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Potkule JB, Kahar SP, Kumar M, Annapure US. Impact of non-thermal techniques on enzyme modifications for their applications in food. Int J Biol Macromol 2024; 275:133566. [PMID: 38960264 DOI: 10.1016/j.ijbiomac.2024.133566] [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: 06/05/2024] [Accepted: 06/28/2024] [Indexed: 07/05/2024]
Abstract
The present review elaborates on the details of the enzyme, its structure, specificity, and the mechanism of action of selected enzymes as well as structural changes and loss or gain of activity after non-thermal treatments for food-based applications. Enzymes are biological catalysts found in various systems such as plants, animals, and microorganisms. Most of the enzymes have their optimum pH, temperature, and substrate or group of substrates. The conformational modification of enzymes either increases or decreases the rate of reaction at different pH, and temperature conditions. Enzymes are modified by different techniques to enhance the activity of enzymes for their commercial applications mainly due to the high cost of enzymes, stability, and difficulties that occur during the use of enzymes in different conditions. On the opposite, enzyme inactivation provides its application to extend the shelf life of fruits and vegetables by denaturation and partial inactivation of enzymes. Hence, the activation and inactivation of enzymes are studied by non-thermal techniques in both the model and the food system. The highly reactive species generated during non-thermal techniques cause chemical and structural modification. The enzyme modifications depend on the type and source of the enzyme, type of technique, and the parameters used.
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Affiliation(s)
- Jayashree B Potkule
- Department of Food Engineering and Technology, Institute of Chemical Technology, Matunga, Mumbai, India
| | - Suraj P Kahar
- Department of Food Engineering and Technology, Institute of Chemical Technology, Matunga, Mumbai, India
| | - Manoj Kumar
- Chemical and Biochemical Processing Division, ICAR - Central Institute for Research on Cotton Technology, Matunga, Mumbai, India
| | - Uday S Annapure
- Department of Food Engineering and Technology, Institute of Chemical Technology, Matunga, Mumbai, India; Institute of Chemical Technology, Marathwada Campus, Jalna, India.
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Bautista-Cruz A, Aquino-Bolaños T, Hernández-Canseco J, Quiñones-Aguilar EE. Cellulolytic Aerobic Bacteria Isolated from Agricultural and Forest Soils: An Overview. BIOLOGY 2024; 13:102. [PMID: 38392320 PMCID: PMC10886624 DOI: 10.3390/biology13020102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 01/29/2024] [Accepted: 01/31/2024] [Indexed: 02/24/2024]
Abstract
This review provides insights into cellulolytic bacteria present in global forest and agricultural soils over a period of 11 years. It delves into the study of soil-dwelling cellulolytic bacteria and the enzymes they produce, cellulases, which are crucial in both soil formation and the carbon cycle. Forests and agricultural activities are significant contributors to the production of lignocellulosic biomass. Forest ecosystems, which are key carbon sinks, contain 20-30% cellulose in their leaf litter. Concurrently, the agricultural sector generates approximately 998 million tons of lignocellulosic waste annually. Predominant genera include Bacillus, Pseudomonas, Stenotrophomonas, and Streptomyces in forests and Bacillus, Streptomyces, Pseudomonas, and Arthrobacter in agricultural soils. Selection of cellulolytic bacteria is based on their hydrolysis ability, using artificial cellulose media and dyes like Congo red or iodine for detection. Some studies also measure cellulolytic activity in vitro. Notably, bacterial cellulose hydrolysis capability may not align with their cellulolytic enzyme production. Enzymes such as GH1, GH3, GH5, GH6, GH8, GH9, GH10, GH12, GH26, GH44, GH45, GH48, GH51, GH74, GH124, and GH148 are crucial, particularly GH48 for crystalline cellulose degradation. Conversely, bacteria with GH5 and GH9 often fail to degrade crystalline cellulose. Accurate identification of cellulolytic bacteria necessitates comprehensive genomic analysis, supplemented by additional proteomic and transcriptomic techniques. Cellulases, known for degrading cellulose, are also significant in healthcare, food, textiles, bio-washing, bleaching, paper production, ink removal, and biotechnology, emphasizing the importance of discovering novel cellulolytic strains in soil.
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Affiliation(s)
- Angélica Bautista-Cruz
- Instituto Politécnico Nacional, CIIDIR-Oaxaca, Hornos 1003, Santa Cruz Xoxocotlán 71230, Oaxaca, Mexico
| | - Teodulfo Aquino-Bolaños
- Instituto Politécnico Nacional, CIIDIR-Oaxaca, Hornos 1003, Santa Cruz Xoxocotlán 71230, Oaxaca, Mexico
| | - Jessie Hernández-Canseco
- Doctoral Programme in Conservation and Use of Natural Resources, Instituto Politécnico Nacional, CIIDIR-Oaxaca, Hornos 1003, Santa Cruz Xoxocotlán 71230, Oaxaca, Mexico
| | - Evangelina Esmeralda Quiñones-Aguilar
- Laboratorio de Fitopatología de Biotecnología Vegetal, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, A.C. Camino Arenero 1227, El Bajío del Arenal, Zapopan 45019, Jalisco, Mexico
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3
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Coluccia M, Besaury L. Acidobacteria members harbour an abundant and diverse carbohydrate-active enzymes (cazyme) and secreted proteasome repertoire, key factors for potential efficient biomass degradation. Mol Genet Genomics 2023:10.1007/s00438-023-02045-x. [PMID: 37335345 DOI: 10.1007/s00438-023-02045-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 06/05/2023] [Indexed: 06/21/2023]
Abstract
The Acidobacteria phylum is a very abundant group (20-30% of microbial communities in soil ecosystems); however, little is known about these microorganisms and their ability to degrade the biomass and lignocellulose due to the difficulty of culturing them. We, therefore, bioinformatically studied the content of lignocellulolytic enzymes (total and predicted secreted enzymes) and secreted peptidases in an in silico library containing 41 Acidobacteria genomes. The results showed a high abundance and diversity of total and secreted Carbohydrate-Active enzymes (cazyme) families among the Acidobacteria compared to known previous degraders. Indeed, the relative abundance of cazymes in some genomes represented more than 6% of the gene coding proteins with at least 300 cazymes. The same observation was made with the predicted secreted peptidases with several families of secreted peptidases, which represented at least 1.5% of the gene coding proteins in several genomes. These results allowed us to highlight the lignocellulolytic potential of the Acidobacteria phylum in the degradation of lignocellulosic biomass, which could explain its high abundance in the environment.
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Affiliation(s)
- Marion Coluccia
- Université de Reims Champagne Ardenne, INRAE, FARE, UMR A 614, Chaire AFERE, 51097, Reims, France
| | - Ludovic Besaury
- Université de Reims Champagne Ardenne, INRAE, FARE, UMR A 614, Chaire AFERE, 51097, Reims, France.
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Gladkov GV, Kimeklis AK, Afonin AM, Lisina TO, Orlova OV, Aksenova TS, Kichko AA, Pinaev AG, Andronov EE. The Structure of Stable Cellulolytic Consortia Isolated from Natural Lignocellulosic Substrates. Int J Mol Sci 2022; 23:ijms231810779. [PMID: 36142684 PMCID: PMC9501375 DOI: 10.3390/ijms231810779] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 08/31/2022] [Accepted: 09/04/2022] [Indexed: 10/27/2022] Open
Abstract
Recycling plant matter is one of the challenges facing humanity today and depends on efficient lignocellulose degradation. Although many bacterial strains from natural substrates demonstrate cellulolytic activities, the CAZymes (Carbohydrate-Active enZYmes) responsible for these activities are very diverse and usually distributed among different bacteria in one habitat. Thus, using microbial consortia can be a solution to rapid and effective decomposition of plant biomass. Four cellulolytic consortia were isolated from enrichment cultures from composting natural lignocellulosic substrates—oat straw, pine sawdust, and birch leaf litter. Enrichment cultures facilitated growth of similar, but not identical cellulose-decomposing bacteria from different substrates. Major components in all consortia were from Proteobacteria, Actinobacteriota and Bacteroidota, but some were specific for different substrates—Verrucomicrobiota and Myxococcota from straw, Planctomycetota from sawdust and Firmicutes from leaf litter. While most members of the consortia were involved in the lignocellulose degradation, some demonstrated additional metabolic activities. Consortia did not differ in the composition of CAZymes genes, but rather in axillary functions, such as ABC-transporters and two-component systems, usually taxon-specific and associated with CAZymes. Our findings show that enrichment cultures can provide reproducible cellulolytic consortia from various lignocellulosic substrates, the stability of which is ensured by tight microbial relations between its components.
