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Ladeveze S, Zurek PJ, Kaminski TS, Emond S, Hollfelder F. Versatile Product Detection via Coupled Assays for Ultrahigh-Throughput Screening of Carbohydrate-Active Enzymes in Microfluidic Droplets. ACS Catal 2023; 13:10232-10243. [PMID: 37560191 PMCID: PMC10407846 DOI: 10.1021/acscatal.3c01609] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 06/06/2023] [Indexed: 08/11/2023]
Abstract
Enzyme discovery and directed evolution are the two major contemporary approaches for the improvement of industrial processes by biocatalysis in various fields. Customization of catalysts for improvement of single enzyme reactions or de novo reaction development is often complex and tedious. The success of screening campaigns relies on the fraction of sequence space that can be sampled, whether for evolving a particular enzyme or screening metagenomes. Ultrahigh-throughput screening (uHTS) based on in vitro compartmentalization in water-in-oil emulsion of picoliter droplets generated in microfluidic systems allows screening rates >1 kHz (or >107 per day). Screening for carbohydrate-active enzymes (CAZymes) catalyzing biotechnologically valuable reactions in this format presents an additional challenge because the released carbohydrates are difficult to monitor in high throughput. Activated substrates with large optically active hydrophobic leaving groups provide a generic optical readout, but the molecular recognition properties of sugars will be altered by the incorporation of such fluoro- or chromophores and their typically higher reactivity, as leaving groups with lowered pKa values compared to native substrates make the observation of promiscuous reactions more likely. To overcome these issues, we designed microdroplet assays in which optically inactive carbohydrate products are made visible by specific cascades: the primary reaction of an unlabeled substrate leads to an optical signal downstream. Successfully implementing such assays at the picoliter droplet scale allowed us to detect glucose, xylose, glucuronic acid, and arabinose as final products of complex oligosaccharide degradation by glycoside hydrolases by absorbance measurements. Enabling the use of uHTS for screening CAZyme reactions that have been thus far elusive will chart a route toward faster and easier development of specific and efficient biocatalysts for biovalorization, directing enzyme discovery by challenging catalysts for reaction with natural rather than model substrates.
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Affiliation(s)
| | - Paul J. Zurek
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB21GA, U.K.
| | | | | | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB21GA, U.K.
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Batth TS, Simonsen JL, Hernández-Rollán C, Brander S, Morth JP, Johansen KS, Nørholm MHH, Hoof JB, Olsen JV. A seven-transmembrane methyltransferase catalysing N-terminal histidine methylation of lytic polysaccharide monooxygenases. Nat Commun 2023; 14:4202. [PMID: 37452022 PMCID: PMC10349129 DOI: 10.1038/s41467-023-39875-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 06/29/2023] [Indexed: 07/18/2023] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are oxidative enzymes that help break down lignocellulose, making them highly attractive for improving biomass utilization in industrial biotechnology. The catalytically essential N-terminal histidine (His1) of LPMOs is post-translationally modified by methylation in filamentous fungi to protect them from auto-oxidative inactivation, however, the responsible methyltransferase enzyme is unknown. Using mass-spectrometry-based quantitative proteomics in combination with systematic CRISPR/Cas9 knockout screening in Aspergillus nidulans, we identify the N-terminal histidine methyltransferase (NHMT) encoded by the gene AN4663. Targeted proteomics confirm that NHMT was solely responsible for His1 methylation of LPMOs. NHMT is predicted to encode a unique seven-transmembrane segment anchoring a soluble methyltransferase domain. Co-localization studies show endoplasmic reticulum residence of NHMT and co-expression in the industrial production yeast Komagataella phaffii with LPMOs results in His1 methylation of the LPMOs. This demonstrates the biotechnological potential of recombinant production of proteins and peptides harbouring this specific post-translational modification.
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Affiliation(s)
- Tanveer S Batth
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen Denmark, Copenhagen, Denmark.
| | - Jonas L Simonsen
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen Denmark, Copenhagen, Denmark
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Cristina Hernández-Rollán
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Søren Brander
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Frederiksberg, Denmark
| | - Jens Preben Morth
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Katja S Johansen
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Frederiksberg, Denmark
| | - Morten H H Nørholm
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark.
| | - Jakob B Hoof
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark.
| | - Jesper V Olsen
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen Denmark, Copenhagen, Denmark.
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Bakshani CR, Cuskin F, Lant NJ, Yau HCL, Willats WGT, Grant Burgess J. Analysis of glycans in a Burnt-on/Baked-on (BoBo) model food soil using Microarray Polymer Profiling (MAPP) and immunofluorescence microscopy. Food Chem 2023; 410:135379. [PMID: 36621331 DOI: 10.1016/j.foodchem.2022.135379] [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: 10/03/2022] [Revised: 12/12/2022] [Accepted: 12/31/2022] [Indexed: 01/03/2023]
Abstract
Burning of food materials during cooking can increase the difficulty in removal from solid surfaces, forming residual food soils. Using molecular probe-based technologies, the aim of this work was to elucidate the composition and relative abundance of glycans within a Burnt-On/Baked-On (BoBo) model food soil and investigate enzyme systems that may facilitate soil breakdown. Microarray Polymer Profiling identified xylan, arabinoxylan, mixed-linkage glucan and mannan as target substrates for the enzymatic cleaning of BoBo residues from surfaces. Indirect immunofluorescence microscopy revealed that burning resulted in extensive structural modifications and degradation of the three-dimensional architecture of constituent polysaccharide matrices. Results from high-throughput enzyme screening indicate that inclusion of xylan depolymerising enzymes in automatic dishwashing detergents may improve cleaning of recalcitrant, plant glycan-rich BoBo soils. Collectively, this study provides new insight into the composition and removal chemistry of complex, multi-component food soils.
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Affiliation(s)
- Cassie R Bakshani
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK.
| | - Fiona Cuskin
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Neil J Lant
- Procter & Gamble, Newcastle Innovation Centre, Newcastle upon Tyne NE12 9TS, UK
| | - Hamish C L Yau
- Procter & Gamble, Newcastle Innovation Centre, Newcastle upon Tyne NE12 9TS, UK
| | - William G T Willats
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - J Grant Burgess
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
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Khani M, Hansen MF, Knøchel S, Rasekh B, Ghasemipanah K, Zamir SM, Nosrati M, Burmølle M. Antifouling potential of enzymes applied to Reverse Osmosis Membranes. Biofilm 2023; 5:100119. [PMID: 37131492 PMCID: PMC10149195 DOI: 10.1016/j.bioflm.2023.100119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 03/31/2023] [Accepted: 03/31/2023] [Indexed: 04/03/2023] Open
Abstract
Many companies in the food industry apply reverse osmosis (RO) membranes to ensure high-quality reuse of water. Biofouling is however, a common, recalcitrant and recurring problem that blocks transport over membranes and decreases the water recovery. Microorganisms adhering to membranes may form biofilm and produce an extracellular matrix, which protects against external stress and ensures continuous attachment. Thus, various agents are tested for their ability to degrade and disperse biofilms. Here, we identified industrially relevant bacterial model communities that form biofilms on RO membranes used for treating process water before reuse. There was a marked difference in the biofilm forming capabilities of bacteria isolated from contaminated RO membranes. One species, Raoultella ornithinolytica, was particularly capable of forming biofilm and was included in most communities. The potential of different enzymes (Trypsin-EDTA, Proteinase K, α-Amylase, β-Mannosidase and Alginate lyase) as biofouling dispersing agents was evaluated at different concentrations (0.05 U/ml and 1.28 U/ml). Among the tested enzymes, β-Mannosidase was the only enzyme able to reduce biofilm formation significantly within 4 h of exposure at 25 °C (0.284 log reduction), and only at the high concentration. Longer exposure duration, however, resulted in significant biofilm reduction by all enzymes tested (0.459-0.717 log reduction) at both low and high concentrations. Using confocal laser scanning microscopy, we quantified the biovolume on RO membranes after treatment with two different enzyme mixtures. The application of proteinase K and β-Mannosidase significantly reduced the amount of attached biomass (43% reduction), and the combination of all five enzymes showed even stronger reducing effect (71% reduction). Overall, this study demonstrates a potential treatment strategy, using matrix-degrading enzymes for biofouled RO membranes in food processing water treatment streams. Future studies on optimization of buffer systems, temperature and other factors could facilitate cleaning operations based on enzymatic treatment extending the lifespan of membranes with a continuous flux.
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Moye J, Schenk T, Hess S. Experimental evidence for enzymatic cell wall dissolution in a microbial protoplast feeder (Orciraptor agilis, Viridiraptoridae). BMC Biol 2022; 20:267. [PMID: 36464670 PMCID: PMC9721047 DOI: 10.1186/s12915-022-01478-x] [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: 08/24/2022] [Accepted: 11/24/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Several protists have evolved the ability to perforate the cell walls of algae and fungi to specifically feed on their cell contents. These phagotrophic "protoplast feeders" represent an interesting mechanistic intermediate between predators and parasites and pose a number of cell biological questions. Although their fascinating feeding behaviour has been observed for the last 150 years, it is still unknown how protoplast feeders produce the well-defined and species-specific perforations in biochemically diverse cell walls. Differential expression analyses of the algivorous flagellate Orciraptor agilis (Viridiraptoridae, Cercozoa, Rhizaria) suggested the involvement of a highly expressed putative glycoside hydrolase of family GH5_5. To assess the importance of this carbohydrate-active enzyme in the feeding act of Orciraptor, we recombinantly produced its catalytic domain and studied the enzymatic activity, cellular localisation and function. RESULTS The GH5_5 catalytic domain from Orciraptor showed pronounced activity on soluble cellulose derivatives and mixed-linkage glucans, with reaction optima comparable to known GH5_5 representatives. Crystalline cellulose was not digested by the enzyme, which suggests a typical endocellulase activity. Immunocytochemistry with a polyclonal antibody raised against the GH5_5 domain revealed that the native endocellulase localises to the contact zone of Orciraptor and the algal cell wall (= perforation zone) and to intracellular granules, which were enriched during attack. Furthermore, the anti-GH5_5 antibody applied to live cells significantly reduced the feeding success of Orciraptor. The cells attacked the algae, which, however, resulted in numerous incomplete perforations. CONCLUSIONS Our experimental data from enzymatic assays, immunocytochemistry and inhibition experiments strongly suggest a key role of the GH5_5 endocellulase in cell wall dissolution by Orciraptor agilis. With that, we provide evidence that the well-defined perforations produced by protoplast feeders are caused by extracellular carbohydrate-active enzymes and made a first step towards establishing the molecular basis of a fascinating, yet poorly understood microbial feeding strategy.
