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Höhmann S, Briol TA, Ihle N, Frick O, Schmid A, Bühler B. Glycolate as alternative carbon source for Escherichia coli. J Biotechnol 2024; 381:76-85. [PMID: 38190849 DOI: 10.1016/j.jbiotec.2024.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 12/20/2023] [Accepted: 01/01/2024] [Indexed: 01/10/2024]
Abstract
The physiology of different Escherichia coli stains was analyzed for growth with glycolate as a potentially promising sustainable sole source of carbon and energy. Different E. coli strains showed large differences regarding lag phases after provision of glycolate. Whereas E. coli W showed fast adaptation, E. coli BW25113, JM101, and BL21 (DE3) needed extensive time for adaption (up to 30 generations) until the attainable µmax was reached, which, at 30 °C, amounted to 0.20-0.25 h-1 for all strains. The overexpression of genes encoding glycolate degradation did neither overcome the need for adaptation of E. coli BL21 (DE3) nor improve growth of E. coli W. Rather, high level expression of proteins involved in uptake and initial degradation steps had an adverse effect on growth. Overall, the results show a promising capacity of E. coli strains for growth on glycolate.
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Affiliation(s)
- Sonja Höhmann
- Department of Solar Materials, Helmholtz Centre for Environmental Research GmbH - UFZ, Leipzig, Germany; Department of Microbial Biotechnology, Helmholtz Centre for Environmental Research GmbH - UFZ, Leipzig, Germany
| | - Tim Arik Briol
- Department of Solar Materials, Helmholtz Centre for Environmental Research GmbH - UFZ, Leipzig, Germany; Department of Microbial Biotechnology, Helmholtz Centre for Environmental Research GmbH - UFZ, Leipzig, Germany
| | - Nadine Ihle
- Department of Solar Materials, Helmholtz Centre for Environmental Research GmbH - UFZ, Leipzig, Germany
| | - Oliver Frick
- Department of Solar Materials, Helmholtz Centre for Environmental Research GmbH - UFZ, Leipzig, Germany
| | - Andreas Schmid
- Department of Solar Materials, Helmholtz Centre for Environmental Research GmbH - UFZ, Leipzig, Germany
| | - Bruno Bühler
- Department of Solar Materials, Helmholtz Centre for Environmental Research GmbH - UFZ, Leipzig, Germany; Department of Microbial Biotechnology, Helmholtz Centre for Environmental Research GmbH - UFZ, Leipzig, Germany.
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2
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Farasati Far B, Isfahani AA, Nasiriyan E, Pourmolaei A, Mahmoudvand G, Karimi Rouzbahani A, Namiq Amin M, Naimi-Jamal MR. An Updated Review on Advances in Hydrogel-Based Nanoparticles for Liver Cancer Treatment. LIVERS 2023. [DOI: 10.3390/livers3020012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/29/2023] Open
Abstract
More than 90% of all liver malignancies are hepatocellular carcinomas (HCCs), for which chemotherapy and immunotherapy are the ideal therapeutic choices. Hepatocellular carcinoma is descended from other liver diseases, such as viral hepatitis, alcoholism, and metabolic syndrome. Normal cells and tissues may suffer damage from common forms of chemotherapy. In contrast to systemic chemotherapy, localized chemotherapy can reduce side effects by delivering a steady stream of chemotherapeutic drugs directly to the tumor site. This highlights the significance of controlled-release biodegradable hydrogels as drug delivery methods for chemotherapeutics. This review discusses using hydrogels as drug delivery systems for HCC and covers thermosensitive, pH-sensitive, photosensitive, dual-sensitive, and glutathione-responsive hydrogels. Compared to conventional systemic chemotherapy, hydrogel-based drug delivery methods are more effective in treating cancer.
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3
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Kamilari E, Stanton C, Reen FJ, Ross RP. Uncovering the Biotechnological Importance of Geotrichum candidum. Foods 2023; 12:foods12061124. [PMID: 36981051 PMCID: PMC10048088 DOI: 10.3390/foods12061124] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/24/2023] [Accepted: 03/02/2023] [Indexed: 03/30/2023] Open
Abstract
Fungi make a fundamental contribution to several biotechnological processes, including brewing, winemaking, and the production of enzymes, organic acids, alcohols, antibiotics, and pharmaceuticals. The present review explores the biotechnological importance of the filamentous yeast-like fungus Geotrichum candidum, a ubiquitous species known for its use as a starter in the dairy industry. To uncover G. candidum's biotechnological role, we performed a search for related work through the scientific indexing internet services, Web of Science and Google Scholar. The following query was used: Geotrichum candidum, producing about 6500 scientific papers from 2017 to 2022. From these, approximately 150 that were associated with industrial applications of G. candidum were selected. Our analysis revealed that apart from its role as a starter in the dairy and brewing industries, this species has been administered as a probiotic nutritional supplement in fish, indicating improvements in developmental and immunological parameters. Strains of this species produce a plethora of biotechnologically important enzymes, including cellulases, β-glucanases, xylanases, lipases, proteases, and α-amylases. Moreover, strains that produce antimicrobial compounds and that are capable of bioremediation were identified. The findings of the present review demonstrate the importance of G. candidum for agrifood- and bio-industries and provide further insights into its potential future biotechnological roles.