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Affiliation(s)
- Grigory V. Gladkov
- All-Russian Research Institute of Agricultural Microbiology, 196608 Saint Petersburg, Russia
- Correspondence: ; Tel.: +7-921-402-65-16
| | - Anastasiia K. Kimeklis
- All-Russian Research Institute of Agricultural Microbiology, 196608 Saint Petersburg, Russia
- Department of Applied Ecology, Saint-Petersburg State University, 199034 Saint Petersburg, Russia
| | - Alexey M. Afonin
- All-Russian Research Institute of Agricultural Microbiology, 196608 Saint Petersburg, Russia
| | - Tatiana O. Lisina
- All-Russian Research Institute of Agricultural Microbiology, 196608 Saint Petersburg, Russia
| | - Olga V. Orlova
- All-Russian Research Institute of Agricultural Microbiology, 196608 Saint Petersburg, Russia
| | - Tatiana S. Aksenova
- All-Russian Research Institute of Agricultural Microbiology, 196608 Saint Petersburg, Russia
| | - Arina A. Kichko
- All-Russian Research Institute of Agricultural Microbiology, 196608 Saint Petersburg, Russia
| | - Alexander G. Pinaev
- All-Russian Research Institute of Agricultural Microbiology, 196608 Saint Petersburg, Russia
| | - Evgeny E. Andronov
- All-Russian Research Institute of Agricultural Microbiology, 196608 Saint Petersburg, Russia
- Dokuchaev Soil Science Institute, 119017 Moscow, Russia
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Si J, Yang C, Ma W, Chen Y, Xie J, Qin X, Hu X, Yu Q. Screen of high efficiency cellulose degrading strains and effects on tea residues dietary fiber modification: Structural properties and adsorption capacities. Int J Biol Macromol 2022; 220:337-347. [PMID: 35985395 DOI: 10.1016/j.ijbiomac.2022.08.092] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 08/11/2022] [Accepted: 08/12/2022] [Indexed: 11/27/2022]
Abstract
In our study, two high efficiency cellulose degrading strains were screened, isolated and identified as Cochliobolus kusanoi and Aspergillus puulaauensis by 18S rDNA gene sequencing. In addition, the composite microbial system was constructed to develop the synergistic effect among different strains. Under the optimum conditions, the yield of soluble dietary fiber from tea residues by mixed fermentation method (MF-SDF) dramatically increased compared to single strain fermentation. The structural analysis demonstrated that all samples possessed the representative infrared absorption peaks of polysaccharides, whereas MF-SDF revealed more loose structure, lower crystallinity and smaller molecular size. For the adsorption capacities indexes, MF-SDF also owned the highest adsorbing capacity for the water molecule, oil molecule, cholesterol molecule and nitrite ion. Overall, our data showed that mixed fermentation method could be better choices to improve the functional properties of dietary fiber, and screening of cellulose degrading strains could provide new thinkings for the study of dietary fiber modification and realize high-quality utilization of crop residues.
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Affiliation(s)
- Jingyu Si
- State Key Laboratory of Food Science and Technology, China-Canada Joint Laboratory of Food Science and Technology (Nanchang), Key Laboratory of Bioactive Polysaccharides of Jiangxi Province, Nanchang University, China
| | - Chaoran Yang
- State Key Laboratory of Food Science and Technology, China-Canada Joint Laboratory of Food Science and Technology (Nanchang), Key Laboratory of Bioactive Polysaccharides of Jiangxi Province, Nanchang University, China
| | - Wenjie Ma
- State Key Laboratory of Food Science and Technology, China-Canada Joint Laboratory of Food Science and Technology (Nanchang), Key Laboratory of Bioactive Polysaccharides of Jiangxi Province, Nanchang University, China
| | - Yi Chen
- State Key Laboratory of Food Science and Technology, China-Canada Joint Laboratory of Food Science and Technology (Nanchang), Key Laboratory of Bioactive Polysaccharides of Jiangxi Province, Nanchang University, China
| | - Jianhua Xie
- State Key Laboratory of Food Science and Technology, China-Canada Joint Laboratory of Food Science and Technology (Nanchang), Key Laboratory of Bioactive Polysaccharides of Jiangxi Province, Nanchang University, China
| | - Xiaoting Qin
- State Key Laboratory of Food Science and Technology, China-Canada Joint Laboratory of Food Science and Technology (Nanchang), Key Laboratory of Bioactive Polysaccharides of Jiangxi Province, Nanchang University, China
| | - Xiaobo Hu
- State Key Laboratory of Food Science and Technology, China-Canada Joint Laboratory of Food Science and Technology (Nanchang), Key Laboratory of Bioactive Polysaccharides of Jiangxi Province, Nanchang University, China
| | - Qiang Yu
- State Key Laboratory of Food Science and Technology, China-Canada Joint Laboratory of Food Science and Technology (Nanchang), Key Laboratory of Bioactive Polysaccharides of Jiangxi Province, Nanchang University, China.
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Guo MW, Zhu L, Li HY, Liu WP, Wu ZN, Wang CH, Liu L, Li ZY, Li J. Mechanism of pod shattering in the forage legume Medicago ruthenica. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 185:260-267. [PMID: 35717734 DOI: 10.1016/j.plaphy.2022.06.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 05/14/2022] [Accepted: 06/11/2022] [Indexed: 06/15/2023]
Abstract
Pod shattering is a seed dispersal strategy and an important agronomical trait in domesticated crops. The relationship between pod shattering and pod morphology in the genus Medicago is well known; however, the detailed mechanism underlying pod dehiscence in Medicago ruthenica, a perennial legume used for forage production, is unknown. Here, the pod ventral sutures of shatter-resistant and shatter-susceptible M. ruthenica genotypes were examined at 8, 12, 16, and 20 d after flowering. The mechanism of pod shattering was analyzed through microscopic observations, polygalacturonase (PG) and cellulase (CE) activity analyses, and RNA-sequencing (RNA-Seq), and the results were verified via reverse transcriptase-quantitative polymerase chain reaction. Pod shattering at the ventral suture in M. ruthenica occurs via a combination of two mechanisms: degradation of the middle lamella at the abscission layers (ALs) and detachment of lignified cells on either side of the ALs triggered by physical forces. Increased PG and CE activities in the pod ventral suture are essential for AL cell-autolysis in the shatter-susceptible genotype. RNA-Seq revealed that 11 genes encoding PG and CE were highly expressed in the ventral sutures of the shatter-susceptible genotype. The expression levels of auxin biosynthesis-related genes decreased in the AL cells and they were negatively associated with pod dehiscence. These results enhance our understanding of the pod shattering mechanism not only in M. ruthenica but also in other leguminous plants.
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Affiliation(s)
- Mao W Guo
- Grassland Research Institute, Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Lin Zhu
- Grassland and Resources Environment Institute, Inner Mongolia Agriculture University, Hohhot, China
| | - Hong Y Li
- Grassland Research Institute, Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Wan P Liu
- Grassland Research Institute, Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Zi N Wu
- Grassland Research Institute, Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Cheng H Wang
- Grassland Supervision Office, Chahar Right Back Banner, Ulanqab, China
| | - Lei Liu
- Grassland Research Institute, Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Zhi Y Li
- Grassland Research Institute, Chinese Academy of Agricultural Sciences, Hohhot, China.
| | - Jun Li
- Grassland Research Institute, Chinese Academy of Agricultural Sciences, Hohhot, China; Key Laboratory of Herbage & Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, China.
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7
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Wilkens C, Vuillemin M, Pilgaard B, Polikarpov I, Morth JP. A GH115 α-glucuronidase structure reveals dimerization-mediated substrate binding and a proton wire potentially important for catalysis. Acta Crystallogr D Struct Biol 2022; 78:658-668. [PMID: 35503213 PMCID: PMC9063842 DOI: 10.1107/s2059798322003527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 03/28/2022] [Indexed: 11/25/2022] Open
Abstract
The crystal structure of a GH115 α-glucuronidase obtained in complex with xylohexaose and Ca2+ reveals that the two molecules constituting the homodimer cooperatively bind the substrate and that a divalent ion is involved in formation of the Michaelis–Menten complex and is likely to contribute to the formation of a protein wire that is essential for catalysis. Xylan is a major constituent of plant cell walls and is a potential source of biomaterials, and the derived oligosaccharides have been shown to have prebiotic effects. Xylans can be highly substituted with different sugar moieties, which pose steric hindrance to the xylanases that catalyse the hydrolysis of the xylan backbone. One such substituent is α-d-glucuronic acid, which is linked to the O2′ position of the β-1,4 d-xylopyranoses composing the main chain of xylans. The xylan-specific α-glucuronidases from glycoside hydrolase family 115 (GH115) specifically catalyse the removal of α-d-glucuronic acid (GlcA) or methylated GlcA (MeGlcA). Here, the molecular basis by which the bacterial GH115 member wtsAgu115A interacts with the main chain of xylan and the indirect involvement of divalent ions in the formation of the Michaelis–Menten complex are described. A crystal structure at 2.65 Å resolution of wtsAgu115A originating from a metagenome from an anaerobic digester fed with wastewater treatment sludge was determined in complex with xylohexaose, and Asp303 was identified as the likely general acid. The residue acting as the general base could not be identified. However, a proton wire connecting the active site to the metal site was observed and hence a previous hypothesis suggesting a Grotthuss-like mechanism cannot be rejected. Only a single molecule was found in the asymmetric unit. However, wtsAgu115A forms a dimer with a symmetry-related molecule in the crystal lattice. The xylohexaose moieties of the xylohexaose are recognized by residues from both protomers, thus creating a xylohexaose recognition site at the dimer interface. The dimer was confirmed by analytical size-exclusion chromatography in solution. Kinetic analysis with aldouronic acids resulted in a Hill coefficient of greater than 2, suggesting cooperativity between the two binding sites. Three Ca2+ ions were identified in the wtsAgu115A structures. One Ca2+ ion is of particular interest as it is coordinated by the residues of the loops that also interact with the substrate. Activity studies showed that the presence of Mg2+ or Mn2+ resulted in a higher activity towards aldouronic acids, while the less restrictive coordination geometry of Ca2+ resulted in a decrease in activity.