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Affiliation(s)
- Jannika Moye
- grid.6190.e0000 0000 8580 3777Institute for Zoology, University of Cologne, Zülpicher Str. 47b, 50674 Cologne, Germany
| | - Tobias Schenk
- grid.6190.e0000 0000 8580 3777Institute for Zoology, University of Cologne, Zülpicher Str. 47b, 50674 Cologne, Germany
| | - Sebastian Hess
- grid.6190.e0000 0000 8580 3777Institute for Zoology, University of Cologne, Zülpicher Str. 47b, 50674 Cologne, Germany
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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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Complete Genome Sequence and Comparative Genome Analysis of Variovorax sp. Strains PAMC28711, PAMC26660, and PAMC28562 and Trehalose Metabolic Pathways in Antarctica Isolates. Int J Microbiol 2022. [DOI: 10.1155/2022/5067074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The complete genomes of Variovorax strains were analyzed and compared along with the genomes of Variovorax strains PAMC28711, PAMC28562, and PAMC26660, Antarctic isolates. The genomic information was collected from the NCBI database and the CAZyme database, and Prokka annotation was used to find the genes that encode for the trehalose metabolic pathway. Likewise, CAZyme annotation (dbCAN2 Meta server) was performed to predict the CAZyme family responsible for trehalose biosynthesis and degradation enzymes. Trehalose has been found to respond to osmotic stress and extreme temperatures. As a result, the study of the trehalose metabolic pathway was carried out in harsh environments such as the Antarctic, where bacteria Variovorax sp. strains PAMC28711, PAMC28562, and PAMC26660 can survive in extreme environments, such as cold temperatures. The trehalose metabolic pathway was analyzed via bioinformatics tools, such as the dbCAN2 Meta server, Prokka annotation, Multiple Sequence Alignment, ANI calculator, and PATRIC database, which helped to predict trehalose biosynthesis and degradation genes’ involvement in the complete genome of Variovorax strains. Likewise, MEGA X was used for evolutionary and conserved genes. The complete genomes of Variovorax strains PAMC28711, PAMC26660, and PAMC28562 are circular chromosomes of length (4,320,000, 7,390,000, and 4,690,000) bp, respectively, with GC content of (66.00, 66.00, and 63.70)%, respectively. The GC content of these three Variovorax strains is lower than that of the other Variovorax strains with complete genomes. Strains PAMC28711 and PAMC28562 exhibit three complete trehalose biosynthetic pathways (OtsA/OtsB, TS, and TreY/TreZ), but strain PAMC26660 only possesses one (OtsA/OtsB). Despite the fact that all three strains contain trehalose, only strain PAMC28711 has two trehaloses according to CAZyme families (GH37 and GH15). Moreover, among the three Antarctica isolates, only strain PAMC28711 exhibits auxiliary activities (AAs), a CAZyme family. To date, although the Variovorax strains are studied for different purposes, the trehalose metabolic pathways in Variovorax strains have not been reported. Further, this study provides additional information regarding trehalose biosynthesis genes and degradation genes (trehalose) as one of the factors facilitating bacterial survival under extreme environments, and this enzyme has shown potential application in biotechnology fields.
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Šuchová K, Fehér C, Ravn JL, Bedő S, Biely P, Geijer C. Cellulose- and xylan-degrading yeasts: Enzymes, applications and biotechnological potential. Biotechnol Adv 2022; 59:107981. [DOI: 10.1016/j.biotechadv.2022.107981] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 05/08/2022] [Accepted: 05/10/2022] [Indexed: 01/23/2023]
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Díaz-García L, Chaparro D, Jiménez H, Gómez-Ramírez LF, Bernal AJ, Burbano-Erazo E, Jiménez DJ. Top-Down Enrichment Strategy to Co-cultivate Lactic Acid and Lignocellulolytic Bacteria From the Megathyrsus maximus Phyllosphere. Front Microbiol 2022; 12:744075. [PMID: 35035382 PMCID: PMC8753987 DOI: 10.3389/fmicb.2021.744075] [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: 07/19/2021] [Accepted: 10/11/2021] [Indexed: 12/15/2022] Open
Abstract
Traditionally, starting inoculants have been applied to improve ensiling of forage used for livestock feed. Here, we aimed to build up a bioinoculant composed of lactic acid-producing and lignocellulolytic bacteria (LB) derived from the Megathyrsus maximus (guinea grass) phyllosphere. For this, the dilution-to-stimulation approach was used, including a sequential modification of the starting culture medium [Man, Rogosa, and Sharpe (MRS) broth] by addition of plant biomass (PB) and elimination of labile carbon sources. Along 10 growth-dilution steps (T1–T10), slight differences were observed in terms of bacterial diversity and composition. After the sixth subculture, the consortium started to degrade PB, decreasing its growth rate. The co-existence of Enterobacteriales (fast growers and highly abundance), Actinomycetales, Bacillales, and Lactobacillales species was observed at the end of the selection process. However, a significant structural change was noticed when the mixed consortium was cultivated in higher volume (500ml) for 8days, mainly increasing the proportion of Paenibacillaceae populations. Interestingly, Actinomycetales, Bacillales, and Lactobacillales respond positively to a pH decrease (4–5), suggesting a relevant role within a further silage process. Moreover, gene-centric metagenomic analysis showed an increase of (hemi)cellulose-degrading enzymes (HDEs) during the enrichment strategy. Reconstruction of metagenome-assembled genomes (MAGs) revealed that Paenibacillus, Cellulosimicrobium, and Sphingomonas appear as key (hemi)cellulolytic members (harboring endo-glucanases/xylanases, arabinofuranosidases, and esterases), whereas Enterococcus and Cellulosimicrobium have the potential to degrade oligosaccharides, metabolize xylose and might produce lactic acid through the phosphoketolase (PK) pathway. Based on this evidence, we conclude that our innovative top-down strategy enriched a unique bacterial consortium that could be useful in biotechnological applications, including the development/design of a synthetic bioinoculant to improve silage processes.
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Affiliation(s)
- Laura Díaz-García
- Microbiomes and Bioenergy Research Group, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Dayanne Chaparro
- Microbiomes and Bioenergy Research Group, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Hugo Jiménez
- Colombian Corporation for Agricultural Research (Agrosavia), Mosquera, Colombia
| | | | - Adriana J Bernal
- Laboratory of Molecular Interactions of Agricultural Microbes, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | | | - Diego Javier Jiménez
- Microbiomes and Bioenergy Research Group, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
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Fernandez-Lopez L, Sanchez-Carrillo S, García-Moyano A, Borchert E, Almendral D, Alonso S, Cea-Rama I, Miguez N, Larsen Ø, Werner J, Makarova KS, Plou FJ, Dahlgren TG, Sanz-Aparicio J, Hentschel U, Bjerga GEK, Ferrer M. The bone-degrading enzyme machinery: From multi-component understanding to the treatment of residues from the meat industry. Comput Struct Biotechnol J 2021; 19:6328-6342. [PMID: 34938409 PMCID: PMC8645421 DOI: 10.1016/j.csbj.2021.11.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 11/17/2021] [Accepted: 11/17/2021] [Indexed: 11/19/2022] Open
Abstract
Characterization of enzymes from bone-degrading marine microbiomes. Enzymes degrade sialo/glyco-proteins at multiple conditions of pH and temperatures. Enzyme cocktails are useful for valorising bone residues in biorefinery industry.
Many microorganisms feed on the tissue and recalcitrant bone materials from dead animals, however little is known about the collaborative effort and characteristics of their enzymes. In this study, microbial metagenomes from symbionts of the marine bone-dwelling worm Osedax mucofloris, and from microbial biofilms growing on experimentally deployed bone surfaces were screened for specialized bone-degrading enzymes. A total of 2,043 taxonomically (closest match within 40 phyla) and functionally (1 proteolytic and 9 glycohydrolytic activities) diverse and non-redundant sequences (median pairwise identity of 23.6%) encoding such enzymes were retrieved. The taxonomic assignation and the median identity of 72.2% to homologous proteins reflect microbial and functional novelty associated to a specialized bone-degrading marine community. Binning suggests that only one generalist hosting all ten targeted activities, working in synergy with multiple specialists hosting a few or individual activities. Collagenases were the most abundant enzyme class, representing 48% of the total hits. A total of 47 diverse enzymes, representing 8 hydrolytic activities, were produced in Escherichia coli, whereof 13 were soluble and active. The biochemical analyses revealed a wide range of optimal pH (4.0–7.0), optimal temperature (5–65 °C), and of accepted substrates, specific to each microbial enzyme. This versatility may contribute to a high environmental plasticity of bone-degrading marine consortia that can be confronted to diverse habitats and bone materials. Through bone-meal degradation tests, we further demonstrated that some of these enzymes, particularly those from Flavobacteriaceae and Marinifilaceae, may be an asset for development of new value chains in the biorefinery industry.
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Key Words
- Bone degradation
- Bone microbiome
- COLL, collagenases (peptidases families U32 and M9)
- Collagenase
- DNS, dinitrosalicylic acid
- FALGPA, N-[3-(2-furyl)acryloyl]-L-leucyl-glycyl-L-prolyl-L-alanine
- Glycosidase
- HEPES, 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
- HMM, Hidden Markov Models
- HPAEC-PAD, High performance anion-exchange chromatography with pulsed amperometric detection
- MAG, Metagenome Assembled Genome
- Metagenomics
- Neu5Ac-GM2, N-acetyl-galactose-β-1,4-[N-acetylneuraminidate-α-2,3-]-galactose-β-1,4-glucose-α-ceramide
- Neu5Ac-GM3, Neu5Acα2-3Galβ1-4Glcβ1-ceramide
- Ni-NTA, nickel-nitrilotriacetic acid
- Osedax mucofloris
- PEPT, peptidase (families S1, S8, S53, M61)
- RHAM, α-rhamnosidases
- SIAL, sialidases
- pNP-NAβGal, pNP-N-acetyl-β-galactosaminide
- pNP-NAβGlu, pNP-N-acetyl-β-glucosaminide
- pNP-Neu5Ac, 2-O-(p-nitrophenyl)-α-acetylneuraminic acid
- pNP-sugars, p-nitrophenyl-sugars
- pNP-αAFur, pNP-α-arabinofuranoside
- pNP-αAPyr, pNP-α-arabinopyranoside
- pNP-αFuc, pNP-α-fucopyranoside
- pNP-αGal, pNP-α-galactopyranoside
- pNP-αGlu, pNP-α-glucopyranoside
- pNP-αMal, pNP-α-maltoside
- pNP-αMan, pNP-α-mannopyranoside
- pNP-αRham, pNP-α-rhamnopyranoside
- pNP-αXyl, pNP-α-xylopyranoside
- pNP-βAPyr, pNP-β-arabinopyranoside
- pNP-βCel, pNP-β-cellobioside
- pNP-βFuc, pNP-β-fucopyranoside
- pNP-βGal, pNP-β-galactopyranoside
- pNP-βGlu, pNP-β-glucopyranoside
- pNP-βGlucur, pNP-β-glucuronide
- pNP-βLac, pNP-β-lactoside
- pNP-βMan, pNP-β-mannopyranoside
- pNP-βXyl, pNP-β-xylopyranoside
- αFUC, α-fucosidases
- αGAL, α-galactosidases
- αMAN, α-mannosidases
- αNAG, α-N-acetyl-hexosaminidases
- βGAL, β-galactosidases
- βGLU, β-glucosidases
- βNAG, β-N-acetyl-hexosaminidases
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Affiliation(s)
| | | | | | - Erik Borchert
- GEOMAR Helmholtz Centre for Ocean Research, 24148 Kiel, Germany
- Corresponding authors at: GEOMAR Helmholtz Centre for Ocean Research, Wischhofstraße 1-3, 24148 Kiel, Germany (E. Borchert). Institute of Catalysis, CSIC, Marie Curie 2, 28049 Madrid, Spain (M. Ferrer).
| | | | | | - Isabel Cea-Rama
- Institute of Physical Chemistry “Rocasolano”, CSIC, 28006 Madrid, Spain
| | - Noa Miguez
- CSIC, Institute of Catalysis, 28049 Madrid, Spain
| | - Øivind Larsen
- NORCE Norwegian Research Centre, P.O. Box 22 Nygårdstangen, 5838 Bergen, Norway
| | - Johannes Werner
- High Performance and Cloud Computing Group, Zentrum für Datenverarbeitung (ZDV), Eberhard Karls University of Tübingen, 72074 Tübingen, Germany
| | - Kira S. Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, 20892 MD, USA
| | | | - Thomas G. Dahlgren
- NORCE Norwegian Research Centre, P.O. Box 22 Nygårdstangen, 5838 Bergen, Norway
| | | | - Ute Hentschel
- GEOMAR Helmholtz Centre for Ocean Research, 24148 Kiel, Germany
- Christian-Albrechts University of Kiel, 24118 Kiel, Germany
| | | | - Manuel Ferrer
- CSIC, Institute of Catalysis, 28049 Madrid, Spain
- Corresponding authors at: GEOMAR Helmholtz Centre for Ocean Research, Wischhofstraße 1-3, 24148 Kiel, Germany (E. Borchert). Institute of Catalysis, CSIC, Marie Curie 2, 28049 Madrid, Spain (M. Ferrer).