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Affiliation(s)
- Eleni Kamilari
- APC Microbiome Ireland, University College Cork, T12 YT20 Cork, Ireland
- School of Microbiology, University College Cork, T12 YT20 Cork, Ireland
| | - Catherine Stanton
- APC Microbiome Ireland, University College Cork, T12 YT20 Cork, Ireland
- School of Microbiology, University College Cork, T12 YT20 Cork, Ireland
- Department of Biosciences, Teagasc Food Research Centre, Moorepark, Fermoy, P61 C996 Co. Cork, Ireland
| | - F Jerry Reen
- School of Microbiology, University College Cork, T12 YT20 Cork, Ireland
- Synthesis and Solid State Pharmaceutical Centre, University College Cork, T12 YT20 Cork, Ireland
| | - R Paul Ross
- APC Microbiome Ireland, University College Cork, T12 YT20 Cork, Ireland
- School of Microbiology, University College Cork, T12 YT20 Cork, Ireland
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4
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Saleh HM, Hassan AI. Use of heterogeneous catalysis in sustainable biofuel production. PHYSICAL SCIENCES REVIEWS 2022. [DOI: 10.1515/psr-2022-0041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Biofuel is a sustainable energy source that may use to replace fossil-based carbon dioxide and mitigate the adverse effects of exhaust emissions. Nowadays, we need to replace petroleum fuels with alternatives from environmentally sustainable sources of increasing importance. Biofuels derived from biomass have gained considerable attention, and thus most of the traditional methods that harm the environment and humans have retreated. Developing an active and stable heterogeneous catalyst is a step of utmost importance in the renewable liquid fuel technology. Thus, there is a great interest in developing methods for producing liquid fuels from non-edible sources. It may also be from dry plant tissues such as agricultural waste. Lignocellulosic biomass can be a sustainable source for producing renewable fuels and chemicals, as well as the replacement of petroleum products. Hence, the researchers aspired to synthesize new catalysts using a cheap technology developed to hydrolyze cellulose and then produce bioethanol without needing expensive enzymes, which may ultimately lead to a lower fuel price. In this paper, we will focus on the recent technologies used to produce sustainable biofuels through inexpensive incentives and innocuous to the environment.
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Affiliation(s)
- Hosam M. Saleh
- Radioisotope Department , Nuclear Research Center, Egyptian Atomic Energy Authority , Cairo , Egypt
| | - Amal I. Hassan
- Radioisotope Department , Nuclear Research Center, Egyptian Atomic Energy Authority , Cairo , Egypt
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5
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Panahabadi R, Ahmadikhah A, McKee LS, Ingvarsson PK, Farrokhi N. Genome-wide association study for lignocellulosic compounds and fermentable sugar in rice straw. THE PLANT GENOME 2022; 15:e20174. [PMID: 34806838 DOI: 10.1002/tpg2.20174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 10/06/2021] [Indexed: 06/13/2023]
Abstract
Cellulose and lignin are the two main components of secondary plant cell walls with substantial impact on stalk in the field and on straw during industrial processing. The amount of fermentable sugar that can be accessed is another important parameter affecting various industrial applications. In the present study, genetic variability of rice (Oryza sativa L.) genotypes for cellulose, lignin, and fermentable sugars contents was analyzed in rice straw. A genome-wide association study of 33,484 single nucleotide polymorphisms (SNPs) with a minor allele frequency (MAF) >0.05 was performed. The genome-wide association study identified seven, three, and three genomic regions to be significantly associated with cellulose, lignin, and fermentable sugar contents, respectively. Candidate genes in the associated genomic regions were enzymes mainly involved in cell wall metabolism. Novel SNP markers associated with cellulose were tagged to GH16, peroxidase, GT6, GT8, and CSLD2. For lignin content, Villin protein, OsWAK1/50/52/53, and GH16 were identified. For fermentable sugar content, UTP-glucose-1-phosphate uridylyltransferase, BRASSINOSTEROID INSENSITIVE 1, and receptor-like protein kinase 5 were found. The results of this study should improve our understanding of the genetic basis of the factors that might be involved in biosynthesis, turnover, and modification of major cell wall components and saccharides in rice straw.