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Biodegradable polyhydroxyalkanoates production from wheat straw by recombinant Halomonas elongata A1. Int J Biol Macromol 2021; 187:675-682. [PMID: 34314798 DOI: 10.1016/j.ijbiomac.2021.07.137] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 07/14/2021] [Accepted: 07/20/2021] [Indexed: 11/22/2022]
Abstract
Waste straw bio-transformation of high value-added macromolecule polyhydroxyalkanoates (PHAs) was significance to environmental sustainable development. As a member of the PHA family, poly-β-hydroxybutyrate (PHB) could be synthesized by Halomonas elongata A1 with maximal yields of 22.8% and 11.8% of bacterial weights using glucose and carboxymethyl cellulose as carbon sources, respectively. To improve PHB production, we generated three recombinant strains, the H. elongata P2 with highest PHB biosynthesis ability. When wheat straw, mixed substrate and oleic acid were individually used as single carbon source, the maximal PHA polymer accumulation in the H. elongata P2 reached 5.2%, 16.5% and 27.5%, respectively, after 84 h of cultivation. This hardness, toughness and crystallization properties of the PHA macromolecule altered dependent on starting substrates, when analyzed by scanning electron microscopy (SEM), Fourier transform infrared spectroscopy (FTIR) and differential scanning calorimetry (DSC). In terms of the hardness and roughness, the PHA produced from mixed substrates was much softer than that from wheat straw but harder than that from oleic acid. The long-chain carbon improved the softness and strength of the produced PHA. Our data indicate that economical substrates, such as straw and waste oil, can be used in the synthesis of multi-functional plastic products with biodegradable properties.
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Revisiting the Phenomenon of Cellulase Action: Not All Endo- and Exo-Cellulase Interactions Are Synergistic. Catalysts 2021. [DOI: 10.3390/catal11020170] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The conventional endo–exo synergism model has extensively been supported in literature, which is based on the perception that endoglucanases (EGs) expose or create accessible sites on the cellulose chain to facilitate the action of processive cellobiohydrolases (CBHs). However, there is a lack of information on why some bacterial and fungal CBHs and EGs do not exhibit synergism. Therefore, the present study evaluated and compared the synergistic relationships between cellulases from different microbial sources and provided insights into how different GH families govern synergism. The results showed that CmixA2 (a mixture of TlCel7A and CtCel5A) displayed the highest effect with BaCel5A (degree of synergy for reducing sugars and glucose of 1.47 and 1.41, respectively) in a protein mass ratio of 75–25%. No synergism was detected between CmixB1/B2 (as well as CmixC1/C2) and any of the EGs, and the combinations did not improve the overall cellulose hydrolysis. These findings further support the hypothesis that “not all endo-to exo-cellulase interactions are synergistic”, and that the extent of synergism is dependent on the composition of cellulase systems from various sources and their compatibility in the cellulase cocktail. This method of screening for maximal compatibility between exo- and endo-cellulases constitutes a critical step towards the design of improved synergistic cellulose-degrading cocktails for industrial-scale biomass degradation.
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Aymé L, Hébert A, Henrissat B, Lombard V, Franche N, Perret S, Jourdier E, Heiss-Blanquet S. Characterization of three bacterial glycoside hydrolase family 9 endoglucanases with different modular architectures isolated from a compost metagenome. Biochim Biophys Acta Gen Subj 2021; 1865:129848. [PMID: 33460770 DOI: 10.1016/j.bbagen.2021.129848] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 01/11/2021] [Accepted: 01/11/2021] [Indexed: 10/22/2022]
Abstract
BACKGROUND Environmental bacteria express a wide diversity of glycoside hydrolases (GH). Screening and characterization of GH from metagenomic sources provides an insight into biomass degradation strategies of non-cultivated prokaryotes. METHODS In the present report, we screened a compost metagenome for lignocellulolytic activities and identified six genes encoding enzymes belonging to family GH9 (GH9a-f). Three of these enzymes (GH9b, GH9d and GH9e) were successfully expressed and characterized. RESULTS A phylogenetic analysis of the catalytic domain of pro- and eukaryotic GH9 enzymes suggested the existence of two major subgroups. Bacterial GH9s displayed a wide variety of modular architectures and those harboring an N-terminal Ig-like domain, such as GH9b and GH9d, segregated from the remainder. We purified and characterized GH9 endoglucanases from both subgroups and examined their stabilities, substrate specificities and product profiles. GH9e exhibited an original hydrolysis pattern, liberating an elevated proportion of oligosaccharides longer than cellobiose. All of the enzymes exhibited processive behavior and a synergistic action on crystalline cellulose. Synergy was also evidenced between GH9d and a GH48 enzyme identified from the same metagenome. CONCLUSIONS The characterized GH9 enzymes displayed different modular architectures and distinct substrate and product profiles. The presence of a cellulose binding domain was shown to be necessary for binding and digestion of insoluble cellulosic substrates, but not for processivity. GENERAL SIGNIFICANCE The identification of six GH9 enzymes from a compost metagenome and the functional variety of three characterized members highlight the importance of this enzyme family in bacterial biomass deconstruction.
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Affiliation(s)
- Laure Aymé
- IFP Energies Nouvelles, 1 - 4 avenue du Bois-Préau, 92852 Rueil-Malmaison, France
| | - Agnès Hébert
- IFP Energies Nouvelles, 1 - 4 avenue du Bois-Préau, 92852 Rueil-Malmaison, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, 163 avenue de Luminy, 13288 Aix Marseille Université, Marseille, France; INRAE, USC1408 Architecture et Fonction des Macromolécules Biologiques (AFMB), 163 avenue de Luminy, 13288 Marseille, France; Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Vincent Lombard
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, 163 avenue de Luminy, 13288 Aix Marseille Université, Marseille, France; INRAE, USC1408 Architecture et Fonction des Macromolécules Biologiques (AFMB), 163 avenue de Luminy, 13288 Marseille, France
| | - Nathalie Franche
- Aix Marseille Université, CNRS, LCB, 31 Chemin Joseph Aiguier, 13009 Marseille, France
| | - Stéphanie Perret
- Aix Marseille Université, CNRS, LCB, 31 Chemin Joseph Aiguier, 13009 Marseille, France
| | - Etienne Jourdier
- IFP Energies Nouvelles, 1 - 4 avenue du Bois-Préau, 92852 Rueil-Malmaison, France
| | - Senta Heiss-Blanquet
- IFP Energies Nouvelles, 1 - 4 avenue du Bois-Préau, 92852 Rueil-Malmaison, France.
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Pan-Genome Analyses of Geobacillus spp. Reveal Genetic Characteristics and Composting Potential. Int J Mol Sci 2020; 21:ijms21093393. [PMID: 32403359 PMCID: PMC7246994 DOI: 10.3390/ijms21093393] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 05/06/2020] [Accepted: 05/06/2020] [Indexed: 12/27/2022] Open
Abstract
The genus Geobacillus is abundant in ecological diversity and is also well-known as an authoritative source for producing various thermostable enzymes. Although it is clear now that Geobacillus evolved from Bacillus, relatively little knowledge has been obtained regarding its evolutionary mechanism, which might also contribute to its ecological diversity and biotechnology potential. Here, a statistical comparison of thirty-two Geobacillus genomes was performed with a specific focus on pan- and core genomes. The pan-genome of this set of Geobacillus strains contained 14,913 genes, and the core genome contained 940 genes. The Clusters of Orthologous Groups (COG) and Carbohydrate-Active Enzymes (CAZymes) analysis revealed that the Geobacillus strains had huge potential industrial application in composting for agricultural waste management. Detailed comparative analyses showed that basic functional classes and housekeeping genes were conserved in the core genome, while genes associated with environmental interaction or energy metabolism were more enriched in the pan-genome. Therefore, the evolution of Geobacillus seems to be guided by environmental parameters. In addition, horizontal gene transfer (HGT) events among different Geobacillus species were detected. Altogether, pan-genome analysis was a useful method for detecting the evolutionary mechanism, and Geobacillus’ evolution was directed by the environment and HGT events.