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11
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Duong HL, Paufler S, Harms H, Maskow T, Schlosser D. Applicability and information value of biocalorimetry for the monitoring of fungal solid-state fermentation of lignocellulosic agricultural by-products. N Biotechnol 2021; 66:97-106. [PMID: 34767975 DOI: 10.1016/j.nbt.2021.11.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 11/02/2021] [Accepted: 11/07/2021] [Indexed: 11/30/2022]
Abstract
The applicability of biocalorimetry for monitoring fungal conversion of lignocellulosic agricultural by-products during solid-state fermentation (SSF) was substantiated through linking the non-invasive measurement of metabolic heat fluxes to conventional invasive determination of fungal activity (growth, substrate degradation, enzyme activity) parameters. For this, the fast-growing, cellulose-utilising ascomycete Stachybotrys chlorohalonata and the comparatively slow-growing litter-decay basidiomycete Stropharia rugosoannulata were investigated as model organisms during growth on solid wheat straw. Both biocalorimetric and non-calorimetric data may suggest R (ruderal)- and C (combative)-selected life history strategies in S. chlorohalonata and S. rugosoannulata, respectively. For both species, a strong linear correlation of the released metabolic heat with the corresponding fungal biomass was observed. Species-specific YQ/X values (metabolic heat released per fungal biomass unit) were obtained, which potentially enable use of biocalorimetric signals for the quantification of fungal biomass during single-species SSF processes. Moreover, YQ/X values may also indicate different fungal life history strategies and therefore be considered as useful parameters aiding fungal ecology research.
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Affiliation(s)
- Hieu Linh Duong
- Department of Environmental Microbiology, Helmholtz-Centre for Environmental Research - UFZ, Permoserstraβe 15, 04318, Leipzig, Germany; Vietnamese-German University (VGU), Le Lai Street, Hoa Phu Ward, Thu Dau Mot City, Binh Duong Province, Viet Nam.
| | - Sven Paufler
- Department of Environmental Microbiology, Helmholtz-Centre for Environmental Research - UFZ, Permoserstraβe 15, 04318, Leipzig, Germany.
| | - Hauke Harms
- Department of Environmental Microbiology, Helmholtz-Centre for Environmental Research - UFZ, Permoserstraβe 15, 04318, Leipzig, Germany.
| | - Thomas Maskow
- Department of Environmental Microbiology, Helmholtz-Centre for Environmental Research - UFZ, Permoserstraβe 15, 04318, Leipzig, Germany.
| | - Dietmar Schlosser
- Department of Environmental Microbiology, Helmholtz-Centre for Environmental Research - UFZ, Permoserstraβe 15, 04318, Leipzig, Germany.
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12
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Combining analytical approaches for better lignocellulosic biomass degradation: a way of improving fungal enzymatic cocktails? Biotechnol Lett 2021; 43:2283-2298. [PMID: 34708264 DOI: 10.1007/s10529-021-03201-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 10/22/2021] [Indexed: 10/20/2022]
Abstract
PURPOSE In this study, a combinatory approach was undertaken to assay the efficiency of fungal enzymatic cocktails from different fermentation conditions to degrade different lignocellulosic biomasses with the aim of finely characterizing fungal enzymatic cocktails. METHODS Enzymatic assays (AZO and pNP-linked substrates and ABTS) were used to assess the composition of the fungal enzymatic cocktails for cellulase, xylanase and laccase activities. Comparisons were made with a new range of chromogenic substrates based on complex biomass (CBS substrates). The saccharification efficiency of the cocktails was evaluated as a quantification of the sugar monomers released from the different biomasses after incubation with the enzymatic cocktails. RESULTS The results obtained showed striking differences between the AZO and pNP-linked substrates and the CBS substrates for the same enzymatic cocktails. On AZO and pNP-linked substrates, different hydrolysis profiles were observed between the different fungi species with Aspergillus oryzae being the most efficient. However, the results on CBS substrates were more contrasted depending on the biomass tested. Altogether, the results highlighted that assessing laccase activities and taking into account the complexity of the biomass to degrade were key in order to provide the best enzymatic cocktails. CONCLUSION The complementary experiments performed in this study showed that different approaches needed to be taken in order to accurately assess the ability of an enzymatic cocktail to be efficient when it comes to lignocellulosic biomass degradation. The saccharification assay proved to be essential to validate the data obtained from both simple and complex substrates.
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13
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Morato NM, Le MT, Holden DT, Graham Cooks R. Automated High-Throughput System Combining Small-Scale Synthesis with Bioassays and Reaction Screening. SLAS Technol 2021; 26:555-571. [PMID: 34697962 DOI: 10.1177/24726303211047839] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The Purdue Make It system is a unique automated platform capable of small-scale in situ synthesis, screening small-molecule reactions, and performing direct label-free bioassays. The platform is based on desorption electrospray ionization (DESI), an ambient ionization method that allows for minimal sample workup and is capable of accelerating reactions in secondary droplets, thus conferring unique advantages compared with other high-throughput screening technologies. By combining DESI with liquid handling robotics, the system achieves throughputs of more than 1 sample/s, handling up to 6144 samples in a single run. As little as 100 fmol/spot of analyte is required to perform both initial analysis by mass spectrometry (MS) and further MSn structural characterization. The data obtained are processed using custom software so that results are easily visualized as interactive heatmaps of reaction plates based on the peak intensities of m/z values of interest. In this paper, we review the system's capabilities as described in previous publications and demonstrate its utilization in two new high-throughput campaigns: (1) the screening of 188 unique combinatorial reactions (24 reaction types, 188 unique reaction mixtures) to determine reactivity trends and (2) label-free studies of the nicotinamide N-methyltransferase enzyme directly from the bioassay buffer. The system's versatility holds promise for several future directions, including the collection of secondary droplets containing the products from successful reaction screening measurements, the development of machine learning algorithms using data collected from compound library screening, and the adaption of a variety of relevant bioassays to high-throughput MS.
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Affiliation(s)
- Nicolás M Morato
- Department of Chemistry and Center for Analytical Instrumentation Development, Purdue University, West Lafayette, IN, USA
| | - MyPhuong T Le
- Department of Chemistry and Center for Analytical Instrumentation Development, Purdue University, West Lafayette, IN, USA
| | - Dylan T Holden
- Department of Chemistry and Center for Analytical Instrumentation Development, Purdue University, West Lafayette, IN, USA
| | - R Graham Cooks
- Department of Chemistry and Center for Analytical Instrumentation Development, Purdue University, West Lafayette, IN, USA
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14
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Wang D, Li Y, Zheng Y, Hsieh YSY. Recent Advances in Screening Methods for the Functional Investigation of Lytic Polysaccharide Monooxygenases. Front Chem 2021; 9:653754. [PMID: 33912540 PMCID: PMC8072006 DOI: 10.3389/fchem.2021.653754] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 02/12/2021] [Indexed: 01/22/2023] Open
Abstract
Lytic polysaccharide monooxygenase (LPMO) is a newly discovered and widely studied enzyme in recent years. These enzymes play a key role in the depolymerization of sugar-based biopolymers (including cellulose, hemicellulose, chitin and starch), and have a positive significance for biomass conversion. LPMO is a copper-dependent enzyme that can oxidize and cleave glycosidic bonds in cellulose and other polysaccharides. Their mechanism of action depends on the correct coordination of copper ions in the active site. There are still difficulties in the analysis of LPMO activity, which often requires multiple methods to be used in concert. In this review, we discussed various LPMO activity analysis methods reported so far, including mature mass spectrometry, chromatography, labeling, and indirect measurements, and summarized the advantages, disadvantages and applicability of different methods.
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Affiliation(s)
- Damao Wang
- College of Food Science, Southwest University, Chongqing, China
| | - Yanping Li
- College of Food Science, Southwest University, Chongqing, China
| | - Yuting Zheng
- College of Food Science, Southwest University, Chongqing, China
| | - Yves S Y Hsieh
- Division of Glycoscience, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology (KTH), AlbaNova University Centre, Stockholm, Sweden.,School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan.,Genomics Research Center, Academia Sinica, Taipei, Taiwan
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15
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Complete Genome Sequence of Pedobacter sp. PAMC26386 and Their Low Temperature Application in Arabinose-containing Polysaccharides Degradation. Curr Microbiol 2021; 78:944-953. [PMID: 33638002 DOI: 10.1007/s00284-021-02364-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 01/29/2021] [Indexed: 10/22/2022]
Abstract
Pedobacter are a representative genus of soil-associated bacteria. Here we have provided the complete genome sequence of Pedobacter sp. PAMC26386 isolated from Antarctic soil, and functionally annotated the genome, describing the unique features of carbohydrate active enzymes (CAZymes) and α-L-arabinofuranosidase (α-L-ABF). The genome of Pedobacter sp. PAMC26386 is circular and comprises 4,796,773 bp, with a 38.2% GC content. The genome encodes 4,175 genes, including 7 rRNA and 44 tRNA genes. We identified 172 genes (8 auxiliary activities, 8 carbohydrate binding modules, 23 carbohydrate esterases, 86 glycoside hydrolases, 42 glycosyl transferases, and 5 polysaccharide lyases) related to CAZymes using the dbCAN2 tool. We checked enzyme activity on 11 substrates using the AZCL assay and obtained strong activity for arabinooligosaccharide and hemicellulose. This includes information regarding α-L-ABF, which is active at low temperatures, based on the annotation results. Our findings on Pedobacter sp. PAMC26386 provide the basis for research in the future. The favorable properties of Pedobacter sp. PAMC26386 make it a good candidate for industrial applications involving low temperatures.
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Koteshwara A, Philip NV, Aranjani JM, Hariharapura RC, Volety Mallikarjuna S. A set of simple methods for detection and extraction of laminarinase. Sci Rep 2021; 11:2489. [PMID: 33510321 PMCID: PMC7844030 DOI: 10.1038/s41598-021-81807-2] [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: 09/10/2020] [Accepted: 12/04/2020] [Indexed: 11/08/2022] Open
Abstract
A carefully designed ammonium sulfate precipitation will simplify extraction of proteins and is considered to be a gold standard among various precipitation methods. Therefore, optimization of ammonium sulfate precipitation can be an important functional step in protein purification. The presence of high amounts of ammonium sulphate precludes direct detection of many enzymatically active proteins including reducing sugar assays (e.g. Nelson-Somogyi, Reissig and 3,5-dinitrosalicylic acid methods) for assessing carbohydrases (e.g. laminarinase (β (1-3)-glucanohydrolase), cellulases and chitinases). In this study, a simple method was developed using laminarin infused agarose plate for the direct analysis of the ammonium sulphate precipitates from Streptomyces rimosus AFM-1. The developed method is simple and convenient that can give accurate results even in presence of ammonium sulfate in the crude precipitates. Laminarin is a translucent substrate requiring the use of a stain to visualize the zones of hydrolysis in a plate assay. A very low-cost and locally available fluorescent optical fabric brightener Tinopal CBS-X has been used as a stain to detect the zones of hydrolysis. We also report simple methods to prepare colloidal chitin and cell free supernatant in this manuscript.
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Affiliation(s)
- Ananthamurthy Koteshwara
- Department of Pharmaceutical Biotechnology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Udupi, Karnataka, 576104, India
| | - Nancy V Philip
- Department of Pharmaceutical Biotechnology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Udupi, Karnataka, 576104, India
| | - Jesil Mathew Aranjani
- Department of Pharmaceutical Biotechnology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Udupi, Karnataka, 576104, India
| | - Raghu Chandrashekhar Hariharapura
- Department of Pharmaceutical Biotechnology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Udupi, Karnataka, 576104, India
| | - Subrahmanyam Volety Mallikarjuna
- Department of Pharmaceutical Biotechnology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Udupi, Karnataka, 576104, India.