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Affiliation(s)
- Rahele Panahabadi
- Faculty of Life Sciences and Biotechnology, Shahid Beheshti Univ., Tehran, Iran
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, Stockholm, 106 91, Sweden
| | | | - Lauren S McKee
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, Stockholm, 106 91, Sweden
- Wallenberg Wood Science Centre, Teknikringen 56-58, Stockholm, 100 44, Sweden
| | - Pär K Ingvarsson
- Linnean Centre for Plant Biology, Dep. of Plant Biology, Swedish Univ. of Agricultural Sciences, Uppsala, Sweden
| | - Naser Farrokhi
- Faculty of Life Sciences and Biotechnology, Shahid Beheshti Univ., Tehran, Iran
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Mahanty A, Giri S, Kar A, Ghosh S. Biocatalytic pretreatment of rice straw by ligninolytic enzymes produced by newly isolated <i>Micrococcus unnanensis</i> strain B4 for downstream cellulolytic saccharification. J GEN APPL MICROBIOL 2022; 68:184-192. [DOI: 10.2323/jgam.2022.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Ayan Mahanty
- Department of Biotechnology, University of North Bengal
| | | | - Akas Kar
- Department of Biotechnology, University of North Bengal
| | - Shilpi Ghosh
- Department of Biotechnology, University of North Bengal
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8
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Identifying metabolic pathway intermediates that modulate the gallate dioxygenase (DesB) from Sphingobium sp. strain SYK-6. Process Biochem 2021. [DOI: 10.1016/j.procbio.2021.01.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Abou-Elyazed AS, Sun Y, El-Nahas AM, Yousif AM. A green approach for enhancing the hydrophobicity of UiO-66(Zr) catalysts for biodiesel production at 298 K. RSC Adv 2020; 10:41283-41295. [PMID: 35516530 PMCID: PMC9057805 DOI: 10.1039/d0ra08217a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 10/28/2020] [Indexed: 12/04/2022] Open
Abstract
Recently, the incorporation of hydrophobicity on the surface of UiO-66(Zr) has received much attention due to the deactivation of hydrophilic active sites of UiO-66(Zr) upon water adsorption. In this work, we report UiO-66(Zr) catalysts with an assortment of surface hydrophobicities fabricated by the solvent-free method to elucidate the impact of the environment framing Lewis acid sites on their catalytic activity in the production of fatty acid methyl ester (biodiesel) via the esterification of fatty acids at room temperature with high selectivity (100%) and good recyclability. A detailed structural analysis of the materials by N2 sorption, FT-IR, SEM, XRD, water contact angle measurement, dynamic liquid scattering (DLS), NMR and TGA revealed the fabrication of stearic acid-grafted UiO-66(Zr) catalysts (10SA/UiO-66) with fine particle size and a highly hydrophobic network. 10SA/UiO-66(Zr) with enhanced hydrophobicity exhibited superior catalytic performance in the esterification of a fatty acid with a long alkyl chain compared with conventional solid acid catalysts and even liquid acid catalysts. Detailed kinetic studies corroborated that the adsorption of lipophilic acids at the Lewis acid sites besides the enhancement of wettability between the reactants was facilitated by the hydrophobic environment, thus significantly motivating the esterification reaction at room temperature. Furthermore, 10SA/UiO-66(Zr) showed good catalytic activity in the esterification of oleic acid in the presence of water (∼10% in the light of acid weight). Recently, the incorporation of hydrophobicity on the surface of UiO-66(Zr) has received much attention due to the deactivation of hydrophilic active sites of UiO-66(Zr) upon water adsorption.![]()
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Affiliation(s)
- Ahmed S Abou-Elyazed
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology Harbin 150001 China +86-45186413708.,Chemistry Department, Faculty of Science, Menoufia University Shebin El-Kom Egypt +20 1064607974
| | - Yinyong Sun
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology Harbin 150001 China +86-45186413708
| | - Ahmed M El-Nahas
- Chemistry Department, Faculty of Science, Menoufia University Shebin El-Kom Egypt +20 1064607974
| | - Ahmed M Yousif
- Chemistry Department, Faculty of Science, Menoufia University Shebin El-Kom Egypt +20 1064607974.,Chemistry Department, College of Science and Arts, Jouf University Alqurayyat Kingdom of Saudi Arabia
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10
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Ndukwe IE, Black I, Heiss C, Azadi P. Evaluating the Utility of Permethylated Polysaccharide Solution NMR Data for Characterization of Insoluble Plant Cell Wall Polysaccharides. Anal Chem 2020; 92:13221-13228. [PMID: 32794693 DOI: 10.1021/acs.analchem.0c02379] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Plant cell wall polysaccharide analysis encompasses the utilization of a variety of analytical tools, including gas and liquid chromatography, mass spectrometry (MS), and nuclear magnetic resonance (NMR) spectroscopy. These methods provide complementary data, which enable confident structural proposals of the many complex polysaccharide structures that exist in the complex matrices of plant cell walls. However, cell walls contain fractions of varying solubilities, and a few techniques are available that can analyze all fractions simultaneously. We have discovered that permethylation affords the complete dissolution of both soluble and insoluble polysaccharide fractions of plant cell walls in organic solvents such as chloroform or acetonitrile, which can then be analyzed by a number of analytical techniques including MS and NMR. In this work, NMR structure analysis of 10 permethylated polysaccharide standards was undertaken to generate chemical shift data providing insights into spectral changes that result from permethylation of polysaccharide residues. This information is of especial relevance to the structure analysis of insoluble polysaccharide materials that otherwise are not easily investigated by solution-state NMR methodologies. The preassigned NMR chemical shift data is shown to be vital for NMR structure analysis of minor polysaccharide components of plant cell walls that are particularly difficult to assign by NMR correlation data alone. With the assigned chemical shift data, we analyzed the permethylated samples of destarched, alcohol-insoluble residues of switchgrass and poplar by two-dimensional NMR spectral profiling. Thus, we identified, in addition to the major polysaccharide components, two minor polysaccharides, namely, <5% 3-linked arabinoxylan (switchgrass) and <2% glucomannan (poplar). In particular, the position of the arabinose residue in the arabinoxylan of the switchgrass sample was confidently assigned based on chemical shift values, which are highly sensitive to local chemical environments. Furthermore, the high resolution afforded by the 1H NMR spectra of the permethylated switchgrass and poplar samples allowed facile relative quantitative analysis of their polysaccharide composition, utilizing only a few milligrams of the cell wall material. The concepts herein developed will thus facilitate NMR structure analysis of insoluble plant cell wall polysaccharides, more so of minor cell wall components that are especially challenging to analyze with current methods.
