylan have attracted great interest in the bioconversion of lignocellulosic biomass, since they have potential in improving the hydrolytic performance and reducing the enzyme costs. Exploring glycoside hydrolases (GHs) with good thermostability and activities on xylan and cellulose would be beneficial to the industrial production of biofuels and bio-based chemicals. RESULTS A novel GH10 enzyme (XynA) identified from a xylanolytic strain Bacillus sp. KW1 was cloned and expressed. Its optimal pH and temperature were determined to be pH 6.0 and 65 °C. Stability analyses revealed that XynA was stable over a broad pH range (pH 6.0-11.0) after being incubated at 25 °C for 24 h. Moreover, XynA retained over 95% activity after heat treatment at 60 °C for 60 h, and its half-lives at 65 °C and 70 °C were about 12 h and 1.5 h, respectively. More importantly, in terms of substrate specificity, XynA exhibits hydrolytic activities towards xylans, microcrystalline cellulose (filter paper and Avicel), carboxymethyl cellulose (CMC), cellobiose, p-nitrophenyl-β-d-cellobioside (pNPC), and p-nitrophenyl-β-d-glucopyranoside (pNPG). Furthermore, the addition of XynA into commercial cellulase in the hydrolysis of pretreated corn stover resulted in remarkable increases (the relative increases may up to 90%) in the release of reducing sugars. Finally, it is worth mentioning that XynA only shows high amino acid sequence identity (88%) with rXynAHJ14, a GH10 xylanase with no activity on CMC. The similarities with other characterized GH10 enzymes, including xylanases and bifunctional xylanase/cellulase enzymes, are no more than 30%. CONCLUSIONS XynA is a novel thermostable GH10 xylanase with a wide substrate spectrum. It displays good stability in a broad range of pH and high temperatures, and exhibits activities towards xylans and a wide variety of cellulosic substrates, which are not found in other GH10 enzymes. The enzyme also has high capacity in saccharification of pretreated corn stover. These characteristics make XynA a good candidate not only for assisting cellulase in lignocellulosic biomass hydrolysis, but also for the research on structure-function relationship of bifunctional xylanase/cellulase.
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Affiliation(s)
- Kui Wang
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine, Guangzhou Higher Education Mega Center, No.232 Outer Ring West Rd., Panyu District, Guangzhou, 510006 Guangdong China
- Key Laboratory of Chinese Medicinal Resource from Lingnan, Ministry of Education, Guangzhou University of Chinese Medicine, Guangzhou Higher Education Mega Center, No.232 Outer Ring West Rd., Panyu District, Guangzhou, 510006 Guangdong China
- Joint Laboratory of National Engineering Research Center for the Pharmaceutics of Traditional Chinese Medicines, Guangzhou University of Chinese Medicine, Guangzhou Higher Education Mega Center, No.232 Outer Ring West Rd., Panyu District, Guangzhou, 510006 Guangdong China
| | - Ruoting Cao
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine, Guangzhou Higher Education Mega Center, No.232 Outer Ring West Rd., Panyu District, Guangzhou, 510006 Guangdong China
- Key Laboratory of Chinese Medicinal Resource from Lingnan, Ministry of Education, Guangzhou University of Chinese Medicine, Guangzhou Higher Education Mega Center, No.232 Outer Ring West Rd., Panyu District, Guangzhou, 510006 Guangdong China
- Joint Laboratory of National Engineering Research Center for the Pharmaceutics of Traditional Chinese Medicines, Guangzhou University of Chinese Medicine, Guangzhou Higher Education Mega Center, No.232 Outer Ring West Rd., Panyu District, Guangzhou, 510006 Guangdong China
| | - Meiling Wang
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine, Guangzhou Higher Education Mega Center, No.232 Outer Ring West Rd., Panyu District, Guangzhou, 510006 Guangdong China
- Key Laboratory of Chinese Medicinal Resource from Lingnan, Ministry of Education, Guangzhou University of Chinese Medicine, Guangzhou Higher Education Mega Center, No.232 Outer Ring West Rd., Panyu District, Guangzhou, 510006 Guangdong China