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Dilution-to-Stimulation/Extinction Method: a Combination Enrichment Strategy To Develop a Minimal and Versatile Lignocellulolytic Bacterial Consortium. Appl Environ Microbiol 2021; 87:AEM.02427-20. [PMID: 33127812 PMCID: PMC7783344 DOI: 10.1128/aem.02427-20] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 10/22/2020] [Indexed: 12/13/2022] Open
Abstract
The significance of our study mainly lies in the development of a combined top-down enrichment strategy (i.e., dilution to stimulation coupled to dilution to extinction) to build a minimal and versatile lignocellulolytic microbial consortium. We demonstrated that mainly two selectively enriched bacterial species (Pseudomonas sp. and Paenibacillus sp.) are required to drive the effective degradation of plant polymers. Our findings can guide the design of a synthetic bacterial consortium that could improve saccharification (i.e., the release of sugars from agricultural plant residues) processes in biorefineries. In addition, they can help to expand our ecological understanding of plant biomass degradation in enriched bacterial systems. The engineering of complex communities can be a successful path to understand the ecology of microbial systems and improve biotechnological processes. Here, we developed a strategy to assemble a minimal and effective lignocellulolytic microbial consortium (MELMC) using a sequential combination of dilution-to-stimulation and dilution-to-extinction approaches. The consortium was retrieved from Andean forest soil and selected through incubation in liquid medium with a mixture of three types of agricultural plant residues. After the dilution-to-stimulation phase, approximately 50 bacterial sequence types, mostly belonging to the Sphingobacteriaceae, Enterobacteriaceae, Pseudomonadaceae, and Paenibacillaceae, were significantly enriched. The dilution-to-extinction method demonstrated that only eight of the bacterial sequence types were necessary to maintain microbial growth and plant biomass consumption. After subsequent stabilization, only two bacterial species (Pseudomonas sp. and Paenibacillus sp.) became highly abundant (>99%) within the MELMC, indicating that these are the key players in degradation. Differences in the composition of bacterial communities between biological replicates indicated that selection, sampling, and/or priority effects could shape the consortium structure. The MELMC can degrade up to ∼13% of corn stover, consuming mostly its (hemi)cellulosic fraction. Tests with chromogenic substrates showed that the MELMC secretes an array of endoenzymes able to degrade xylan, arabinoxylan, carboxymethyl cellulose, and wheat straw. Additionally, the metagenomic profile inferred from the phylogenetic composition along with an analysis of carbohydrate-active enzymes of 20 bacterial genomes support the potential of the MELMC to deconstruct plant polysaccharides. This capacity was mainly attributed to the presence of Paenibacillus sp. IMPORTANCE The significance of our study mainly lies in the development of a combined top-down enrichment strategy (i.e., dilution to stimulation coupled to dilution to extinction) to build a minimal and versatile lignocellulolytic microbial consortium. We demonstrated that mainly two selectively enriched bacterial species (Pseudomonas sp. and Paenibacillus sp.) are required to drive the effective degradation of plant polymers. Our findings can guide the design of a synthetic bacterial consortium that could improve saccharification (i.e., the release of sugars from agricultural plant residues) processes in biorefineries. In addition, they can help to expand our ecological understanding of plant biomass degradation in enriched bacterial systems.
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Karnaouri A, Zerva A, Christakopoulos P, Topakas E. Screening of Recombinant Lignocellulolytic Enzymes Through Rapid Plate Assays. Methods Mol Biol 2021; 2178:479-503. [PMID: 33128767 DOI: 10.1007/978-1-0716-0775-6_30] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In the search for novel biomass-degrading enzymes through mining microbial genomes, it is necessary to apply functional tests during high-throughput screenings, which are capable of detecting enzymatic activities directly by way of plate assay. Using the most efficient expression systems of Escherichia coli and Pichia pastoris, the production of a high amount of His-tagged recombinant proteins could be thrived, allowing the one-step isolation by affinity chromatography. Here, we describe simple and efficient assay techniques for the detection of various biomass-degrading enzymatic activities on agar plates, such as cellulolytic, hemicellulolytic, and ligninolytic activities and their isolation using immobilized-metal affinity chromatography.
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Affiliation(s)
- Anthi Karnaouri
- Industrial Biotechnology and Biocatalysis Group, Biotechnology Laboratory, Department of Synthesis and Development of Industrial Processes, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Anastasia Zerva
- Industrial Biotechnology and Biocatalysis Group, Biotechnology Laboratory, Department of Synthesis and Development of Industrial Processes, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Paul Christakopoulos
- Biochemical Process Engineering, Chemical Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, Luleå, Sweden
| | - Evangelos Topakas
- Industrial Biotechnology and Biocatalysis Group, Biotechnology Laboratory, Department of Synthesis and Development of Industrial Processes, School of Chemical Engineering, National Technical University of Athens, Athens, Greece.
- Biochemical Process Engineering, Chemical Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, Luleå, Sweden.
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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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Elhussiny NI, Khattab AENA, El-Refai HA, Mohamed SS, Shetaia YM, Amin HA. Biotransesterification capabilities of Mucorales whole-cell lipase isolates and mutants. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2020. [DOI: 10.1016/j.bcab.2020.101722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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21
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Oda Y, Asatsuma S, Nakasone H, Matsuoka K. Sucrose starvation induces the degradation of proteins in trans-Golgi network and secretory vesicle cluster in tobacco BY-2 cells. Biosci Biotechnol Biochem 2020; 84:1652-1666. [PMID: 32338160 DOI: 10.1080/09168451.2020.1756736] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 04/14/2020] [Indexed: 10/24/2022]
Abstract
Endomembrane transport system begins at the endoplasmic reticulum (ER), continues to the Golgi apparatus and subsequent compartment called trans-Golgi network (TGN). We found that SUT2, a tobacco sucrose-transporter ortholog and was localized in the TGN, decreased significantly under a sucrose-starvation condition. The tobacco SNARE protein SYP41, localized in the TGN and secretory vesicle cluster (SVC), also decreased under the starvation. Similarly, the SCAMP2-RFP fusion protein, which is localized in TGN, SVC, and plasma membrane (PM), was distributed solely in the PM under the starvation. Under the same starvation condition, protein secretion was not arrested but pectin deposition to cell wall was suppressed. These data indicated that the protein composition in TGN and existence of the SVC are regulated by sugar availability. Furthermore, our findings as well as the involvement of SVC in pectin secretion suggested that synthesis and transport of pectin are regulated by the level of extracellular sugars. ABBREVIATIONS ER: endoplasmic reticulum; GI-TGN: Golgi-released independent TGN; GFP: green fluorescent protein; mRFP: monomeric red fluorescent protein; P4H1.1: prolyl 4-hydroxylase 1.1; PM: plasma membrane; SCAMP2: secretory carrier membrane protein 2; SUT2: sucrose transporter 2; SVC: secretory vesicle cluster; SYP41: syntaxin of plant 41; TGN: trans-Golgi network; YFP: yellow fluorescent protein.
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Affiliation(s)
- Yamato Oda
- Department of Bioscience and Biotechnology, Graduate School of Bioenvironmental Sciences, Kyushu University , Fukuoka, Japan
| | - Satoru Asatsuma
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University , Fukuoka, Japan
- RIKEN Plant Science Center , Yokohama, Japan
| | - Hiroaki Nakasone
- Department of Bioscience and Biotechnology, Graduate School of Bioenvironmental Sciences, Kyushu University , Fukuoka, Japan
| | - Ken Matsuoka
- Department of Bioscience and Biotechnology, Graduate School of Bioenvironmental Sciences, Kyushu University , Fukuoka, Japan
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University , Fukuoka, Japan
- RIKEN Plant Science Center , Yokohama, Japan
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Irla M, Drejer EB, Brautaset T, Hakvåg S. Establishment of a functional system for recombinant production of secreted proteins at 50 °C in the thermophilic Bacillus methanolicus. Microb Cell Fact 2020; 19:151. [PMID: 32723337 PMCID: PMC7389648 DOI: 10.1186/s12934-020-01409-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 07/20/2020] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND The suitability of bacteria as microbial cell factories is dependent on several factors such as price of feedstock, product range, production yield and ease of downstream processing. The facultative methylotroph Bacillus methanolicus is gaining interest as a thermophilic cell factory for production of value-added products from methanol. The aim of this study was to expand the capabilities of B. methanolicus as a microbial cell factory by establishing a system for secretion of recombinant proteins. RESULTS Native and heterologous signal peptides were tested for secretion of α-amylases and proteases, and we have established the use of the thermostable superfolder green fluorescent protein (sfGFP) as a valuable reporter protein in B. methanolicus. We demonstrated functional production and secretion of recombinant proteases, α-amylases and sfGFP in B. methanolicus MGA3 at 50 °C and showed that the choice of signal peptide for optimal secretion efficiency varies between proteins. In addition, we showed that heterologous production and secretion of α-amylase from Geobacillus stearothermophilus enables B. methanolicus to grow in minimal medium with starch as the sole carbon source. An in silico signal peptide library consisting of 169 predicted peptides from B. methanolicus was generated and will be useful for future studies, but was not experimentally investigated any further here. CONCLUSION A functional system for recombinant production of secreted proteins at 50 °C has been established in the thermophilic B. methanolicus. In addition, an in silico signal peptide library has been generated, that together with the tools and knowledge presented in this work will be useful for further development of B. methanolicus as a host for recombinant protein production and secretion at 50 °C.
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Affiliation(s)
- Marta Irla
- Department of Biotechnology and Food Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Eivind B Drejer
- Department of Biotechnology and Food Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Trygve Brautaset
- Department of Biotechnology and Food Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Sigrid Hakvåg
- Department of Biotechnology and Food Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.
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Elhussiny NI, Khattab AENA, El-Refai HA, Mohamed SS, Shetaia YM, Amin HA. Assessment of waste frying oil transesterification capacities of local isolated Aspergilli species and mutants. MYCOSCIENCE 2020. [DOI: 10.1016/j.myc.2020.01.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Enzymes to unravel bioproducts architecture. Biotechnol Adv 2020; 41:107546. [PMID: 32275940 DOI: 10.1016/j.biotechadv.2020.107546] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 02/20/2020] [Accepted: 04/03/2020] [Indexed: 11/20/2022]
Abstract
Enzymes are essential and ubiquitous biocatalysts involved in various metabolic pathways and used in many industrial processes. Here, we reframe enzymes not just as biocatalysts transforming bioproducts but also as sensitive probes for exploring the structure and composition of complex bioproducts, like meat tissue, dairy products and plant materials, in both food and non-food bioprocesses. This review details the global strategy and presents the most recent investigations to prepare and use enzymes as relevant probes, with a focus on glycoside-hydrolases involved in plant deconstruction and proteases and lipases involved in food digestion. First, to expand the enzyme repertoire to fit bioproduct complexity, novel enzymes are mined from biodiversity and can be artificially engineered. Enzymes are further characterized by exploring sequence/structure/dynamics/function relationships together with the environmental factors influencing enzyme interactions with their substrates. Then, the most advanced experimental and theoretical approaches developed for exploring bioproducts at various scales (from nanometer to millimeter) using active and inactive enzymes as probes are illustrated. Overall, combining multimodal and multiscale approaches brings a better understanding of native-form or transformed bioproduct architecture and composition, and paves the way to mainstream the use of enzymes as probes.
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Keller MB, Felby C, Labate CA, Pellegrini VOA, Higasi P, Singh RK, Polikarpov I, Blossom BM. A simple enzymatic assay for the quantification of C1-specific cellulose oxidation by lytic polysaccharide monooxygenases. Biotechnol Lett 2020; 42:93-102. [PMID: 31745843 PMCID: PMC6940319 DOI: 10.1007/s10529-019-02760-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 11/08/2019] [Indexed: 11/24/2022]
Abstract
OBJECTIVE The development of an enzymatic assay for the specific quantification of the C1-oxidation product, i.e. gluconic acid of cellulose active lytic polysaccharide monooxygenases (LPMOs). RESULTS In combination with a β-glucosidase, the spectrophotometrical assay can reliably quantify the specific C1- oxidation product of LPMOs acting on cellulose. It is applicable for a pure cellulose model substrate as well as lignocellulosic biomass. The enzymatic assay compares well with the quantification performed by HPAEC-PAD. In addition, we show that simple boiling is not sufficient to inactivate LPMOs and we suggest to apply a metal chelator in addition to boiling or to drastically increase pH for proper inactivation. CONCLUSIONS We conclude that the versatility of this simple enzymatic assay makes it useful in a wide range of experiments in basic and applied LPMO research and without the need for expensive instrumentation, e.g. HPAEC-PAD.