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Affiliation(s)
- Ikenna E Ndukwe
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, Georgia 30602, United States
| | - Ian Black
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, Georgia 30602, United States
| | - Christian Heiss
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, Georgia 30602, United States
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, Georgia 30602, United States
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Antonopoulou G, Alexandropoulou M, Ntaikou I, Lyberatos G. From waste to fuel: Energy recovery from household food waste via its bioconversion to energy carriers based on microbiological processes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 732:139230. [PMID: 32438165 DOI: 10.1016/j.scitotenv.2020.139230] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 04/23/2020] [Accepted: 05/03/2020] [Indexed: 06/11/2023]
Abstract
In the present study the bioconversion of dried household food waste (FORBI) to energy carriers was investigated aiming to its sustainable management and valorization. FORBI was either directly fermented towards ethanol and hydrogen or was previously subjected to extraction with water resulting to a liquid fraction (extract) rich in sugars and a solid residue, which were then fermented separately. Subsequently, the effluents were assessed as substrates for methane production via anaerobic digestion (AD). Mono-cultures and co-cultures of C5 and C6 yeasts were used for the alcoholic fermentation whereas for the production of hydrogen, mixed acidogenic consortia were used. Taking into account the optimum yields of biofuels, the amount of recoverable energy was estimated based for each different approach. The maximum ethanol yield was 0.16 g ethanol per kg of FORBI and it was achieved for separate fermentation of liquid and solid fractions of the waste. The highest hydrogen yield that was observed was 210.44 L ± 4.02 H2/kg TS FORBI for 1% solids loading and supplementation with cellulolytic enzymes. Direct AD of either the whole FORBI or its individual fractions led to lower overall energy recovery, compared to that obtained when fermentation and subsequent AD were applied. The recoverable energy was estimated for the different exploitation approaches of the waste. The maximum achieved recoverable energy was 21.49 ± 0.57 MJ/kg.
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Affiliation(s)
- Georgia Antonopoulou
- School of Chemical Engineering, National Technical University of Athens, Zografou Campus, GR 15780 Athens, Greece; Institute of Chemical Engineering Sciences, Foundation for Research and Technology, GR 26504 Patras, Greece
| | - Maria Alexandropoulou
- School of Chemical Engineering, National Technical University of Athens, Zografou Campus, GR 15780 Athens, Greece; Institute of Chemical Engineering Sciences, Foundation for Research and Technology, GR 26504 Patras, Greece
| | - Ioanna Ntaikou
- School of Chemical Engineering, National Technical University of Athens, Zografou Campus, GR 15780 Athens, Greece; Institute of Chemical Engineering Sciences, Foundation for Research and Technology, GR 26504 Patras, Greece.
| | - Gerasimos Lyberatos
- School of Chemical Engineering, National Technical University of Athens, Zografou Campus, GR 15780 Athens, Greece; Institute of Chemical Engineering Sciences, Foundation for Research and Technology, GR 26504 Patras, Greece
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12
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Marcotuli I, Colasuonno P, Hsieh YSY, Fincher GB, Gadaleta A. Non-Starch Polysaccharides in Durum Wheat: A Review. Int J Mol Sci 2020; 21:ijms21082933. [PMID: 32331292 PMCID: PMC7215680 DOI: 10.3390/ijms21082933] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/16/2020] [Accepted: 04/17/2020] [Indexed: 02/06/2023] Open
Abstract
Durum wheat is one of most important cereal crops that serves as a staple dietary component for humans and domestic animals. It provides antioxidants, proteins, minerals and dietary fibre, which have beneficial properties for humans, especially as related to the health of gut microbiota. Dietary fibre is defined as carbohydrate polymers that are non-digestible in the small intestine. However, this dietary component can be digested by microorganisms in the large intestine and imparts physiological benefits at daily intake levels of 30–35 g. Dietary fibre in cereal grains largely comprises cell wall polymers and includes insoluble (cellulose, part of the hemicellulose component and lignin) and soluble (arabinoxylans and (1,3;1,4)-β-glucans) fibre. More specifically, certain components provide immunomodulatory and cholesterol lowering activity, faecal bulking effects, enhanced absorption of certain minerals, prebiotic effects and, through these effects, reduce the risk of type II diabetes, cardiovascular disease and colorectal cancer. Thus, dietary fibre is attracting increasing interest from cereal processors, producers and consumers. Compared with other components of the durum wheat grain, fibre components have not been studied extensively. Here, we have summarised the current status of knowledge on the genetic control of arabinoxylan and (1,3;1,4)-β-glucan synthesis and accumulation in durum wheat grain. Indeed, the recent results obtained in durum wheat open the way for the improvement of these important cereal quality parameters.