- Joint Laboratory of National Engineering Research Center for the Pharmaceutics of Traditional Chinese Medicines, Guangzhou University of Chinese Medicine, Guangzhou Higher Education Mega Center, No.232 Outer Ring West Rd., Panyu District, Guangzhou, 510006 Guangdong China
| | - Qibin Lin
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine, Guangzhou Higher Education Mega Center, No.232 Outer Ring West Rd., Panyu District, Guangzhou, 510006 Guangdong China
- Key Laboratory of Chinese Medicinal Resource from Lingnan, Ministry of Education, Guangzhou University of Chinese Medicine, Guangzhou Higher Education Mega Center, No.232 Outer Ring West Rd., Panyu District, Guangzhou, 510006 Guangdong China
- Joint Laboratory of National Engineering Research Center for the Pharmaceutics of Traditional Chinese Medicines, Guangzhou University of Chinese Medicine, Guangzhou Higher Education Mega Center, No.232 Outer Ring West Rd., Panyu District, Guangzhou, 510006 Guangdong China
| | - Ruoting Zhan
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine, Guangzhou Higher Education Mega Center, No.232 Outer Ring West Rd., Panyu District, Guangzhou, 510006 Guangdong China
- Key Laboratory of Chinese Medicinal Resource from Lingnan, Ministry of Education, Guangzhou University of Chinese Medicine, Guangzhou Higher Education Mega Center, No.232 Outer Ring West Rd., Panyu District, Guangzhou, 510006 Guangdong China
- Joint Laboratory of National Engineering Research Center for the Pharmaceutics of Traditional Chinese Medicines, Guangzhou University of Chinese Medicine, Guangzhou Higher Education Mega Center, No.232 Outer Ring West Rd., Panyu District, Guangzhou, 510006 Guangdong China
| | - Hui Xu
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine, Guangzhou Higher Education Mega Center, No.232 Outer Ring West Rd., Panyu District, Guangzhou, 510006 Guangdong China
- Key Laboratory of Chinese Medicinal Resource from Lingnan, Ministry of Education, Guangzhou University of Chinese Medicine, Guangzhou Higher Education Mega Center, No.232 Outer Ring West Rd., Panyu District, Guangzhou, 510006 Guangdong China
- Joint Laboratory of National Engineering Research Center for the Pharmaceutics of Traditional Chinese Medicines, Guangzhou University of Chinese Medicine, Guangzhou Higher Education Mega Center, No.232 Outer Ring West Rd., Panyu District, Guangzhou, 510006 Guangdong China
| | - Sidi Wang
- College of Fundamental Medical Science, Guangzhou University of Chinese Medicine, Guangzhou Higher Education Mega Center, No.232 Outer Ring West Rd., Panyu District, Guangzhou, 510006 Guangdong China
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Ren Z, You W, Wu S, Poetsch A, Xu C. Secretomic analyses of Ruminiclostridium papyrosolvens reveal its enzymatic basis for lignocellulose degradation. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:183. [PMID: 31338125 PMCID: PMC6628489 DOI: 10.1186/s13068-019-1522-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 07/05/2019] [Indexed: 05/07/2023]
Abstract
BACKGROUND Efficient biotechnological conversion of lignocellulosic biomass to valuable products, such as transportation biofuels, is ecologically attractive, yet requires substantially improved mechanistic understanding and optimization to become economically feasible. Cellulolytic clostridia, such as Ruminiclostridium papyrosolvens (previously Clostridium papyrosolvens), produce a wide variety of carbohydrate-active enzymes (CAZymes) including extracellular multienzyme complexes-cellulosomes with different specificities for enhanced cellulosic biomass degradation. Identification of the secretory components, especially CAZymes, during bacterial growth on lignocellulose and their influence on bacterial catalytic capabilities provide insight into construction of potent cellulase systems of cell factories tuned or optimized for the targeted substrate by matching the type and abundance of enzymes and corresponding transporters. RESULTS In this study, we firstly predicted a total of 174 putative CAZymes from the genome of R. papyrosolvens, including 74 cellulosomal components. To explore profile of secreted proteins involved in lignocellulose degradation, we compared the secretomes of R. papyrosolvens grown on different