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Affiliation(s)
- M B Keller
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Copenhagen, Denmark
| | - C Felby
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Copenhagen, Denmark
| | - C A Labate
- Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - V O A Pellegrini
- São Carlos Institute of Physics, University of São Paulo, São Carlos, Brazil
| | - P Higasi
- São Carlos Institute of Physics, University of São Paulo, São Carlos, Brazil
| | - R K Singh
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - I Polikarpov
- São Carlos Institute of Physics, University of São Paulo, São Carlos, Brazil
| | - B M Blossom
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Copenhagen, Denmark.
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Hannachi E, Bouratbine A, Mousli M. Enhancing the detection of Toxoplasma gondii via an anti-SAG1 scFv-alkaline phosphatase immunoconjugate. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2019; 23:e00360. [PMID: 31341791 PMCID: PMC6630058 DOI: 10.1016/j.btre.2019.e00360] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 06/29/2019] [Accepted: 06/30/2019] [Indexed: 12/11/2022]
Abstract
The purpose of this study was to implement a fluorometric method for enhancing the detection sensitivity of Toxoplasma gondii in biological fluids. To address this challenge, we designed and produced a recombinant immunoconjugate tool based on a single-chain antibody fragment anti-T. gondii SAG1 antigen (scFvSG15) genetically fused to the bacterial alkaline phosphatase (AP) using 4-methyl-umbelliferyl-phosphate as fluorogenic substrate. The anti-SAG1 scFv-AP conjugate was fully bifunctional and was used successfully in different assays including immunoblot, fluorometric ELISA and direct immunofluorescence. The fluorometric immunoassay afforded an extremely low detection limit (1 tachyzoite/well), which was in agreement with the real-time PCR control test. The immunofluorescence imaging has provided captivating visual evidence of T. gondii detection. These results strongly suggest that the recombinant anti-SAG1-AP conjugate generated here might serve as useful and highly sensitive immunoassay probe to direct detect T. gondii in a one-step procedure, opening up new perspectives for diagnosis of toxoplasmosis.
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Affiliation(s)
| | | | - Mohamed Mousli
- Laboratoire de Parasitologie Médicale, Biotechnologies et Biomolécules, LR11-IPT06, Institut Pasteur de Tunis, Université Tunis El-Manar, 13 Place Pasteur -BP74, 1002 Tunis-Belvédère, Tunisia
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da Costa RR, Hu H, Li H, Poulsen M. Symbiotic Plant Biomass Decomposition in Fungus-Growing Termites. INSECTS 2019; 10:E87. [PMID: 30925664 PMCID: PMC6523192 DOI: 10.3390/insects10040087] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 03/05/2019] [Accepted: 03/06/2019] [Indexed: 01/25/2023]
Abstract
Termites are among the most successful animal groups, accomplishing nutrient acquisition through long-term associations and enzyme provisioning from microbial symbionts. Fungus farming has evolved only once in a single termite sub-family: Macrotermitinae. This sub-family has become a dominant decomposer in the Old World; through enzymatic contributions from insects, fungi, and bacteria, managed in an intricate decomposition pathway, the termites obtain near-complete utilisation of essentially any plant substrate. Here we review recent insights into our understanding of the process of plant biomass decomposition in fungus-growing termites. To this end, we outline research avenues that we believe can help shed light on how evolution has shaped the optimisation of plant-biomass decomposition in this complex multipartite symbiosis.
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Affiliation(s)
- Rafael R da Costa
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen East, Denmark.
| | - Haofu Hu
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen East, Denmark.
| | - Hongjie Li
- Department of Bacteriology, University of Wisconsin⁻Madison, Madison, WI 53706, USA.
| | - Michael Poulsen
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen East, Denmark.
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Puentes-Téllez PE, Falcao Salles J. Construction of Effective Minimal Active Microbial Consortia for Lignocellulose Degradation. MICROBIAL ECOLOGY 2018; 76:419-429. [PMID: 29392382 PMCID: PMC6061470 DOI: 10.1007/s00248-017-1141-5] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 12/29/2017] [Indexed: 06/02/2023]
Abstract
Enriched microbial communities, obtained from environmental samples through selective processes, can effectively contribute to lignocellulose degradation. Unfortunately, fully controlled industrial degradation processes are difficult to reach given the intrinsically dynamic nature and complexity of the microbial communities, composed of a large number of culturable and unculturable species. The use of less complex but equally effective microbial consortia could improve their applications by allowing for more controlled industrial processes. Here, we combined ecological theory and enrichment principles to develop an effective lignocellulose-degrading minimal active microbial Consortia (MAMC). Following an enrichment of soil bacteria capable of degrading lignocellulose material from sugarcane origin, we applied a reductive-screening approach based on molecular phenotyping, identification, and metabolic characterization to obtain a selection of 18 lignocellulose-degrading strains representing four metabolic functional groups. We then generated 65 compositional replicates of MAMC containing five species each, which vary in the number of functional groups, metabolic potential, and degradation capacity. The characterization of the MAMC according to their degradation capacities and functional diversity measurements revealed that functional diversity positively correlated with the degradation of the most complex lignocellulosic fraction (lignin), indicating the importance of metabolic complementarity, whereas cellulose and hemicellulose degradation were either negatively or not affected by functional diversity. The screening method described here successfully led to the selection of effective MAMC, whose degradation potential reached up 96.5% of the degradation rates when all 18 species were present. A total of seven assembled synthetic communities were identified as the most effective MAMC. A consortium containing Stenotrophomonas maltophilia, Paenibacillus sp., Microbacterium sp., Chryseobacterium taiwanense, and Brevundimonas sp. was found to be the most effective degrading synthetic community.
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Affiliation(s)
- Pilar Eliana Puentes-Téllez
- Microbial Community Ecology, GELIFES - Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
- Department of Biology, Institute of Environmental Biology, Ecology and Biodiversity Group, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Joana Falcao Salles
- Microbial Community Ecology, GELIFES - Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.
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Daas MJA, Nijsse B, van de Weijer AHP, Groenendaal BWAJ, Janssen F, van der Oost J, van Kranenburg R. Engineering Geobacillus thermodenitrificans to introduce cellulolytic activity; expression of native and heterologous cellulase genes. BMC Biotechnol 2018; 18:42. [PMID: 29945583 PMCID: PMC6020330 DOI: 10.1186/s12896-018-0453-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 06/14/2018] [Indexed: 11/28/2022] Open
Abstract
Background Consolidated bioprocessing (CBP) is a cost-effective approach for the conversion of lignocellulosic biomass to biofuels and biochemicals. The enzymatic conversion of cellulose to glucose requires the synergistic action of three types of enzymes: exoglucanases, endoglucanases and β-glucosidases. The thermophilic, hemicellulolytic Geobacillus thermodenitrificans T12 was shown to harbor desired features for CBP, although it lacks the desired endo and exoglucanases required for the conversion of cellulose. Here, we report the expression of both endoglucanase and exoglucanase encoding genes by G. thermodenitrificans T12, in an initial attempt to express cellulolytic enzymes that complement the enzymatic machinery of this strain. Results A metagenome screen was performed on 73 G. thermodenitrificans strains using HMM profiles of all known CAZy families that contain endo and/or exoglucanases. Two putative endoglucanases, GE39 and GE40, belonging to glucoside hydrolase family 5 (GH5) were isolated and expressed in both E. coli and G. thermodenitrificans T12. Structure modeling of GE39 revealed a folding similar to a GH5 exo-1,3-β-glucanase from S. cerevisiae. However, we determined GE39 to be a β-xylosidase having pronounced activity towards p-nitrophenyl-β-d-xylopyranoside. Structure modelling of GE40 revealed its protein architecture to be similar to a GH5 endoglucanase from B. halodurans, and its endoglucanase activity was confirmed by enzymatic activity against 2-hydroxyethylcellulose, carboxymethylcellulose and barley β-glucan. Additionally, we introduced expression constructs into T12 containing Geobacillus sp. 70PC53 endoglucanase gene celA and both endoglucanase genes (M1 and M2) from Geobacillus sp. WSUCF1. Finally, we introduced expression constructs into T12 containing the C. thermocellum exoglucanases celK and celS genes and the endoglucanase celC gene. Conclusions We identified a novel G. thermodenitrificans β-xylosidase (GE39) and a novel endoglucanase (GE40) using a metagenome screen based on multiple HMM profiles. We successfully expressed both genes in E. coli and functionally expressed the GE40 endoglucanase in G. thermodenitrificans T12. Additionally, the heterologous production of active CelK, a C. thermocellum derived exoglucanase, and CelA, a Geobacillus derived endoglucanase, was demonstrated with strain T12. The native hemicellulolytic activity and the heterologous cellulolytic activity described in this research provide a good basis for the further development of G. thermodenitrificans T12 as a host for consolidated bioprocessing. Electronic supplementary material The online version of this article (10.1186/s12896-018-0453-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Martinus J A Daas
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708, WE, Wageningen, The Netherlands
| | - Bart Nijsse
- Laboratory of Systems and Synthetic Biology, Wageningen University, Stippeneng 4, 6708, WE, Wageningen, The Netherlands
| | | | - Bart W A J Groenendaal
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708, WE, Wageningen, The Netherlands
| | - Fons Janssen
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708, WE, Wageningen, The Netherlands
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708, WE, Wageningen, The Netherlands
| | - Richard van Kranenburg
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708, WE, Wageningen, The Netherlands. .,Corbion, Arkelsedijk 46, 4206, AC, Gorinchem, The Netherlands.
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Breslmayr E, Hanžek M, Hanrahan A, Leitner C, Kittl R, Šantek B, Oostenbrink C, Ludwig R. A fast and sensitive activity assay for lytic polysaccharide monooxygenase. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:79. [PMID: 29588664 PMCID: PMC5865291 DOI: 10.1186/s13068-018-1063-6] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 02/24/2018] [Indexed: 05/02/2023]
Abstract
BACKGROUND Lytic polysaccharide monooxygenases (LPMO) release a spectrum of cleavage products from their polymeric substrates cellulose, hemicellulose, or chitin. The correct identification and quantitation of these released products is the basis of MS/HPLC-based detection methods for LPMO activity. The duration, effort, and intricate analysis allow only specialized laboratories to measure LPMO activity in day-to-day work. A spectrophotometric assay will simplify the screening for LPMO in culture supernatants, help monitor recombinant LPMO expression and purification, and support enzyme characterization. RESULTS Based on a newly discovered peroxidase activity of LPMO, we propose a fast, robust, and sensitive spectrophotometric activity assay using 2,6-dimethoxyphenol (2,6-DMP) and H2O2. The fast enzymatic assay (300 s) consists of 1 mM 2,6-DMP as chromogenic substrate, 100 µM H2O2 as cosubstrate, and an adequate activity of LPMO in a suitable buffer. The high molar absorption coefficient of the formed product coerulignone (ε469 = 53,200 M-1 cm-1) makes the assay sensitive and allows reliable activity measurements of LPMO in concentrations of approx. 0.5-50 mg L-1. CONCLUSIONS The activity assay based on 2,6-DMP detects a novel peroxidase activity of LPMO. This activity can be accurately measured and used for enzyme screening, production, and purification, and can also be applied to study binding constants or thermal stability. However, the assay has to be used with care in crude extracts, because other enzymes such as laccase or peroxidase will interfere with the assay. We also want to stress that the peroxidase activity is a homogeneous reaction with soluble substrates and should not be correlated to heterogeneous LPMO activity on polymeric substrates.