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Affiliation(s)
- Ilaria Marcotuli
- Department of Agricultural and Environmental Science, University of Bari ‘Aldo Moro’, Via G. Amendola 165/A, 70126 Bari, Italy;
- Correspondence: (I.M.); (A.G.)
| | - Pasqualina Colasuonno
- Department of Agricultural and Environmental Science, University of Bari ‘Aldo Moro’, Via G. Amendola 165/A, 70126 Bari, Italy;
| | - Yves S. Y. Hsieh
- Division of Glycoscience, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology (KTH), SE106 91 Stockholm, Sweden;
| | - Geoffrey B. Fincher
- ARC Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA 5064, Australia;
| | - Agata Gadaleta
- Department of Agricultural and Environmental Science, University of Bari ‘Aldo Moro’, Via G. Amendola 165/A, 70126 Bari, Italy;
- Correspondence: (I.M.); (A.G.)
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Kao MR, Kuo HW, Lee CC, Huang KY, Huang TY, Li CW, Chen CW, Wang AHJ, Yu SM, Ho THD. Chaetomella raphigera β-glucosidase D2-BGL has intriguing structural features and a high substrate affinity that renders it an efficient cellulase supplement for lignocellulosic biomass hydrolysis. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:258. [PMID: 31700541 PMCID: PMC6825360 DOI: 10.1186/s13068-019-1599-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 10/22/2019] [Indexed: 05/17/2023]
Abstract
BACKGROUND To produce second-generation biofuels, enzymatic catalysis is required to convert cellulose from lignocellulosic biomass into fermentable sugars. β-Glucosidases finalize the process by hydrolyzing cellobiose into glucose, so the efficiency of cellulose hydrolysis largely depends on the quantity and quality of these enzymes used during saccharification. Accordingly, to reduce biofuel production costs, new microbial strains are needed that can produce highly efficient enzymes on a large scale. RESULTS We heterologously expressed the fungal β-glucosidase D2-BGL from a Taiwanese indigenous fungus Chaetomella raphigera in Pichia pastoris for constitutive production by fermentation. Recombinant D2-BGL presented significantly higher substrate affinity than the commercial β-glucosidase Novozyme 188 (N188; K m = 0.2 vs 2.14 mM for p-nitrophenyl β-d-glucopyranoside and 0.96 vs 2.38 mM for cellobiose). When combined with RUT-C30 cellulases, it hydrolyzed acid-pretreated lignocellulosic biomasses more efficiently than the commercial cellulase mixture CTec3. The extent of conversion from cellulose to glucose was 83% for sugarcane bagasse and 63% for rice straws. Compared to N188, use of D2-BGL halved the time necessary to produce maximal levels of ethanol by a semi-simultaneous saccharification and fermentation process. We upscaled production of recombinant D2-BGL to 33.6 U/mL within 15 days using a 1-ton bioreactor. Crystal structure analysis revealed that D2-BGL belongs to glycoside hydrolase (GH) family 3. Removing the N-glycosylation N68 or O-glycosylation T431 residues by site-directed mutagenesis negatively affected enzyme production in P. pastoris. The F256 substrate-binding residue in D2-BGL is located in a shorter loop surrounding the active site pocket relative to that of Aspergillus β-glucosidases, and this short loop is responsible for its high substrate affinity toward cellobiose. CONCLUSIONS D2-BGL is an efficient supplement for lignocellulosic biomass saccharification, and we upscaled production of this enzyme using a 1-ton bioreactor. Enzyme production could be further improved using optimized fermentation, which could reduce biofuel production costs. Our structure analysis of D2-BGL offers new insights into GH3 β-glucosidases, which will be useful for strain improvements via a structure-based mutagenesis approach.