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12
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Brandes R, de Souza L, Carminatti C, Recouvreux D. Production with a High Yield of Bacterial Cellulose Nanocrystals by Enzymatic Hydrolysis. INTERNATIONAL JOURNAL OF NANOSCIENCE 2019. [DOI: 10.1142/s0219581x19500157] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Bacterial cellulose nanocrystals are highly crystalline structures with nanoscopic scale dimensions that have received increased attention in the nanocomposites area. Its properties, such as large surface area, low density, mechanical strength and ease of modification, are attractive to the preparation many kinds of nanomaterials applied multifunctional in various fields. Besides, the cellulose nanocrystals are from abundant and renewable sources that are biodegradable. An altemative method is to obtain bacterial cellulose nanocrystal by enzymatic hydrolysis because it is, less expensive, it does not use chemicals and it requires much less energy. In this sense, the primary objective of this study was to produce bacterial cellulose using glycerol as a carbon source and isolate nanocrystals from bacterial cellulose using the enzymatic hydrolysis. This study also investigated the yield of nanocrystals depending on the weight of the bacterial cellulose hydrogel, keeping constant some enzymes. The study shows us that the enzymatic method has the best performance when using cellulose hydrogel 2[Formula: see text]g to 40[Formula: see text][Formula: see text]L cellulase enzyme (endoglucanase) and 1[Formula: see text]mL of citrate buffer. Also, it was observed that the yield of nanocrystals decrease with increasing time required for the hydrolysis.
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Affiliation(s)
- Ricardo Brandes
- Polymer and Composite Materials Laboratory, Federal University of Santa Catarina, Joinville SC 89218080, Brazil
| | - Leticia de Souza
- Polymer and Composite Materials Laboratory, Federal University of Santa Catarina, Joinville SC 89218080, Brazil
| | - Claudimir Carminatti
- Polymer and Composite Materials Laboratory, Federal University of Santa Catarina, Joinville SC 89218080, Brazil
| | - Derce Recouvreux
- Polymer and Composite Materials Laboratory, Federal University of Santa Catarina, Joinville SC 89218080, Brazil
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13
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Evans ED, Pentelute BL. Studies on a landscape of perfluoroaromatic-reactive peptides. Org Biomol Chem 2019; 17:1862-1868. [PMID: 30065992 DOI: 10.1039/c8ob01678j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We investigated 26 midsized peptides (∼30 amino acids in length) selected using mRNA display to perform a nucleophilic aromatic substitution reaction (SNAr). Analysis suggested a diverse set of reactive sequences with significant differences in primary sequence, secondary structure and even predicted tertiary structural features. Several of the sequences displayed rapid kinetics allowing for near complete labeling in under one hour. Rosetta ab initio structure prediction of these sequences suggested a landscape of structural features, ranging from beta-sheet-based sequences to those possessing more alpha-helical-like character. Circular dichroism spectroscopy confirmed elements of the structure predictions for the majority of peptides. This analysis additionally uncovered that several peptides underwent secondary structure alterations upon reaction. These results suggest a broad sequence and structural landscape of SNAr active peptides along with a potentially important feature of these biopolymers.
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Affiliation(s)
- Ethan D Evans
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.
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14
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Dos Santos AC, Ximenes E, Kim Y, Ladisch MR. Lignin-Enzyme Interactions in the Hydrolysis of Lignocellulosic Biomass. Trends Biotechnol 2018; 37:518-531. [PMID: 30477739 DOI: 10.1016/j.tibtech.2018.10.010] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 10/22/2018] [Accepted: 10/25/2018] [Indexed: 12/20/2022]
Abstract
Lignin is central to overcoming recalcitrance in the enzyme hydrolysis of lignocellulose. While the term implies a physical barrier in the cell wall structure, there are also important biochemical components that direct interactions between lignin and the hydrolytic enzymes that attack cellulose in plant cell walls. Progress toward a deeper understanding of the lignin synthesis pathway - and the consistency between a range of observations over the past 40 years in the very extensive literature on cellulose hydrolysis - is resulting in advances in reducing a major impediment to cellulose conversion: the cost of enzymes. This review addresses lignin and its role in the hydrolysis of hardwood and other lignocellulosic residues.
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Affiliation(s)
- Antonio Carlos Dos Santos
- Laboratory of Renewable Resources Engineering, Purdue University, West Lafayette, IN 47907, USA; Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA
| | - Eduardo Ximenes
- Laboratory of Renewable Resources Engineering, Purdue University, West Lafayette, IN 47907, USA; Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA
| | - Youngmi Kim
- Department of Agricultural Engineering Technology, University of Wisconsin, River Falls, WI 54022, USA
| | - Michael R Ladisch
- Laboratory of Renewable Resources Engineering, Purdue University, West Lafayette, IN 47907, USA; Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA; Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907, USA; www.purdue.edu/LORRE.
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15
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Nishitani Y, Horiuchi A, Aslam M, Kanai T, Atomi H, Miki K. Crystal structures of an archaeal chitinase ChiD and its ligand complexes. Glycobiology 2018; 28:418-426. [PMID: 29800365 DOI: 10.1093/glycob/cwy024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 03/20/2018] [Indexed: 11/13/2022] Open
Abstract
Chitinase D (designated as Pc-ChiD) was found in a hyperthermophilic archaeon, Pyrococcus chitonophagus (previously described as Thermococcus chitonophagus), that was isolated from media containing only chitin as carbon source. Pc-ChiD displays chitinase activity and is thermostable at temperatures up to 95°C, suggesting its potential for industrial use. Pc-ChiD has a secretion signal peptide and two chitin-binding domains (ChBDs) in the N-terminal domain. However, the C-terminal domain shares no sequence similarity with previously identified saccharide-degrading enzymes and does not contain the DXDXE motif conserved in the glycoside hydrolase (GH) 18 family chitinases. To elucidate its overall structure and reaction mechanism, we determined the first crystal structures of Pc-ChiD, both in the ligand-free form and in complexes with substrates. Structure analyses revealed that the C-terminal domain of Pc-ChiD, Pc-ChiD(ΔBD), consists of a third putative substrate-binding domain, which cannot be predicted from the amino acid sequence, and a catalytic domain structurally similar to that found in not the GH18 family but the GH23 family. Based on the similarity with GH23 family chitinase, the catalytic residues of Pc-ChiD were predicted and confirmed by mutagenesis analyses. Moreover, the specific C-terminal 100 residues of Pc-ChiD are important to fix the putative substrate-binding domain next to the catalytic domain, contributing to the structure stability as well as the long chitin chain binding. Our findings reveal the structure of a unique archaeal chitinase that is distinct from previously known members of the GH23 family.
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Affiliation(s)
- Yuichi Nishitani
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Ayumi Horiuchi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Mehwish Aslam
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Tamotsu Kanai
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan.,JST, CREST, Gobancho 7, Chiyoda-ku, Tokyo 102-0076, Japan
| | - Haruyuki Atomi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan.,JST, CREST, Gobancho 7, Chiyoda-ku, Tokyo 102-0076, Japan
| | - Kunio Miki
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.,JST, CREST, Gobancho 7, Chiyoda-ku, Tokyo 102-0076, Japan
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16
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Leis B, Held C, Andreeßen B, Liebl W, Graubner S, Schulte LP, Schwarz WH, Zverlov VV. Optimizing the composition of a synthetic cellulosome complex for the hydrolysis of softwood pulp: identification of the enzymatic core functions and biochemical complex characterization. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:220. [PMID: 30116297 PMCID: PMC6083626 DOI: 10.1186/s13068-018-1220-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 07/31/2018] [Indexed: 05/30/2023]
Abstract
BACKGROUND The development of efficient cellulase blends is a key factor for cost-effectively valorizing biomass in a new bio-economy. Today, the enzymatic hydrolysis of plant-derived polysaccharides is mainly accomplished with fungal cellulases, whereas potentially equally effective cellulose-degrading systems from bacteria have not been developed. Particularly, a thermostable multi-enzyme cellulase complex, the cellulosome from the anaerobic cellulolytic bacterium Clostridium thermocellum is promising of being applied as cellulolytic nano-machinery for the production of fermentable sugars from cellulosic biomass. RESULTS In this study, 60 cellulosomal components were recombinantly produced in E. coli and systematically permuted in synthetic complexes to study the function-activity relationship of all available enzymes on Kraft pulp from pine wood as the substrate. Starting from a basic exo/endoglucanase complex, we were able to identify additional functional classes such as mannanase and xylanase for optimal activity on the substrate. Based on these results, we predicted a synthetic cellulosome complex consisting of seven single components (including the scaffoldin protein and a β-glucosidase) and characterized it biochemically. We obtained a highly thermostable complex with optimal activity around 60-65 °C and an optimal pH in agreement with the optimum of the native cellulosome (pH 5.8). Remarkably, a fully synthetic complex containing 47 single cellulosomal components showed comparable activity with a commercially available fungal enzyme cocktail on the softwood pulp substrate. CONCLUSIONS Our results show that synthetic bacterial multi-enzyme complexes based on the cellulosome of C. thermocellum can be applied as a versatile platform for the quick adaptation and efficient degradation of a substrate of interest.