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Affiliation(s)
- Erik Breslmayr
- Department of Food Science and Technology, Vienna Institute of Biotechnology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
- Department of Material Science and Process Engineering, Institute of Molecular Modeling and Simulation, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Marija Hanžek
- Department of Food Science and Technology, Vienna Institute of Biotechnology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
- Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Aoife Hanrahan
- Department of Food Science and Technology, Vienna Institute of Biotechnology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Christian Leitner
- Department of Food Science and Technology, Vienna Institute of Biotechnology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Roman Kittl
- Department of Food Science and Technology, Vienna Institute of Biotechnology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Božidar Šantek
- Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Chris Oostenbrink
- Department of Material Science and Process Engineering, Institute of Molecular Modeling and Simulation, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Roland Ludwig
- Department of Food Science and Technology, Vienna Institute of Biotechnology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
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Enzyme Activities at Different Stages of Plant Biomass Decomposition in Three Species of Fungus-Growing Termites. Appl Environ Microbiol 2018; 84:AEM.01815-17. [PMID: 29269491 PMCID: PMC5812949 DOI: 10.1128/aem.01815-17] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 12/07/2017] [Indexed: 11/20/2022] Open
Abstract
Fungus-growing termites rely on mutualistic fungi of the genus Termitomyces and gut microbes for plant biomass degradation. Due to a certain degree of symbiont complementarity, this tripartite symbiosis has evolved as a complex bioreactor, enabling decomposition of nearly any plant polymer, likely contributing to the success of the termites as one of the main plant decomposers in the Old World. In this study, we evaluated which plant polymers are decomposed and which enzymes are active during the decomposition process in two major genera of fungus-growing termites. We found a diversity of active enzymes at different stages of decomposition and a consistent decrease in plant components during the decomposition process. Furthermore, our findings are consistent with the hypothesis that termites transport enzymes from the older mature parts of the fungus comb through young worker guts to freshly inoculated plant substrate. However, preliminary fungal RNA sequencing (RNA-seq) analyses suggest that this likely transport is supplemented with enzymes produced in situ. Our findings support that the maintenance of an external fungus comb, inoculated with an optimal mixture of plant material, fungal spores, and enzymes, is likely the key to the extraordinarily efficient plant decomposition in fungus-growing termites. IMPORTANCE Fungus-growing termites have a substantial ecological footprint in the Old World (sub)tropics due to their ability to decompose dead plant material. Through the establishment of an elaborate plant biomass inoculation strategy and through fungal and bacterial enzyme contributions, this farming symbiosis has become an efficient and versatile aerobic bioreactor for plant substrate conversion. Since little is known about what enzymes are expressed and where they are active at different stages of the decomposition process, we used enzyme assays, transcriptomics, and plant content measurements to shed light on how this decomposition of plant substrate is so effectively accomplished.
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Schückel J, Kračun SK. Two-Dimensional High-Throughput Endo-Enzyme Screening Assays Based on Chromogenic Polysaccharide Hydrogel and Complex Biomass Substrates. Methods Mol Biol 2018; 1796:201-217. [PMID: 29856056 DOI: 10.1007/978-1-4939-7877-9_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
In this chapter, we present a two-dimensional approach for high-throughput screening of endo-cellulases as well as other endo-acting enzymes. The method is based on chromogenic substrates, produced either from purified or complex material, providing valuable information about enzyme activity toward its target as well as that same target in a context of complex natural material normally encountered in bioindustrial settings. The enzymes that can be tested using this assay can be from virtually any source: in purified form, directly from microbial cultures or even from raw materials, enabling study of the interplay between enzyme mixtures such as synergistic or inhibitory effects. By using the method of analysis described in this chapter, enzymes can be screened and evaluated quickly and information pertinent to both the inherent properties of the enzyme itself as well as predictions about its performance on complex biomass samples can be obtained.
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Díez-Buitrago B, Briz N, Liz-Marzán LM, Pavlov V. Biosensing strategies based on enzymatic reactions and nanoparticles. Analyst 2018; 143:1727-1734. [DOI: 10.1039/c7an02067h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Application of new nanomaterials to detection of enzymatic activities allows the development of new sensitive and selective bioanalytical assays based on enzymes for recognition and signal amplification.
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Affiliation(s)
| | - Nerea Briz
- Tecnalia
- 20009 Donostia-San Sebastián
- Spain
| | - Luis M. Liz-Marzán
- CIC BiomaGUNE
- 20014 Donostia-San Sebastián
- Spain
- Ikerbasque
- Basque Foundation for Science
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Knapp A, Ripphahn M, Volkenborn K, Skoczinski P, Jaeger KE. Activity-independent screening of secreted proteins using split GFP. J Biotechnol 2017; 258:110-116. [PMID: 28619616 DOI: 10.1016/j.jbiotec.2017.05.024] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 05/31/2017] [Accepted: 05/31/2017] [Indexed: 01/16/2023]
Abstract
The large-scale industrial production of proteins requires efficient secretion, as provided, for instance, by the Sec system of Gram-positive bacteria. Protein engineering approaches to optimize secretion often involve the screening of large libraries, e.g. comprising a target protein fused to many different signal peptides. Respective high-throughput screening methods are usually based on photometric or fluorimetric assays enabling fast and simple determination of enzymatic activities. Here, we report on an alternative method for quantification of secreted proteins based on the split GFP assay. We analyzed the secretion by Bacillus subtilis of a homologous lipase and a heterologous cutinase by determination of GFP fluorescence and enzyme activity assays. Furthermore, we identified from a signal peptide library a variant of the biotechnologically relevant B. subtilis protein swollenin EXLX1 with up to 5-fold increased secretion. Our results demonstrate that the split GFP assay can be used to monitor secretion of enzymatic and non-enzymatic proteins in B. subtilis in a high-throughput manner.
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Affiliation(s)
- Andreas Knapp
- Institute of Molecular Enzyme Technology, Heinrich -Heine -University Düsseldorf, Forschungszentrum Jülich, D-52426 Jülich, Germany
| | - Myriam Ripphahn
- Institute of Molecular Enzyme Technology, Heinrich -Heine -University Düsseldorf, Forschungszentrum Jülich, D-52426 Jülich, Germany
| | - Kristina Volkenborn
- Institute of Molecular Enzyme Technology, Heinrich -Heine -University Düsseldorf, Forschungszentrum Jülich, D-52426 Jülich, Germany
| | - Pia Skoczinski
- Institute of Molecular Enzyme Technology, Heinrich -Heine -University Düsseldorf, Forschungszentrum Jülich, D-52426 Jülich, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich -Heine -University Düsseldorf, Forschungszentrum Jülich, D-52426 Jülich, Germany; Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, D-52428 Jülich, Germany.
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Mravec J, Guo X, Hansen AR, Schückel J, Kračun SK, Mikkelsen MD, Mouille G, Johansen IE, Ulvskov P, Domozych DS, Willats WGT. Pea Border Cell Maturation and Release Involve Complex Cell Wall Structural Dynamics. PLANT PHYSIOLOGY 2017; 174:1051-1066. [PMID: 28400496 PMCID: PMC5462005 DOI: 10.1104/pp.16.00097] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 04/06/2017] [Indexed: 05/21/2023]
Abstract
The adhesion of plant cells is vital for support and protection of the plant body and is maintained by a variety of molecular associations between cell wall components. In some specialized cases, though, plant cells are programmed to detach, and root cap-derived border cells are examples of this. Border cells (in some species known as border-like cells) provide an expendable barrier between roots and the environment. Their maturation and release is an important but poorly characterized cell separation event. To gain a deeper insight into the complex cellular dynamics underlying this process, we undertook a systematic, detailed analysis of pea (Pisum sativum) root tip cell walls. Our study included immunocarbohydrate microarray profiling, monosaccharide composition determination, Fourier-transformed infrared microspectroscopy, quantitative reverse transcription-PCR of cell wall biosynthetic genes, analysis of hydrolytic activities, transmission electron microscopy, and immunolocalization of cell wall components. Using this integrated glycobiology approach, we identified multiple novel modes of cell wall structural and compositional rearrangement during root cap growth and the release of border cells. Our findings provide a new level of detail about border cell maturation and enable us to develop a model of the separation process. We propose that loss of adhesion by the dissolution of homogalacturonan in the middle lamellae is augmented by an active biophysical process of cell curvature driven by the polarized distribution of xyloglucan and extensin epitopes.
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Affiliation(s)
- Jozef Mravec
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg 1871, Denmark (J.M., X.G., A.R.H., J.S., S.K.K., M.D.M., I.E.J., P.U.);
- Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318 Institut National de la Recherche Agronomique/AgroParisTech, Saclay Plant Sciences, Institut National de la Recherche Agronomique Centre de Versailles, 78026 Versailles cedex, France (G.M.);
- Department of Biology and Skidmore Microscopy Imaging Center, Skidmore College, Saratoga Springs, New York 12866 (D.S.D.); and
- School of Agriculture, Food, and Rural Development, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom (W.G.T.W.)
| | - Xiaoyuan Guo
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg 1871, Denmark (J.M., X.G., A.R.H., J.S., S.K.K., M.D.M., I.E.J., P.U.)
- Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318 Institut National de la Recherche Agronomique/AgroParisTech, Saclay Plant Sciences, Institut National de la Recherche Agronomique Centre de Versailles, 78026 Versailles cedex, France (G.M.)
- Department of Biology and Skidmore Microscopy Imaging Center, Skidmore College, Saratoga Springs, New York 12866 (D.S.D.); and
- School of Agriculture, Food, and Rural Development, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom (W.G.T.W.)
| | - Aleksander Riise Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg 1871, Denmark (J.M., X.G., A.R.H., J.S., S.K.K., M.D.M., I.E.J., P.U.)
- Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318 Institut National de la Recherche Agronomique/AgroParisTech, Saclay Plant Sciences, Institut National de la Recherche Agronomique Centre de Versailles, 78026 Versailles cedex, France (G.M.)
- Department of Biology and Skidmore Microscopy Imaging Center, Skidmore College, Saratoga Springs, New York 12866 (D.S.D.); and
- School of Agriculture, Food, and Rural Development, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom (W.G.T.W.)
| | - Julia Schückel
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg 1871, Denmark (J.M., X.G., A.R.H., J.S., S.K.K., M.D.M., I.E.J., P.U.)
- Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318 Institut National de la Recherche Agronomique/AgroParisTech, Saclay Plant Sciences, Institut National de la Recherche Agronomique Centre de Versailles, 78026 Versailles cedex, France (G.M.)
- Department of Biology and Skidmore Microscopy Imaging Center, Skidmore College, Saratoga Springs, New York 12866 (D.S.D.); and
- School of Agriculture, Food, and Rural Development, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom (W.G.T.W.)
| | - Stjepan Krešimir Kračun
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg 1871, Denmark (J.M., X.G., A.R.H., J.S., S.K.K., M.D.M., I.E.J., P.U.)
- Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318 Institut National de la Recherche Agronomique/AgroParisTech, Saclay Plant Sciences, Institut National de la Recherche Agronomique Centre de Versailles, 78026 Versailles cedex, France (G.M.)
- Department of Biology and Skidmore Microscopy Imaging Center, Skidmore College, Saratoga Springs, New York 12866 (D.S.D.); and
- School of Agriculture, Food, and Rural Development, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom (W.G.T.W.)
| | - Maria Dalgaard Mikkelsen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg 1871, Denmark (J.M., X.G., A.R.H., J.S., S.K.K., M.D.M., I.E.J., P.U.)
- Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318 Institut National de la Recherche Agronomique/AgroParisTech, Saclay Plant Sciences, Institut National de la Recherche Agronomique Centre de Versailles, 78026 Versailles cedex, France (G.M.)