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Affiliation(s)
- Mu-Rong Kao
- Molecular and Cell Biology, Taiwan International Graduate Program, Academia Sinica and National Defense Medical Center, Taipei, Taiwan, ROC
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, ROC
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan, ROC
| | - Hsion-Wen Kuo
- Department of Environmental Science and Engineering, Tunghai University, Taichung, Taiwan, ROC
| | - Cheng-Chung Lee
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan, ROC
| | - Kuan-Ying Huang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan, ROC
| | - Ting-Yen Huang
- Department of Bioengineering, Tatung University, Taipei, Taiwan, ROC
| | - Chen-Wei Li
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan, ROC
| | - C. Will Chen
- Department of Bioengineering, Tatung University, Taipei, Taiwan, ROC
| | | | - Su-May Yu
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, ROC
- Biotechnology Center, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Tuan-Hua David Ho
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan, ROC
- Biotechnology Center, National Chung Hsing University, Taichung, Taiwan, ROC
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Midorikawa GEO, Correa CL, Noronha EF, Filho EXF, Togawa RC, Costa MMDC, Silva-Junior OB, Grynberg P, Miller RNG. Analysis of the Transcriptome in Aspergillus tamarii During Enzymatic Degradation of Sugarcane Bagasse. Front Bioeng Biotechnol 2018; 6:123. [PMID: 30280097 PMCID: PMC6153317 DOI: 10.3389/fbioe.2018.00123] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 08/20/2018] [Indexed: 11/13/2022] Open
Abstract
The production of bioethanol from non-food agricultural residues represents an alternative energy source to fossil fuels for incorporation into the world's economy. Within the context of bioconversion of plant biomass into renewable energy using improved enzymatic cocktails, Illumina RNA-seq transcriptome profiling was conducted on a strain of Aspergillus tamarii, efficient in biomass polysaccharide degradation, in order to identify genes encoding proteins involved in plant biomass saccharification. Enzyme production and gene expression was compared following growth in liquid and semi-solid culture with steam-exploded sugarcane bagasse (SB) (1% w/v) and glucose (1% w/v) employed as contrasting sole carbon sources. Enzyme production following growth in liquid minimum medium supplemented with SB resulted in 0.626 and 0.711 UI.mL-1 xylanases after 24 and 48 h incubation, respectively. Transcriptome profiling revealed expression of over 7120 genes, with groups of genes modulated according to solid or semi-solid culture, as well as according to carbon source. Gene ontology analysis of genes expressed following SB hydrolysis revealed enrichment in xyloglucan metabolic process and xylan, pectin and glucan catabolic process, indicating up-regulation of genes involved in xylanase secretion. According to carbohydrate-active enzyme (CAZy) classification, 209 CAZyme-encoding genes were identified with significant differential expression on liquid or semi-solid SB, in comparison to equivalent growth on glucose as carbon source. Up-regulated CAZyme-encoding genes related to cellulases (CelA, CelB, CelC, CelD) and hemicellulases (XynG1, XynG2, XynF1, XylA, AxeA, arabinofuranosidase) showed up to a 10-fold log2FoldChange in expression levels. Five genes from the AA9 (GH61) family, related to lytic polysaccharide monooxygenase (LPMO), were also identified with significant expression up-regulation. The transcription factor gene XlnR, involved in induction of hemicellulases, showed up-regulation on liquid and semi-solid SB culture. Similarly, the gene ClrA, responsible for regulation of cellulases, showed increased expression on liquid SB culture. Over 150 potential transporter genes were also identified with increased expression on liquid and semi-solid SB culture. This first comprehensive analysis of the transcriptome of A. tamarii contributes to our understanding of genes and regulatory systems involved in cellulose and hemicellulose degradation in this fungus, offering potential for application in improved enzymatic cocktail development for plant biomass degradation in biorefinery applications.
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Affiliation(s)
| | - Camila Louly Correa
- Departamento de Biologia Celular, Universidade de Brasília, Brasília, Brazil
| | | | | | - Roberto Coiti Togawa
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, Brasília, Brazil
| | | | | | - Priscila Grynberg
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, Brasília, Brazil
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Raghavendran V, Nitsos C, Matsakas L, Rova U, Christakopoulos P, Olsson L. A comparative study of the enzymatic hydrolysis of batch organosolv-pretreated birch and spruce biomass. AMB Express 2018; 8:114. [PMID: 29992363 PMCID: PMC6039347 DOI: 10.1186/s13568-018-0643-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 07/05/2018] [Indexed: 01/09/2023] Open
Abstract
A shift towards a sustainable and green society is vital to reduce the negative effects of climate change associated with increased CO2 emissions. Lignocellulosic biomass is both renewable and abundant, but is recalcitrant to deconstruction. Among the methods of pretreatment available, organosolv (OS) delignifies cellulose efficiently, significantly improving its digestibility by enzymes. We have assessed the hydrolysability of the cellulose-rich solid fractions from OS-pretreated spruce and birch at 2% w/v loading (dry matter). Almost complete saccharification of birch was possible with 80 mg enzyme preparation/gsolids (12 FPU/gsolids), while the saccharification yield for spruce was only 70%, even when applying 60 FPU/gsolids. As the cellulose content is enriched by OS, the yield of glucose was higher than in their steam-exploded counterparts. The hydrolysate was a transparent liquid due to the absence of phenolics and was also free from inhibitors. OS pretreatment holds potential for use in a large-scale, closed-loop biorefinery producing fuels from the cellulose fraction and platform chemicals from the hemicellulose and lignin fractions respectively.
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16
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Gallifuoco A, Taglieri L, Scimia F, Papa AA, Di Giacomo G. Hydrothermal conversions of waste biomass: Assessment of kinetic models using liquid-phase electrical conductivity measurements. WASTE MANAGEMENT (NEW YORK, N.Y.) 2018; 77:586-592. [PMID: 29801969 DOI: 10.1016/j.wasman.2018.05.033] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 03/22/2018] [Accepted: 05/17/2018] [Indexed: 06/08/2023]
Abstract
This experimental study proposes the systematic monitoring of liquid phase electrical conductivity as a new technique for evaluating kinetic models for hydrothermal conversion of biomass. The application to the hydrothermal carbonization of three different wooden materials is validated by batch experiments at 200 °C, up to 120 min of reaction time, and at a 7:1 water to solid ratio. Whatever the biomass, the time course of electrical conductivity follows a unique law, unquestionably corresponding to the evolution of solid-phase carbon content. The model tested comes from literature, and is a simple first-order pattern. The network of elementary steps satisfactorily explains the experimental data. The evidence reported demonstrates that the electrical conductivity should become a standard measurement. In fact, this lumped parameter is for the first time used for predicting the time variation of furfural, an important compound ubiquitously found in the HTC liquid phases. Ordered trends also appear from experiments at higher temperatures, up to 440 °C, but the method highlights a different behavior. The observed discrepancies give useful feedback for steering the upgrading of kinetic equations toward a more structured model, which necessarily should account for the bio-crude. Additional runs with potato peels, an entirely different kind of biomass were used here as a stress test for the method, and as expected gave different results. This new response correctly signals that another model is required for describing the process applied to starchy materials, and confirms the power of the proposed technique as a tool for build-up suitable kinetic models.