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Affiliation(s)
- Benedikt Leis
- Department of Microbiology, Technische Universität München, TUM School of Life Sciences Weihenstephan, Emil-Ramann-Str. 4, 85354 Freising, Germany
- Present Address: Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Winchester Str. 2, 35394 Gießen, Germany
| | - Claudia Held
- Department of Microbiology, Technische Universität München, TUM School of Life Sciences Weihenstephan, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Björn Andreeßen
- Department of Microbiology, Technische Universität München, TUM School of Life Sciences Weihenstephan, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Wolfgang Liebl
- Department of Microbiology, Technische Universität München, TUM School of Life Sciences Weihenstephan, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Sigrid Graubner
- Department of Microbiology, Technische Universität München, TUM School of Life Sciences Weihenstephan, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Louis-Philipp Schulte
- Department of Microbiology, Technische Universität München, TUM School of Life Sciences Weihenstephan, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Wolfgang H. Schwarz
- Department of Microbiology, Technische Universität München, TUM School of Life Sciences Weihenstephan, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Vladimir V. Zverlov
- Department of Microbiology, Technische Universität München, TUM School of Life Sciences Weihenstephan, Emil-Ramann-Str. 4, 85354 Freising, Germany
- Institute of Molecular Genetics, Russian Academy of Science, Kurchatov Sq. 2, Moscow, 123182 Russia
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17
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Urresti S, Cartmell A, Liu F, Walton PH, Davies GJ. Structural studies of the unusual metal-ion site of the GH124 endoglucanase from Ruminiclostridium thermocellum. Acta Crystallogr F Struct Biol Commun 2018; 74:496-505. [PMID: 30084399 PMCID: PMC6096483 DOI: 10.1107/s2053230x18006842] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 05/03/2018] [Indexed: 12/20/2022] Open
Abstract
The recent discovery of `lytic' polysaccharide monooxygenases, copper-dependent enzymes for biomass degradation, has provided new impetus for the analysis of unusual metal-ion sites in carbohydrate-active enzymes. In this context, the CAZY family GH124 endoglucanase from Ruminiclostridium thermocellum contains an unusual metal-ion site, which was originally modelled as a Ca2+ site but features aspartic acid, asparagine and two histidine imidazoles as coordinating residues, which are more consistent with a transition-metal binding environment. It was sought to analyse whether the GH124 metal-ion site might accommodate other metals. It is demonstrated through thermal unfolding experiments that this metal-ion site can accommodate a range of transition metals (Fe2+, Cu2+, Mn2+ and Ni2+), whilst the three-dimensional structure and mass spectrometry show that one of the histidines is partially covalently modified and is present as a 2-oxohistidine residue; a feature that is rarely observed but that is believed to be involved in an `off-switch' to transition-metal binding. Atomic resolution (<1.1 Å) complexes define the metal-ion site and also reveal the binding of an unusual fructosylated oligosaccharide, which was presumably present as a contaminant in the cellohexaose used for crystallization. Although it has not been possible to detect a biological role for the unusual metal-ion site, this work highlights the need to study some of the many metal-ion sites in carbohydrate-active enzymes that have long been overlooked or previously mis-assigned.
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Affiliation(s)
- Saioa Urresti
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, England
| | - Alan Cartmell
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE1 7RU, England
| | - Feng Liu
- Department of Chemistry, University of British Columbia, Vancouver V6T 1Z1, Canada
| | - Paul H. Walton
- Department of Chemistry, University of York, York YO10 5DD, England
| | - Gideon J. Davies
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, England
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18
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Escuder-Rodríguez JJ, DeCastro ME, Cerdán ME, Rodríguez-Belmonte E, Becerra M, González-Siso MI. Cellulases from Thermophiles Found by Metagenomics. Microorganisms 2018; 6:microorganisms6030066. [PMID: 29996513 PMCID: PMC6165527 DOI: 10.3390/microorganisms6030066] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 07/04/2018] [Accepted: 07/05/2018] [Indexed: 01/05/2023] Open
Abstract
Cellulases are a heterogeneous group of enzymes that synergistically catalyze the hydrolysis of cellulose, the major component of plant biomass. Such reaction has biotechnological applications in a broad spectrum of industries, where they can provide a more sustainable model of production. As a prerequisite for their implementation, these enzymes need to be able to operate in the conditions the industrial process requires. Thus, cellulases retrieved from extremophiles, and more specifically those of thermophiles, are likely to be more appropriate for industrial needs in which high temperatures are involved. Metagenomics, the study of genes and gene products from the whole community genomic DNA present in an environmental sample, is a powerful tool for bioprospecting in search of novel enzymes. In this review, we describe the cellulolytic systems, we summarize their biotechnological applications, and we discuss the strategies adopted in the field of metagenomics for the discovery of new cellulases, focusing on those of thermophilic microorganisms.
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Affiliation(s)
- Juan-José Escuder-Rodríguez
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía, Facultade de Ciencias, Universidade da Coruña, 15071 A Corunna, Spain.
| | - María-Eugenia DeCastro
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía, Facultade de Ciencias, Universidade da Coruña, 15071 A Corunna, Spain.
| | - María-Esperanza Cerdán
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía, Facultade de Ciencias, Universidade da Coruña, 15071 A Corunna, Spain.
| | - Esther Rodríguez-Belmonte
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía, Facultade de Ciencias, Universidade da Coruña, 15071 A Corunna, Spain.
| | - Manuel Becerra
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía, Facultade de Ciencias, Universidade da Coruña, 15071 A Corunna, Spain.
| | - María-Isabel González-Siso
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía, Facultade de Ciencias, Universidade da Coruña, 15071 A Corunna, Spain.
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19
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Tan YN, Li Q. Microbial production of rhamnolipids using sugars as carbon sources. Microb Cell Fact 2018; 17:89. [PMID: 29884194 PMCID: PMC5994124 DOI: 10.1186/s12934-018-0938-3] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 05/31/2018] [Indexed: 12/27/2022] Open
Abstract
Rhamnolipids are a class of biosurfactants with effective surface-active properties. The high cost of microbial production of rhamnolipids largely affects their commercial applications. To reduce the production post, research has been carried out in screening more powerful strains, engineering microbes with higher biosurfactant yields and exploring cheaper substrates to reduce the production cost. Extensive refining is required for biosurfactant production using oils and oil-containing wastes, necessitating the use of complex and expensive biosurfactant recovery methods such as extraction with solvents or acid precipitation. As raw materials normally can account for 10-30% of the overall production cost, sugars have been proven to be an alternative carbon source for microbial production of rhamnolipids due to its lower costs and straightforward processing techniques. Studies have thus been focused on using tropical agroindustrial crop residues as renewable substrates. Herein, we reviewed studies that are using sugar-containing substrates as carbon sources for producing rhamnolipids. We speculate that sugars derived from agricultural wastes rich in cellulose and sugar-containing wastes are potential carbon sources in fermentation while challenges still remain in large scales.
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Affiliation(s)
- Yun Nian Tan
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, Singapore, 637459 Singapore
- Institute of Chemical and Engineering Sciences, Agency for Science, Technology and Research, 1 Pesek Road, Singapore, Jurong Island 627833 Singapore
| | - Qingxin Li
- Institute of Chemical and Engineering Sciences, Agency for Science, Technology and Research, 1 Pesek Road, Singapore, Jurong Island 627833 Singapore
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20
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You X, Qin Z, Li YX, Yan QJ, Li B, Jiang ZQ. Structural and biochemical insights into the substrate-binding mechanism of a novel glycoside hydrolase family 134 β-mannanase. Biochim Biophys Acta Gen Subj 2018; 1862:1376-1388. [DOI: 10.1016/j.bbagen.2018.03.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Revised: 03/08/2018] [Accepted: 03/10/2018] [Indexed: 12/11/2022]
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21
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Orłowski A, Artzi L, Cazade PA, Gunnoo M, Bayer EA, Thompson D. On the distinct binding modes of expansin and carbohydrate-binding module proteins on crystalline and nanofibrous cellulose: implications for cellulose degradation by designer cellulosomes. Phys Chem Chem Phys 2018. [DOI: 10.1039/c7cp07764e] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Transformation of cellulose into monosaccharides can be achieved by hydrolysis of the cellulose chains, carried out by a special group of enzymes known as cellulases.