- Department of Biology and Skidmore Microscopy Imaging Center, Skidmore College, Saratoga Springs, New York 12866 (D.S.D.); and
- School of Agriculture, Food, and Rural Development, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom (W.G.T.W.)
| | - Grégory Mouille
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg 1871, Denmark (J.M., X.G., A.R.H., J.S., S.K.K., M.D.M., I.E.J., P.U.)
- Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318 Institut National de la Recherche Agronomique/AgroParisTech, Saclay Plant Sciences, Institut National de la Recherche Agronomique Centre de Versailles, 78026 Versailles cedex, France (G.M.)
- Department of Biology and Skidmore Microscopy Imaging Center, Skidmore College, Saratoga Springs, New York 12866 (D.S.D.); and
- School of Agriculture, Food, and Rural Development, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom (W.G.T.W.)
| | - Ida Elisabeth Johansen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg 1871, Denmark (J.M., X.G., A.R.H., J.S., S.K.K., M.D.M., I.E.J., P.U.)
- Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318 Institut National de la Recherche Agronomique/AgroParisTech, Saclay Plant Sciences, Institut National de la Recherche Agronomique Centre de Versailles, 78026 Versailles cedex, France (G.M.)
- Department of Biology and Skidmore Microscopy Imaging Center, Skidmore College, Saratoga Springs, New York 12866 (D.S.D.); and
- School of Agriculture, Food, and Rural Development, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom (W.G.T.W.)
| | - Peter Ulvskov
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg 1871, Denmark (J.M., X.G., A.R.H., J.S., S.K.K., M.D.M., I.E.J., P.U.)
- Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318 Institut National de la Recherche Agronomique/AgroParisTech, Saclay Plant Sciences, Institut National de la Recherche Agronomique Centre de Versailles, 78026 Versailles cedex, France (G.M.)
- Department of Biology and Skidmore Microscopy Imaging Center, Skidmore College, Saratoga Springs, New York 12866 (D.S.D.); and
- School of Agriculture, Food, and Rural Development, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom (W.G.T.W.)
| | - David S Domozych
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg 1871, Denmark (J.M., X.G., A.R.H., J.S., S.K.K., M.D.M., I.E.J., P.U.)
- Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318 Institut National de la Recherche Agronomique/AgroParisTech, Saclay Plant Sciences, Institut National de la Recherche Agronomique Centre de Versailles, 78026 Versailles cedex, France (G.M.)
- Department of Biology and Skidmore Microscopy Imaging Center, Skidmore College, Saratoga Springs, New York 12866 (D.S.D.); and
- School of Agriculture, Food, and Rural Development, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom (W.G.T.W.)
| | - William George Tycho Willats
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg 1871, Denmark (J.M., X.G., A.R.H., J.S., S.K.K., M.D.M., I.E.J., P.U.);
- Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318 Institut National de la Recherche Agronomique/AgroParisTech, Saclay Plant Sciences, Institut National de la Recherche Agronomique Centre de Versailles, 78026 Versailles cedex, France (G.M.);
- Department of Biology and Skidmore Microscopy Imaging Center, Skidmore College, Saratoga Springs, New York 12866 (D.S.D.); and
- School of Agriculture, Food, and Rural Development, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom (W.G.T.W.)
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Badino SF, Christensen SJ, Kari J, Windahl MS, Hvidt S, Borch K, Westh P. Exo-exo synergy between Cel6A and Cel7A fromHypocrea jecorina: Role of carbohydrate binding module and the endo-lytic character of the enzymes. Biotechnol Bioeng 2017; 114:1639-1647. [DOI: 10.1002/bit.26276] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 02/17/2017] [Accepted: 02/21/2017] [Indexed: 01/08/2023]
Affiliation(s)
- Silke F. Badino
- Research Unit for Functional Biomaterials; Department of Science and Environment; INM; Roskilde University; 1 Universitetsvej, Build. 28C, DK-4000 Roskilde Denmark
| | - Stefan J. Christensen
- Research Unit for Functional Biomaterials; Department of Science and Environment; INM; Roskilde University; 1 Universitetsvej, Build. 28C, DK-4000 Roskilde Denmark
| | - Jeppe Kari
- Research Unit for Functional Biomaterials; Department of Science and Environment; INM; Roskilde University; 1 Universitetsvej, Build. 28C, DK-4000 Roskilde Denmark
| | - Michael S. Windahl
- Research Unit for Functional Biomaterials; Department of Science and Environment; INM; Roskilde University; 1 Universitetsvej, Build. 28C, DK-4000 Roskilde Denmark
- Novozymes A/S; Bagsvaerd Denmark
| | - Søren Hvidt
- Research Unit for Functional Biomaterials; Department of Science and Environment; INM; Roskilde University; 1 Universitetsvej, Build. 28C, DK-4000 Roskilde Denmark
| | | | - Peter Westh
- Research Unit for Functional Biomaterials; Department of Science and Environment; INM; Roskilde University; 1 Universitetsvej, Build. 28C, DK-4000 Roskilde Denmark
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Vuong TV, Liu B, Sandgren M, Master ER. Microplate-Based Detection of Lytic Polysaccharide Monooxygenase Activity by Fluorescence-Labeling of Insoluble Oxidized Products. Biomacromolecules 2017; 18:610-616. [DOI: 10.1021/acs.biomac.6b01790] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Thu V. Vuong
- Department
of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
| | - Bing Liu
- Department
of Molecular Sciences, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
| | - Mats Sandgren
- Department
of Molecular Sciences, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
| | - Emma R. Master
- Department
of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
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DeCastro ME, Rodríguez-Belmonte E, González-Siso MI. Metagenomics of Thermophiles with a Focus on Discovery of Novel Thermozymes. Front Microbiol 2016; 7:1521. [PMID: 27729905 PMCID: PMC5037290 DOI: 10.3389/fmicb.2016.01521] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 09/12/2016] [Indexed: 11/24/2022] Open
Abstract
Microbial populations living in environments with temperatures above 50°C (thermophiles) have been widely studied, increasing our knowledge in the composition and function of these ecological communities. Since these populations express a broad number of heat-resistant enzymes (thermozymes), they also represent an important source for novel biocatalysts that can be potentially used in industrial processes. The integrated study of the whole-community DNA from an environment, known as metagenomics, coupled with the development of next generation sequencing (NGS) technologies, has allowed the generation of large amounts of data from thermophiles. In this review, we summarize the main approaches commonly utilized for assessing the taxonomic and functional diversity of thermophiles through metagenomics, including several bioinformatics tools and some metagenome-derived methods to isolate their thermozymes.
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Affiliation(s)
- María-Eugenia DeCastro
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía Celular e Molecular, Facultade de Ciencias, Universidade da Coruña A Coruña, Spain
| | - Esther Rodríguez-Belmonte
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía Celular e Molecular, Facultade de Ciencias, Universidade da Coruña A Coruña, Spain
| | - María-Isabel González-Siso
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía Celular e Molecular, Facultade de Ciencias, Universidade da Coruña A Coruña, Spain
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Schückel J, Kračun SK, Willats WGT. High-throughput Screening of Carbohydrate-degrading Enzymes Using Novel Insoluble Chromogenic Substrate Assay Kits. J Vis Exp 2016. [PMID: 27684747 PMCID: PMC5092035 DOI: 10.3791/54286] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Carbohydrates active enzymes (CAZymes) have multiple roles in vivo and are widely used for industrial processing in the biofuel, textile, detergent, paper and food industries. A deeper understanding of CAZymes is important from both fundamental biology and industrial standpoints. Vast numbers of CAZymes exist in nature (especially in microorganisms) and hundreds of thousands have been cataloged and described in the carbohydrate active enzyme database (CAZy). However, the rate of discovery of putative enzymes has outstripped our ability to biochemically characterize their activities. One reason for this is that advances in genome and transcriptome sequencing, together with associated bioinformatics tools allow for rapid identification of candidate CAZymes, but technology for determining an enzyme's biochemical characteristics has advanced more slowly. To address this technology gap, a novel high-throughput assay kit based on insoluble chromogenic substrates is described here. Two distinct substrate types were produced: Chromogenic Polymer Hydrogel (CPH) substrates (made from purified polysaccharides and proteins) and Insoluble Chromogenic Biomass (ICB) substrates (made from complex biomass materials). Both CPH and ICB substrates are provided in a 96-well high-throughput assay system. The CPH substrates can be made in four different colors, enabling them to be mixed together and thus increasing assay throughput. The protocol describes a 96-well plate assay and illustrates how this assay can be used for screening the activities of enzymes, enzyme cocktails, and broths.
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Affiliation(s)
- Julia Schückel
- Department for Plant and Environmental Sciences, University of Copenhagen;
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Characterization of three plant biomass-degrading microbial consortia by metagenomics- and metasecretomics-based approaches. Appl Microbiol Biotechnol 2016; 100:10463-10477. [PMID: 27418359 PMCID: PMC5119850 DOI: 10.1007/s00253-016-7713-3] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 06/16/2016] [Accepted: 06/27/2016] [Indexed: 02/01/2023]
Abstract
The selection of microbes by enrichment on plant biomass has been proposed as an efficient way to develop new strategies for lignocellulose saccharification. Here, we report an in-depth analysis of soil-derived microbial consortia that were trained to degrade once-used wheat straw (WS1-M), switchgrass (SG-M) and corn stover (CS-M) under aerobic and mesophilic conditions. Molecular fingerprintings, bacterial 16S ribosomal RNA (rRNA) gene amplicon sequencing and metagenomic analyses showed that the three microbial consortia were taxonomically distinct. Based on the taxonomic affiliation of protein-encoding sequences, members of the Bacteroidetes (e.g. Chryseobacterium, Weeksella, Flavobacterium and Sphingobacterium) were preferentially selected on WS1-M, whereas SG-M and CS-M favoured members of the Proteobacteria (e.g. Caulobacter, Brevundimonas, Stenotrophomonas and Xanthomonas). The highest degradation rates of lignin (~59 %) were observed with SG-M, whereas CS-M showed a high consumption of cellulose and hemicellulose. Analyses of the carbohydrate-active enzymes in the three microbial consortia showed the dominance of glycosyl hydrolases (e.g. of families GH3, GH43, GH13, GH10, GH29, GH28, GH16, GH4 and GH92). In addition, proteins of families AA6, AA10 and AA2 were detected. Analysis of secreted protein fractions (metasecretome) for each selected microbial consortium mainly showed the presence of enzymes able to degrade arabinan, arabinoxylan, xylan, β-glucan, galactomannan and rhamnogalacturonan. Notably, these metasecretomes contain enzymes that enable us to produce oligosaccharides directly from wheat straw, sugarcane bagasse and willow. Thus, the underlying microbial consortia constitute valuable resources for the production of enzyme cocktails for the efficient saccharification of plant biomass.
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Gunnoo M, Cazade PA, Galera-Prat A, Nash MA, Czjzek M, Cieplak M, Alvarez B, Aguilar M, Karpol A, Gaub H, Carrión-Vázquez M, Bayer EA, Thompson D. Nanoscale Engineering of Designer Cellulosomes. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2016; 28:5619-47. [PMID: 26748482 DOI: 10.1002/adma.201503948] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 10/01/2015] [Indexed: 05/27/2023]
Abstract
Biocatalysts showcase the upper limit obtainable for high-speed molecular processing and transformation. Efforts to engineer functionality in synthetic nanostructured materials are guided by the increasing knowledge of evolving architectures, which enable controlled molecular motion and precise molecular recognition. The cellulosome is a biological nanomachine, which, as a fundamental component of the plant-digestion machinery from bacterial cells, has a key potential role in the successful development of environmentally-friendly processes to produce biofuels and fine chemicals from the breakdown of biomass waste. Here, the progress toward so-called "designer cellulosomes", which provide an elegant alternative to enzyme cocktails for lignocellulose breakdown, is reviewed. Particular attention is paid to rational design via computational modeling coupled with nanoscale characterization and engineering tools. Remaining challenges and potential routes to industrial application are put forward.