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Affiliation(s)
- Alberto Gallifuoco
- University of L'Aquila, Department of Industrial and Information Engineering & Economics, Via G. Gronchi, 18, 67100 L'Aquila, Italy.
| | - Luca Taglieri
- University of L'Aquila, Department of Industrial and Information Engineering & Economics, Via G. Gronchi, 18, 67100 L'Aquila, Italy.
| | - Francesca Scimia
- University of L'Aquila, Department of Industrial and Information Engineering & Economics, Via G. Gronchi, 18, 67100 L'Aquila, Italy.
| | - Alessandro Antonio Papa
- University of L'Aquila, Department of Industrial and Information Engineering & Economics, Via G. Gronchi, 18, 67100 L'Aquila, Italy.
| | - Gabriele Di Giacomo
- University of L'Aquila, Department of Industrial and Information Engineering & Economics, Via G. Gronchi, 18, 67100 L'Aquila, Italy.
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Lepcha K, Ghosh S. Glycoside hydrolases from a thermophilic microbial consortium and their implication in the saccharification of agroresidues. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2018. [DOI: 10.1016/j.bcab.2018.05.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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18
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Guo H, Chang Y, Lee DJ. Enzymatic saccharification of lignocellulosic biorefinery: Research focuses. BIORESOURCE TECHNOLOGY 2018; 252:198-215. [PMID: 29329774 DOI: 10.1016/j.biortech.2017.12.062] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Revised: 12/19/2017] [Accepted: 12/20/2017] [Indexed: 06/07/2023]
Abstract
To realize lignocellulosic biorefinery is of global interest, with enzymatic saccharification presenting an essential stage to convert polymeric sugars to mono-sugars for fermentation use. This mini-review summarizes qualitatively the research focuses discussed the review articles presented in the past 22 months and other relevant papers. The research focuses on pretreatment with improved efficiency, enhanced enzyme production with high yields and high extreme tolerance, feasible combined saccharification and fermentation processes, detailed mechanisms corresponding to the enzymatic saccharification in lignocellulosic biorefinery, and the costs are discussed.
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Affiliation(s)
- Hongliang Guo
- College of Food Engineering, Harbin University of Commerce, Harbin 150076, China
| | - Yingju Chang
- Department of Chemical Engineering, National Taiwan University, Taipei 10617, Taiwan
| | - Duu-Jong Lee
- Department of Chemical Engineering, National Taiwan University, Taipei 10617, Taiwan; Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei 10607, Taiwan; State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China.
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Devaux MF, Jamme F, André W, Bouchet B, Alvarado C, Durand S, Robert P, Saulnier L, Bonnin E, Guillon F. Synchrotron Time-Lapse Imaging of Lignocellulosic Biomass Hydrolysis: Tracking Enzyme Localization by Protein Autofluorescence and Biochemical Modification of Cell Walls by Microfluidic Infrared Microspectroscopy. FRONTIERS IN PLANT SCIENCE 2018. [PMID: 29515611 PMCID: PMC5826215 DOI: 10.3389/fpls.2018.00200] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Tracking enzyme localization and following the local biochemical modification of the substrate should help explain the recalcitrance of lignocellulosic plant cell walls to enzymatic degradation. Time-lapse studies using conventional imaging require enzyme labeling and following the biochemical modifications of biopolymers found in plant cell walls, which cannot be easily achieved. In the present work, synchrotron facilities have been used to image the enzymatic degradation of lignocellulosic biomass without labeling the enzyme or the cell walls. Multichannel autofluorescence imaging of the protein and phenolic compounds after excitation at 275 nm highlighted the presence or absence of enzymes on cell walls and made it possible to track them during the reaction. Image analysis was used to quantify the fluorescence intensity variations. Consistent variations in the enzyme concentration were found locally for cell cavities and their surrounding cell walls. Microfluidic FT-IR microspectroscopy allowed for time-lapse tracking of local changes in the polysaccharides in cell walls during degradation. Hemicellulose degradation was found to occur prior to cellulose degradation using a Celluclast® preparation. Combining the fluorescence and FT-IR information yielded the conclusion that enzymes did not bind to lignified cell walls, which were consequently not degraded. Fluorescence multiscale imaging and FT-IR microspectroscopy showed an unexpected variability both in the initial biochemical composition and the degradation pattern, highlighting micro-domains in the cell wall of a given cell. Fluorescence intensity quantification showed that the enzymes were not evenly distributed, and their amount increased progressively on degradable cell walls. During degradation, adjacent cells were separated and the cell wall fragmented until complete degradation.