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Affiliation(s)
- Adam Orłowski
- Department of Physics
- Bernal Institute
- University of Limerick
- Ireland
| | - Lior Artzi
- Department of Biomolecular Sciences
- The Weizmann Institute of Science
- Rehovot
- Israel
| | | | | | - Edward A. Bayer
- Department of Biomolecular Sciences
- The Weizmann Institute of Science
- Rehovot
- Israel
| | - Damien Thompson
- Department of Physics
- Bernal Institute
- University of Limerick
- Ireland
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22
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Ben-David Y, Dassa B, Bensoussan L, Bayer EA, Moraïs S. Methods for Discovery of Novel Cellulosomal Cellulases Using Genomics and Biochemical Tools. Methods Mol Biol 2018; 1796:67-84. [PMID: 29856047 DOI: 10.1007/978-1-4939-7877-9_6] [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: 12/17/2023]
Abstract
Cell wall degradation by cellulases is extensively explored owing to its potential contribution to biofuel production. The cellulosome is an extracellular multienzyme complex that can degrade the plant cell wall very efficiently, and cellulosomal enzymes are therefore of great interest. The cellulosomal cellulases are defined as enzymes that contain a dockerin module, which can interact with a cohesin module contained in multiple copies in a noncatalytic protein, termed scaffoldin. The assembly of the cellulosomal cellulases into the cellulosomal complex occurs via specific protein-protein interactions. Cellulosome systems have been described initially only in several anaerobic cellulolytic bacteria. However, owing to ongoing genome sequencing and metagenomic projects, the discovery of novel cellulosome-producing bacteria and the description of their cellulosomal genes have dramatically increased in the recent years. In this chapter, methods for discovery of novel cellulosomal cellulases from a DNA sequence by bioinformatics and biochemical tools are described. Their biochemical characterization is also described, including both the enzymatic activity of the putative cellulases and their assembly into mature designer cellulosomes.
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Affiliation(s)
- Yonit Ben-David
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Bareket Dassa
- Department of Immunology, The Weizmann Institute of Science, Rehovot, Israel
| | - Lizi Bensoussan
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Edward A Bayer
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Sarah Moraïs
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel.
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23
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Svartström O, Alneberg J, Terrapon N, Lombard V, de Bruijn I, Malmsten J, Dalin AM, El Muller E, Shah P, Wilmes P, Henrissat B, Aspeborg H, Andersson AF. Ninety-nine de novo assembled genomes from the moose (Alces alces) rumen microbiome provide new insights into microbial plant biomass degradation. ISME JOURNAL 2017; 11:2538-2551. [PMID: 28731473 DOI: 10.1038/ismej.2017.108] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 05/05/2017] [Accepted: 05/30/2017] [Indexed: 12/25/2022]
Abstract
The moose (Alces alces) is a ruminant that harvests energy from fiber-rich lignocellulose material through carbohydrate-active enzymes (CAZymes) produced by its rumen microbes. We applied shotgun metagenomics to rumen contents from six moose to obtain insights into this microbiome. Following binning, 99 metagenome-assembled genomes (MAGs) belonging to 11 prokaryotic phyla were reconstructed and characterized based on phylogeny and CAZyme profile. The taxonomy of these MAGs reflected the overall composition of the metagenome, with dominance of the phyla Bacteroidetes and Firmicutes. Unlike in other ruminants, Spirochaetes constituted a significant proportion of the community and our analyses indicate that the corresponding strains are primarily pectin digesters. Pectin-degrading genes were also common in MAGs of Ruminococcus, Fibrobacteres and Bacteroidetes and were overall overrepresented in the moose microbiome compared with other ruminants. Phylogenomic analyses revealed several clades within the Bacteriodetes without previously characterized genomes. Several of these MAGs encoded a large numbers of dockerins, a module usually associated with cellulosomes. The Bacteroidetes dockerins were often linked to CAZymes and sometimes encoded inside polysaccharide utilization loci, which has never been reported before. The almost 100 CAZyme-annotated genomes reconstructed in this study provide an in-depth view of an efficient lignocellulose-degrading microbiome and prospects for developing enzyme technology for biorefineries.
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Affiliation(s)
- Olov Svartström
- School of Biotechnology, Division of Industrial Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Johannes Alneberg
- School of Biotechnology, Division of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Nicolas Terrapon
- CNRS UMR 7257, Aix-Marseille University, 13288 Marseille, France.,INRA, USC 1408 AFMB, 13288 Marseille, France
| | - Vincent Lombard
- CNRS UMR 7257, Aix-Marseille University, 13288 Marseille, France.,INRA, USC 1408 AFMB, 13288 Marseille, France
| | - Ino de Bruijn
- School of Biotechnology, Division of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Jonas Malmsten
- Department of Pathology and Wildlife Diseases, National Veterinary Institute, Uppsala, Sweden.,Division of Reproduction, Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Ann-Marie Dalin
- Division of Reproduction, Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Emilie El Muller
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Pranjul Shah
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Bernard Henrissat
- CNRS UMR 7257, Aix-Marseille University, 13288 Marseille, France.,INRA, USC 1408 AFMB, 13288 Marseille, France.,Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Henrik Aspeborg
- School of Biotechnology, Division of Industrial Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Anders F Andersson
- School of Biotechnology, Division of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
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24
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Molecular Insight into Evolution of Symbiosis between Breast-Fed Infants and a Member of the Human Gut Microbiome Bifidobacterium longum. Cell Chem Biol 2017; 24:515-524.e5. [PMID: 28392148 DOI: 10.1016/j.chembiol.2017.03.012] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 02/13/2017] [Accepted: 03/13/2017] [Indexed: 12/23/2022]
Abstract
Breast-fed infants generally have a bifidobacteria-rich microbiota with recent studies indicating that human milk oligosaccharides (HMOs) selectively promote bifidobacterial growth. Bifidobacterium bifidum possesses a glycoside hydrolase family 20 lacto-N-biosidase for liberating lacto-N-biose I from lacto-N-tetraose, an abundant HMO unique to human milk, while Bifidobacterium longum subsp. longum has a non-classified enzyme (LnbX). Here, we determined the crystal structure of the catalytic domain of LnbX and provide evidence for creation of a novel glycoside hydrolase family, GH136. The structure, in combination with inhibition and mutation studies, provides insight into the molecular mechanism and broader substrate specificity of this enzyme. Moreover, through genetic studies, we show that lnbX is indispensable for B. longum growth on lacto-N-tetraose and is a key genetic factor for persistence in the gut of breast-fed infants. Overall, this study reveals possible evolutionary routes for the emergence of symbiosis between humans and bifidobacterial species in the infant gut.
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Abe K, Nakajima M, Yamashita T, Matsunaga H, Kamisuki S, Nihira T, Takahashi Y, Sugimoto N, Miyanaga A, Nakai H, Arakawa T, Fushinobu S, Taguchi H. Biochemical and structural analyses of a bacterial endo-β-1,2-glucanase reveal a new glycoside hydrolase family. J Biol Chem 2017; 292:7487-7506. [PMID: 28270506 DOI: 10.1074/jbc.m116.762724] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 03/04/2017] [Indexed: 11/06/2022] Open
Abstract
β-1,2-Glucan is an extracellular cyclic or linear polysaccharide from Gram-negative bacteria, with important roles in infection and symbiosis. Despite β-1,2-glucan's importance in bacterial persistence and pathogenesis, only a few reports exist on enzymes acting on both cyclic and linear β-1,2-glucan. To this end, we purified an endo-β-1,2-glucanase to homogeneity from cell extracts of the environmental species Chitinophaga arvensicola, and an endo-β-1,2-glucanase candidate gene (Cpin_6279) was cloned from the related species Chitinophaga pinensis The Cpin_6279 protein specifically hydrolyzed linear β-1,2-glucan with polymerization degrees of ≥5 and a cyclic counterpart, indicating that Cpin_6279 is an endo-β-1,2-glucananase. Stereochemical analysis demonstrated that the Cpin_6279-catalyzed reaction proceeds via an inverting mechanism. Cpin_6279 exhibited no significant sequence similarity with known glycoside hydrolases (GHs), and thus the enzyme defines a novel GH family, GH144. The crystal structures of the ligand-free and complex forms of Cpin_6279 with glucose (Glc) and sophorotriose (Glc-β-1,2-Glc-β-1,2-Glc) determined up to 1.7 Å revealed that it has a large cavity appropriate for polysaccharide degradation and adopts an (α/α)6-fold slightly similar to that of GH family 15 and 8 enzymes. Mutational analysis indicated that some of the highly conserved acidic residues in the active site are important for catalysis, and the Cpin_6279 active-site architecture provided insights into the substrate recognition by the enzyme. The biochemical characterization and crystal structure of this novel GH may enable discovery of other β-1,2-glucanases and represent a critical advance toward elucidating structure-function relationships of GH enzymes.