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Affiliation(s)
- Melissabye Gunnoo
- Materials and Surface Science Institute and Department of Physics and Energy, University of Limerick, Limerick, Ireland
| | - Pierre-André Cazade
- Materials and Surface Science Institute and Department of Physics and Energy, University of Limerick, Limerick, Ireland
| | - Albert Galera-Prat
- Instituto Cajal, Consejo Superior de Investigaciones Cientificas (CSIC), IMDEA Nanociencias and CIBERNED, Madrid, Spain
| | - Michael A Nash
- Lehrstuhl für Angewandte Physik and Center for Nanoscience, Ludwig-Maximilians-University, 80799, Munich, Germany
| | - Mirjam Czjzek
- Sorbonne Universités, UPMC, Université Paris 06, and Centre National de la Recherche Scientifique, UMR 8227, Integrative Biology of Marine Models, Station Biologique, de Roscoff, CS 90074, F-29688, Roscoff cedex, Bretagne, France
| | - Marek Cieplak
- Laboratory of Biological Physics, Institute of Physics, Polish Academy of Sciences, Warsaw, Poland
| | - Beatriz Alvarez
- Biopolis S.L., Parc Científic de la Universitat de Valencia, Edificio 2, C/Catedrático Agustín Escardino 9, 46980, Paterna (Valencia), Spain
| | - Marina Aguilar
- Abengoa, S.A., Palmas Altas, Calle Energía Solar nº 1, 41014, Seville, Spain
| | - Alon Karpol
- Designer Energy Ltd., 2 Bergman St., Tamar Science Park, Rehovot, 7670504, Israel
| | - Hermann Gaub
- Lehrstuhl für Angewandte Physik and Center for Nanoscience, Ludwig-Maximilians-University, 80799, Munich, Germany
| | - Mariano Carrión-Vázquez
- Instituto Cajal, Consejo Superior de Investigaciones Cientificas (CSIC), IMDEA Nanociencias and CIBERNED, Madrid, Spain
| | - Edward A Bayer
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Damien Thompson
- Materials and Surface Science Institute and Department of Physics and Energy, University of Limerick, Limerick, Ireland
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Maruthamuthu M, Jiménez DJ, Stevens P, van Elsas JD. A multi-substrate approach for functional metagenomics-based screening for (hemi)cellulases in two wheat straw-degrading microbial consortia unveils novel thermoalkaliphilic enzymes. BMC Genomics 2016; 17:86. [PMID: 26822785 PMCID: PMC4730625 DOI: 10.1186/s12864-016-2404-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 01/18/2016] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Functional metagenomics is a promising strategy for the exploration of the biocatalytic potential of microbiomes in order to uncover novel enzymes for industrial processes (e.g. biorefining or bleaching pulp). Most current methodologies used to screen for enzymes involved in plant biomass degradation are based on the use of single substrates. Moreover, highly diverse environments are used as metagenomic sources. However, such methods suffer from low hit rates of positive clones and hence the discovery of novel enzymatic activities from metagenomes has been hampered. RESULTS Here, we constructed fosmid libraries from two wheat straw-degrading microbial consortia, denoted RWS (bred on untreated wheat straw) and TWS (bred on heat-treated wheat straw). Approximately 22,000 clones from each library were screened for (hemi)cellulose-degrading enzymes using a multi-chromogenic substrate approach. The screens yielded 71 positive clones for both libraries, giving hit rates of 1:440 and 1:1,047 for RWS and TWS, respectively. Seven clones (NT2-2, T5-5, NT18-17, T4-1, 10BT, NT18-21 and T17-2) were selected for sequence analyses. Their inserts revealed the presence of 18 genes encoding enzymes belonging to twelve different glycosyl hydrolase families (GH2, GH3, GH13, GH17, GH20, GH27, GH32, GH39, GH53, GH58, GH65 and GH109). These encompassed several carbohydrate-active gene clusters traceable mainly to Klebsiella related species. Detailed functional analyses showed that clone NT2-2 (containing a beta-galactosidase of ~116 kDa) had highest enzymatic activity at 55 °C and pH 9.0. Additionally, clone T5-5 (containing a beta-xylosidase of ~86 kDa) showed > 90% of enzymatic activity at 55 °C and pH 10.0. CONCLUSIONS This study employed a high-throughput method for rapid screening of fosmid metagenomic libraries for (hemi)cellulose-degrading enzymes. The approach, consisting of screens on multi-substrates coupled to further analyses, revealed high hit rates, as compared with recent other studies. Two clones, 10BT and T4-1, required the presence of multiple substrates for detectable activity, indicating a new avenue in library activity screening. Finally, clones NT2-2, T5-5 and NT18-17 were found to encode putative novel thermo-alkaline enzymes, which could represent a starting point for further biotechnological applications.
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Affiliation(s)
- Mukil Maruthamuthu
- Department of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747AG, Groningen, The Netherlands.
| | - Diego Javier Jiménez
- Department of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747AG, Groningen, The Netherlands.
| | - Patricia Stevens
- Department of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747AG, Groningen, The Netherlands.
| | - Jan Dirk van Elsas
- Department of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747AG, Groningen, The Netherlands.
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Fong M, Berrin JG, Paës G. Investigation of the binding properties of a multi-modular GH45 cellulase using bioinspired model assemblies. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:12. [PMID: 26788125 PMCID: PMC4717654 DOI: 10.1186/s13068-016-0428-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 01/05/2016] [Indexed: 05/09/2023]
Abstract
BACKGROUND Enzymes degrading plant biomass polymers are widely used in biotechnological applications. Their efficiency can be limited by non-specific interactions occurring with some chemical motifs. In particular, the lignin component is known to bind enzymes irreversibly. In order to determine interactions of enzymes with their substrates, experiments are usually performed on isolated simple polymers which are not representative of plant cell wall complexity. But when using natural plant substrates, the role of individual chemical and structural features affecting enzyme-binding properties is also difficult to decipher. RESULTS We have designed and used lignified model assemblies of plant cell walls as templates to characterize binding properties of multi-modular cellulases. These three-dimensional assemblies are modulated in their composition using the three principal polymers found in secondary plant cell walls (cellulose, hemicellulose, and lignin). Binding properties of enzymes are obtained from the measurement of their mobility that depends on their interactions with the polymers and chemical motifs of the assemblies. The affinity of the multi-modular GH45 cellulase was characterized using a statistical analysis to determine the role played by each assembly polymer. Presence of hemicellulose had much less impact on affinity than cellulose and model lignin. Depending on the number of CBMs appended to the cellulase catalytic core, binding properties toward cellulose and lignin were highly contrasted. CONCLUSIONS Model assemblies bring new insights into the molecular determinants that are responsible for interactions between enzymes and substrate without the need of complex analysis. Consequently, we believe that model bioinspired assemblies will provide relevant information for the design and optimization of enzyme cocktails in the context of biorefineries.
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Affiliation(s)
- Monica Fong
- />UMR0614, Fractionnement des AgroRessources et Environnement, INRA, 2 esplanade Roland-Garros, 51100 Reims, France
- />UMR0614, Fractionnement des AgroRessources et Environnement, University of Reims Champagne Ardenne, 2 esplanade Roland-Garros, 51100 Reims, France
| | - Jean-Guy Berrin
- />UMR1163, Biodiversité et Biotechnologie Fongiques, INRA, 13288 Marseille, France
- />UMR1163, Biodiversité et Biotechnologie Fongiques, Aix Marseille Université, 13288 Marseille, France
- />UMR1163, Biodiversité et Biotechnologie Fongiques, Polytech’Marseille, 13288 Marseille, France
| | - Gabriel Paës
- />UMR0614, Fractionnement des AgroRessources et Environnement, INRA, 2 esplanade Roland-Garros, 51100 Reims, France
- />UMR0614, Fractionnement des AgroRessources et Environnement, University of Reims Champagne Ardenne, 2 esplanade Roland-Garros, 51100 Reims, France
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Ferrer M, Martínez-Martínez M, Bargiela R, Streit WR, Golyshina OV, Golyshin PN. Estimating the success of enzyme bioprospecting through metagenomics: current status and future trends. Microb Biotechnol 2016; 9:22-34. [PMID: 26275154 PMCID: PMC4720405 DOI: 10.1111/1751-7915.12309] [Citation(s) in RCA: 127] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 06/26/2015] [Accepted: 07/02/2015] [Indexed: 12/01/2022] Open
Abstract
Recent reports have suggested that the establishment of industrially relevant enzyme collections from environmental genomes has become a routine procedure. Across the studies assessed, a mean number of approximately 44 active clones were obtained in an average size of approximately 53,000 clones tested using naïve screening protocols. This number could be significantly increased in shorter times when novel metagenome enzyme sequences obtained by direct sequencing are selected and subjected to high-throughput expression for subsequent production and characterization. The pre-screening of clone libraries by naïve screens followed by the pyrosequencing of the inserts allowed for a 106-fold increase in the success rate of identifying genes encoding enzymes of interest. However, a much longer time, usually on the order of years, is needed from the time of enzyme identification to the establishment of an industrial process. If the hit frequency for the identification of enzymes performing at high turnover rates under real application conditions could be increased while still covering a high natural diversity, the very expensive and time-consuming enzyme optimization phase would likely be significantly shortened. At this point, it is important to review the current knowledge about the success of fine-tuned naïve- and sequence-based screening protocols for enzyme selection and to describe the environments worldwide that have already been subjected to enzyme screen programmes through metagenomic tools. Here, we provide such estimations and suggest the current challenges and future actions needed before environmental enzymes can be successfully introduced into the market.
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Affiliation(s)
- Manuel Ferrer
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), Marie Curie 2, 28049, Madrid, Spain
| | - Mónica Martínez-Martínez
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), Marie Curie 2, 28049, Madrid, Spain
| | - Rafael Bargiela
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), Marie Curie 2, 28049, Madrid, Spain
| | - Wolfgang R Streit
- Biozentrum Klein Flottbek, Universität Hamburg, Ohnhorststraße 18, D-22609, Hamburg, Germany
| | - Olga V Golyshina
- School of Biological Sciences, Bangor University, LL57 2UW, Gwynedd, UK
| | - Peter N Golyshin
- School of Biological Sciences, Bangor University, LL57 2UW, Gwynedd, UK
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Lytic Polysaccharide Monooxygenases in Biomass Conversion. Trends Biotechnol 2015; 33:747-761. [DOI: 10.1016/j.tibtech.2015.09.006] [Citation(s) in RCA: 197] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 08/28/2015] [Accepted: 09/08/2015] [Indexed: 01/02/2023]
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White biotechnology: State of the art strategies for the development of biocatalysts for biorefining. Biotechnol Adv 2015; 33:1653-70. [PMID: 26303096 DOI: 10.1016/j.biotechadv.2015.08.004] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 07/31/2015] [Accepted: 08/17/2015] [Indexed: 12/31/2022]
Abstract
White biotechnology is a term that is now often used to describe the implementation of biotechnology in the industrial sphere. Biocatalysts (enzymes and microorganisms) are the key tools of white biotechnology, which is considered to be one of the key technological drivers for the growing bioeconomy. Biocatalysts are already present in sectors such as the chemical and agro-food industries, and are used to manufacture products as diverse as antibiotics, paper pulp, bread or advanced polymers. This review proposes an original and global overview of highly complementary fields of biotechnology at both enzyme and microorganism level. A certain number of state of the art approaches that are now being used to improve the industrial fitness of biocatalysts particularly focused on the biorefinery sector are presented. The first part deals with the technologies that underpin the development of industrial biocatalysts, notably the discovery of new enzymes and enzyme improvement using directed evolution techniques. The second part describes the toolbox available by the cell engineer to shape the metabolism of microorganisms. And finally the last part focuses on the 'omic' technologies that are vital for understanding and guide microbial engineering toward more efficient microbial biocatalysts. Altogether, these techniques and strategies will undoubtedly help to achieve the challenging task of developing consolidated bioprocessing (i.e. CBP) readily available for industrial purpose.
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