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Affiliation(s)
- Marie-Françoise Devaux
- UR1268 Biopolymères Interactions et Assemblages, Institut National de la Recherche Agronomique Pays de la Loire, Nantes, France
- *Correspondence: Marie-Françoise Devaux
| | | | | | - Brigitte Bouchet
- UR1268 Biopolymères Interactions et Assemblages, Institut National de la Recherche Agronomique Pays de la Loire, Nantes, France
| | - Camille Alvarado
- UR1268 Biopolymères Interactions et Assemblages, Institut National de la Recherche Agronomique Pays de la Loire, Nantes, France
| | - Sylvie Durand
- UR1268 Biopolymères Interactions et Assemblages, Institut National de la Recherche Agronomique Pays de la Loire, Nantes, France
| | - Paul Robert
- UR1268 Biopolymères Interactions et Assemblages, Institut National de la Recherche Agronomique Pays de la Loire, Nantes, France
| | - Luc Saulnier
- UR1268 Biopolymères Interactions et Assemblages, Institut National de la Recherche Agronomique Pays de la Loire, Nantes, France
| | - Estelle Bonnin
- UR1268 Biopolymères Interactions et Assemblages, Institut National de la Recherche Agronomique Pays de la Loire, Nantes, France
| | - Fabienne Guillon
- UR1268 Biopolymères Interactions et Assemblages, Institut National de la Recherche Agronomique Pays de la Loire, Nantes, France
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Zhan P, Tang K, Chen X, Yu L. Complete genome sequence of Maribacter sp. T28, a polysaccharide-degrading marine flavobacteria. J Biotechnol 2017; 259:1-5. [DOI: 10.1016/j.jbiotec.2017.08.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 08/09/2017] [Accepted: 08/09/2017] [Indexed: 01/12/2023]
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21
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Ladevèze S, Haon M, Villares A, Cathala B, Grisel S, Herpoël-Gimbert I, Henrissat B, Berrin JG. The yeast Geotrichum candidum encodes functional lytic polysaccharide monooxygenases. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:215. [PMID: 28919928 PMCID: PMC5596469 DOI: 10.1186/s13068-017-0903-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Accepted: 09/07/2017] [Indexed: 05/08/2023]
Abstract
BACKGROUND Lytic polysaccharide monooxygenases (LPMOs) are a class of powerful oxidative enzymes that have revolutionized our understanding of lignocellulose degradation. Fungal LPMOs of the AA9 family target cellulose and hemicelluloses. AA9 LPMO-coding genes have been identified across a wide range of fungal saprotrophs (Ascomycotina, Basidiomycotina, etc.), but so far they have not been found in more basal lineages. Recent genome analysis of the yeast Geotrichum candidum (Saccharomycotina) revealed the presence of several LPMO genes, which belong to the AA9 family. RESULTS In this study, three AA9 LPMOs from G. candidum were successfully produced and biochemically characterized. The use of native signal peptides was well suited to ensure correct processing and high recombinant production of GcLPMO9A, GcLPMO9B, and GcLPMO9C in Pichia pastoris. We show that GcLPMO9A and GcLPMO9B were both active on cellulose and xyloglucan, releasing a mixture of soluble C1- and C4-oxidized oligosaccharides from cellulose. All three enzymes disrupted cellulose fibers and significantly improved the saccharification of pretreated lignocellulosic biomass upon addition to a commercial cellulase cocktail. CONCLUSIONS The unique enzymatic arsenal of G. candidum compared to other yeasts could be beneficial for plant cell wall decomposition in a saprophytic or pathogenic context. From a biotechnological point of view, G. candidum LPMOs are promising candidates to further enhance enzyme cocktails used in biorefineries such as consolidated bioprocessing.
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Affiliation(s)
- Simon Ladevèze
- INRA, Aix Marseille University BBF, Biodiversité et Biotechnologie Fongiques, 13288 Marseille, France
| | - Mireille Haon
- INRA, Aix Marseille University BBF, Biodiversité et Biotechnologie Fongiques, 13288 Marseille, France
| | - Ana Villares
- INRA, UR1268 Biopolymères Interactions Assemblages, 44316 Nantes, France
| | - Bernard Cathala
- INRA, UR1268 Biopolymères Interactions Assemblages, 44316 Nantes, France
| | - Sacha Grisel
- INRA, Aix Marseille University BBF, Biodiversité et Biotechnologie Fongiques, 13288 Marseille, France
| | - Isabelle Herpoël-Gimbert
- INRA, Aix Marseille University BBF, Biodiversité et Biotechnologie Fongiques, 13288 Marseille, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, UMR7857, CNRS, Aix-Marseille University, 13288 Marseille, France
- USC1408, Architecture et Fonction des Macromolécules Biologiques, INRA, 13288 Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jedda, 21589 Saudi Arabia
| | - Jean-Guy Berrin
- INRA, Aix Marseille University BBF, Biodiversité et Biotechnologie Fongiques, 13288 Marseille, France
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