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Affiliation(s)
- Koichi Abe
- From the Department of Biotechnology, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657.,the Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510
| | - Masahiro Nakajima
- the Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510,
| | | | - Hiroki Matsunaga
- the Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510
| | - Shinji Kamisuki
- the Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510.,the School of Veterinary Medicine, Azabu University, 1-17-71 Fuchinobe, Chuoh-ku, Sagamihara 229-8501
| | - Takanori Nihira
- the Faculty of Agriculture, Niigata University, Niigata 950-2181, and
| | - Yuta Takahashi
- the Faculty of Agriculture, Niigata University, Niigata 950-2181, and
| | - Naohisa Sugimoto
- the Faculty of Agriculture, Niigata University, Niigata 950-2181, and
| | - Akimasa Miyanaga
- the Department of Chemistry, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8551, Japan
| | - Hiroyuki Nakai
- the Faculty of Agriculture, Niigata University, Niigata 950-2181, and
| | - Takatoshi Arakawa
- From the Department of Biotechnology, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657
| | - Shinya Fushinobu
- From the Department of Biotechnology, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657
| | - Hayao Taguchi
- the Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510
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26
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Leis B, Held C, Bergkemper F, Dennemarck K, Steinbauer R, Reiter A, Mechelke M, Moerch M, Graubner S, Liebl W, Schwarz WH, Zverlov VV. Comparative characterization of all cellulosomal cellulases from Clostridium thermocellum reveals high diversity in endoglucanase product formation essential for complex activity. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:240. [PMID: 29075324 PMCID: PMC5651568 DOI: 10.1186/s13068-017-0928-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 10/10/2017] [Indexed: 05/06/2023]
Abstract
BACKGROUND Clostridium thermocellum is a paradigm for efficient cellulose degradation and a promising organism for the production of second generation biofuels. It owes its high degradation rate on cellulosic substrates to the presence of supra-molecular cellulase complexes, cellulosomes, which comprise over 70 different single enzymes assembled on protein-backbone molecules of the scaffold protein CipA. RESULTS Although all 24 single-cellulosomal cellulases were described previously, we present the first comparative catalogue of all these enzymes together with a comprehensive analysis under identical experimental conditions, including enzyme activity, binding characteristics, substrate specificity, and product analysis. In the course of our study, we encountered four types of distinct enzymatic hydrolysis modes denoted by substrate specificity and hydrolysis product formation: (i) exo-mode cellobiohydrolases (CBH), (ii) endo-mode cellulases with no specific hydrolysis pattern, endoglucanases (EG), (iii) processive endoglucanases with cellotetraose as intermediate product (pEG4), and (iv) processive endoglucanases with cellobiose as the main product (pEG2). These modes are shown on amorphous cellulose and on model cello-oligosaccharides (with degree of polymerization DP 3 to 6). Artificial mini-cellulosomes carrying combinations of cellulases showed their highest activity when all four endoglucanase-groups were incorporated into a single complex. Such a modeled nonavalent complex (n = 9 enzymes bound to the recombinant scaffolding protein CipA) reached half of the activity of the native cellulosome. Comparative analysis of the protein architecture and structure revealed characteristics that play a role in product formation and enzyme processivity. CONCLUSIONS The identification of a new endoglucanase type expands the list of known cellulase functions present in the cellulosome. Our study shows that the variety of processivities in the enzyme complex is a key enabler of its high cellulolytic efficiency. The observed synergistic effect may pave the way for a better understanding of the enzymatic interactions and the design of more active lignocellulose-degrading cellulase cocktails in the future.
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Affiliation(s)
- Benedikt Leis
- Department of Microbiology, Technische Universität München, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Claudia Held
- Department of Microbiology, Technische Universität München, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Fabian Bergkemper
- Department of Microbiology, Technische Universität München, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Katharina Dennemarck
- Department of Microbiology, Technische Universität München, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Robert Steinbauer
- Department of Microbiology, Technische Universität München, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Alarich Reiter
- Department of Microbiology, Technische Universität München, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Matthias Mechelke
- Department of Microbiology, Technische Universität München, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Matthias Moerch
- Department of Microbiology, Technische Universität München, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Sigrid Graubner
- Department of Microbiology, Technische Universität München, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Wolfgang Liebl
- Department of Microbiology, Technische Universität München, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Wolfgang H. Schwarz
- Department of Microbiology, Technische Universität München, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Vladimir V. Zverlov
- Department of Microbiology, Technische Universität München, Emil-Ramann-Str. 4, 85354 Freising, Germany
- Institute of Molecular Genetics, Russian Academy of Science, Kurchatov Sq. 2, Moscow, 123182 Russia
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27
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Jin Y, Petricevic M, John A, Raich L, Jenkins H, Portela
De Souza L, Cuskin F, Gilbert H, Rovira C, Goddard-Borger ED, Williams SJ, Davies GJ. A β-Mannanase with a Lysozyme-like Fold and a Novel Molecular Catalytic Mechanism. ACS CENTRAL SCIENCE 2016; 2:896-903. [PMID: 28058278 PMCID: PMC5200933 DOI: 10.1021/acscentsci.6b00232] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Indexed: 06/06/2023]
Abstract
The enzymatic cleavage of β-1,4-mannans is achieved by endo-β-1,4-mannanases, enzymes involved in germination of seeds and microbial hemicellulose degradation, and which have increasing industrial and consumer product applications. β-Mannanases occur in a range of families of the CAZy sequence-based glycoside hydrolase (GH) classification scheme including families 5, 26, and 113. In this work we reveal that β-mannanases of the newly described GH family 134 differ from other mannanase families in both their mechanism and tertiary structure. A representative GH family 134 endo-β-1,4-mannanase from a Streptomyces sp. displays a fold closely related to that of hen egg white lysozyme but acts with inversion of stereochemistry. A Michaelis complex with mannopentaose, and a product complex with mannotriose, reveal ligands with pyranose rings distorted in an unusual inverted chair conformation. Ab initio quantum mechanics/molecular mechanics metadynamics quantified the energetically accessible ring conformations and provided evidence in support of a 1C4 → 3H4‡ → 3S1 conformational itinerary along the reaction coordinate. This work, in concert with that on GH family 124 cellulases, reveals how the lysozyme fold can be co-opted to catalyze the hydrolysis of different polysaccharides in a mechanistically distinct manner.
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Affiliation(s)
- Yi Jin
- York
Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, YO10 5DD, U.K.
| | - Marija Petricevic
- School of Chemistry and Bio21 Molecular Science
and Biotechnology
Institute and Department of Medical Biology, University
of Melbourne, Parkville, Victoria 3010, Australia
| | - Alan John
- School of Chemistry and Bio21 Molecular Science
and Biotechnology
Institute and Department of Medical Biology, University
of Melbourne, Parkville, Victoria 3010, Australia
- ACRF
Chemical Biology Division, The Walter and
Eliza Hall Institute of Medical Research, Parkville, Victoria 3010, Australia
| | - Lluís Raich
- Departament
de Química Inorgànica i Orgànica (Secció
de Química Orgànica) & IQTCUB, Universitat de Barcelona, 08028 Barcelona, Spain
| | - Huw Jenkins
- York
Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, YO10 5DD, U.K.
| | - Leticia Portela
De Souza
- York
Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, YO10 5DD, U.K.
| | - Fiona Cuskin
- Institute
for Cell and Molecular Biosciences, The Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, U.K.
| | - Harry
J. Gilbert
- Institute
for Cell and Molecular Biosciences, The Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, U.K.
| | - Carme Rovira
- Departament
de Química Inorgànica i Orgànica (Secció
de Química Orgànica) & IQTCUB, Universitat de Barcelona, 08028 Barcelona, Spain
- Institució
Catalana de Recerca i Estudis Avançats (ICREA), 08020 Barcelona, Spain
| | - Ethan D. Goddard-Borger
- School of Chemistry and Bio21 Molecular Science
and Biotechnology
Institute and Department of Medical Biology, University
of Melbourne, Parkville, Victoria 3010, Australia
- ACRF
Chemical Biology Division, The Walter and
Eliza Hall Institute of Medical Research, Parkville, Victoria 3010, Australia
| | - Spencer J. Williams
- School of Chemistry and Bio21 Molecular Science
and Biotechnology
Institute and Department of Medical Biology, University
of Melbourne, Parkville, Victoria 3010, Australia
| | - Gideon J. Davies
- York
Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, YO10 5DD, U.K.