substrates using label-free quantitative proteomics. CAZymes, extracellular solute-binding proteins (SBPs) of transport systems and proteins involved in spore formation were enriched in the secretome of corn stover for lignocellulose degradation. Furthermore, compared with free CAZymes, complex CAZymes (cellulosomal components) had larger fluctuations in variety and abundance of enzymes among four carbon sources. In particular, cellulosomal proteins encoded by the cip-cel operon and the xyl-doc gene cluster had the highest abundance with corn stover as substrate. Analysis of differential expression of CAZymes revealed a substrate-dependent secretion pattern of CAZymes, which was consistent with their catalytic activity from each secretome determined on different cellulosic substrates. The results suggest that the expression of CAZymes is regulated by the type of substrate in the growth medium. CONCLUSIONS In the present study, our results demonstrated the complexity of the lignocellulose degradation systems of R. papyrosolvens and showed the potency of its biomass degradation activity. Differential proteomic analyses and activity assays of CAZymes secreted by R. papyrosolvens suggested a distinct environment-sensing strategy for cellulose utilization in which R. papyrosolvens modulated the composition of the CAZymes, especially cellulosome, according to the degradation state of its natural substrate.
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Affiliation(s)
- Zhenxing Ren
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, 030006 Shanxi China
- Institute of Applied Chemistry, Shanxi University, Taiyuan, 030006 Shanxi China
| | - Wuxin You
- Department of Plant Biochemistry, Ruhr University Bochum, 44801 Bochum, Germany
| | - Shasha Wu
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, 030006 Shanxi China
| | - Ansgar Poetsch
- Department of Plant Biochemistry, Ruhr University Bochum, 44801 Bochum, Germany
- School of Biomedical and Healthcare Sciences, University of Plymouth, Plymouth, PL48AA UK
| | - Chenggang Xu
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, 030006 Shanxi China
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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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Multidisciplinary involvement and potential of thermophiles. Folia Microbiol (Praha) 2018; 64:389-406. [PMID: 30386965 DOI: 10.1007/s12223-018-0662-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 10/25/2018] [Indexed: 12/15/2022]
Abstract
The full biotechnological exploitation of thermostable enzymes in industrial processes is necessary for their commercial interest and industrious value. The heat-tolerant and heat-resistant enzymes are a key for efficient and cost-effective translation of substrates into useful products for commercial applications. The thermophilic, hyperthermophilic, and microorganisms adapted to extreme temperatures (i.e., low-temperature lovers or psychrophiles) are a rich source of thermostable enzymes with broad-ranging thermal properties, which have structural and functional stability to underpin a variety of technologies. These enzymes are under scrutiny for their great biotechnological potential. Temperature is one of the most critical parameters that shape microorganisms and their biomolecules for stability under harsh environmental conditions. This review describes in detail the sources of thermophiles and thermostable enzymes from prokaryotes and eukaryotes (microbial cell factories). Furthermore, the review critically examines perspectives to improve modern biocatalysts, its production and performance aiming to increase their value for biotechnology through higher standards, specificity, resistance, lowing costs, etc. These thermostable and thermally adapted extremophilic enzymes have been used in a wide range of industries that span all six enzyme classes. Thus, in particular, target of this review paper is to show the possibility of both high-value-low-volume (e.g., fine-chemical synthesis) and low-value-high-volume by-products (e.g., fuels) by minimizing changes to current industrial processes.
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