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28
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Enzymatic diversity of the Clostridium thermocellum cellulosome is crucial for the degradation of crystalline cellulose and plant biomass. Sci Rep 2016; 6:35709. [PMID: 27759119 PMCID: PMC5069625 DOI: 10.1038/srep35709] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 10/03/2016] [Indexed: 01/18/2023] Open
Abstract
The cellulosome is a supramolecular multienzyme complex comprised of a wide variety of polysaccharide-degrading enzymes and scaffold proteins. The cellulosomal enzymes that bind to the scaffold proteins synergistically degrade crystalline cellulose. Here, we report in vitro reconstitution of the Clostridium thermocellum cellulosome from 40 cellulosomal components and the full-length scaffoldin protein that binds to nine enzyme molecules. These components were each synthesized using a wheat germ cell-free protein synthesis system and purified. Cellulosome complexes were reconstituted from 3, 12, 30, and 40 components based on their contents in the native cellulosome. The activity of the enzyme-saturated complex indicated that greater enzymatic variety generated more synergy for the degradation of crystalline cellulose and delignified rice straw. Surprisingly, a less complete enzyme complex displaying fewer than nine enzyme molecules was more efficient for the degradation of delignified rice straw than the enzyme-saturated complex, despite the fact that the enzyme-saturated complex exhibited maximum synergy for the degradation of crystalline cellulose. These results suggest that greater enzymatic diversity of the cellulosome is crucial for the degradation of crystalline cellulose and plant biomass, and that efficient degradation of different substrates by the cellulosome requires not only a different enzymatic composition, but also different cellulosome structures.
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29
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Mayes HB, Knott BC, Crowley MF, Broadbelt LJ, Ståhlberg J, Beckham GT. Who's on base? Revealing the catalytic mechanism of inverting family 6 glycoside hydrolases. Chem Sci 2016; 7:5955-5968. [PMID: 30155195 PMCID: PMC6091422 DOI: 10.1039/c6sc00571c] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 05/29/2016] [Indexed: 12/16/2022] Open
Abstract
In several important classes of inverting carbohydrate-active enzymes, the identity of the catalytic base remains elusive, including in family 6 Glycoside Hydrolase (GH6) enzymes, which are key components of cellulase cocktails for cellulose depolymerization. Despite many structural and kinetic studies with both wild-type and mutant enzymes, especially on the Trichoderma reesei (Hypocrea jecorina) GH6 cellulase (TrCel6A), the catalytic base in the single displacement inverting mechanism has not been definitively identified in the GH6 family. Here, we employ transition path sampling to gain insight into the catalytic mechanism, which provides unbiased atomic-level understanding of key order parameters involved in cleaving the strong glycosidic bond. Our hybrid quantum mechanics and molecular mechanics (QM/MM) simulations reveal a network of hydrogen bonding that aligns two active site water molecules that play key roles in hydrolysis: one water molecule drives the reaction by nucleophilic attack on the substrate and a second shuttles a proton to the putative base (D175) via a short water wire. We also investigated the case where the putative base is mutated to an alanine, an enzyme that is experimentally still partially active. The simulations predict that proton hopping along a water wire via a Grotthuss mechanism provides a mechanism of catalytic rescue. Further simulations reveal that substrate processive motion is 'driven' by strong electrostatic interactions with the protein at the product sites and that the -1 sugar adopts a 2SO ring configuration as it reaches its binding site. This work thus elucidates previously elusive steps in the processive catalytic mechanism of this important class of enzymes.
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Affiliation(s)
- Heather B Mayes
- Department of Chemical and Biological Engineering , Northwestern University , Evanston , IL 60208 , USA
- National Bioenergy Center , National Renewable Energy Laboratory , Golden , CO 80401 , USA .
| | - Brandon C Knott
- National Bioenergy Center , National Renewable Energy Laboratory , Golden , CO 80401 , USA .
| | - Michael F Crowley
- Biosciences Center , National Renewable Energy Laboratory , Golden , CO 80401 , USA
| | - Linda J Broadbelt
- Department of Chemical and Biological Engineering , Northwestern University , Evanston , IL 60208 , USA
| | - Jerry Ståhlberg
- Department of Chemistry and Biotechnology , Swedish University of Agricultural Sciences , SE-75007 , Uppsala , Sweden .
| | - Gregg T Beckham
- National Bioenergy Center , National Renewable Energy Laboratory , Golden , CO 80401 , USA .
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30
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Borah AJ, Agarwal M, Poudyal M, Goyal A, Moholkar VS. Mechanistic investigation in ultrasound induced enhancement of enzymatic hydrolysis of invasive biomass species. BIORESOURCE TECHNOLOGY 2016; 213:342-349. [PMID: 26898160 DOI: 10.1016/j.biortech.2016.02.024] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2016] [Revised: 02/05/2016] [Accepted: 02/06/2016] [Indexed: 06/05/2023]
Abstract
This study has assessed four invasive weeds, viz. Saccharum spontaneum (SS), Mikania micrantha (MM), Lantana camara (LC) and Eichhornia crassipes (EC) for enzymatic hydrolysis prior to bioalcohol fermentation. Enzymatic hydrolysis of pretreated biomasses of weeds has been conducted with mechanical agitation and sonication under constant (non-optimum) conditions. Profiles of total reducible sugar release have been fitted to HCH-1 model of enzymatic hydrolysis using Genetic Algorithm. Trends in parameters of this model reveal physical mechanism of ultrasound-induced enhancement of enzymatic hydrolysis. Sonication accelerates hydrolysis kinetics by ∼10-fold. This effect is contributed by several causes, attributed to intense micro-convection generated during sonication: (1) increase in reaction velocity, (2) increase in enzyme-substrate affinity, (3) reduction in product inhibition, and (4) enhancement of enzyme activity due to conformational changes in its secondary structure. Enhancement effect of sonication is revealed to be independent of conditions of enzymatic hydrolysis - whether optimum or non-optimum.
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Affiliation(s)
- Arup Jyoti Borah
- Center for Energy, Indian Institute of Technology Guwahati, Guwahati 781 039, Assam, India
| | - Mayank Agarwal
- Department of Chemical Engineering, Indian Institute of Technology Guwahati, Guwahati 781 039, Assam, India
| | - Manisha Poudyal
- Department of Molecular Biology and Biotechnology, Tezpur University, Napaam, Tezpur 784028, Assam, India
| | - Arun Goyal
- Center for Energy, Indian Institute of Technology Guwahati, Guwahati 781 039, Assam, India; Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781 039, Assam, India
| | - Vijayanand S Moholkar
- Center for Energy, Indian Institute of Technology Guwahati, Guwahati 781 039, Assam, India; Department of Chemical Engineering, Indian Institute of Technology Guwahati, Guwahati 781 039, Assam, India.
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31
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Functional and modular analyses of diverse endoglucanases from Ruminococcus albus 8, a specialist plant cell wall degrading bacterium. Sci Rep 2016; 6:29979. [PMID: 27439730 PMCID: PMC4954948 DOI: 10.1038/srep29979] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 06/24/2016] [Indexed: 11/09/2022] Open
Abstract
Ruminococcus albus 8 is a specialist plant cell wall degrading ruminal bacterium capable of utilizing hemicellulose and cellulose. Cellulose degradation requires a suite of enzymes including endoglucanases, exoglucanases, and β-glucosidases. The enzymes employed by R. albus 8 in degrading cellulose are yet to be completely elucidated. Through bioinformatic analysis of a draft genome sequence of R. albus 8, seventeen putatively cellulolytic genes were identified. The genes were heterologously expressed in E. coli, and purified to near homogeneity. On biochemical analysis with cellulosic substrates, seven of the gene products (Ra0185, Ra0259, Ra0325, Ra0903, Ra1831, Ra2461, and Ra2535) were identified as endoglucanases, releasing predominantly cellobiose and cellotriose. Each of the R. albus 8 endoglucanases, except for Ra0259 and Ra0325, bound to the model crystalline cellulose Avicel, confirming functional carbohydrate binding modules (CBMs). The polypeptides for Ra1831 and Ra2535 were found to contain distantly related homologs of CBM65. Mutational analysis of residues within the CBM65 of Ra1831 identified key residues required for binding. Phylogenetic analysis of the endoglucanases revealed three distinct subfamilies of glycoside hydrolase family 5 (GH5). Our results demonstrate that this fibrolytic bacterium uses diverse GH5 catalytic domains appended with different CBMs, including novel forms of CBM65, to degrade cellulose.
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32
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Cellulose and hemicellulose decomposition by forest soil bacteria proceeds by the action of structurally variable enzymatic systems. Sci Rep 2016; 6:25279. [PMID: 27125755 PMCID: PMC4850484 DOI: 10.1038/srep25279] [Citation(s) in RCA: 192] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 04/14/2016] [Indexed: 12/22/2022] Open
Abstract
Evidence shows that bacteria contribute actively to the decomposition of cellulose and hemicellulose in forest soil; however, their role in this process is still unclear. Here we performed the screening and identification of bacteria showing potential cellulolytic activity from litter and organic soil of a temperate oak forest. The genomes of three cellulolytic isolates previously described as abundant in this ecosystem were sequenced and their proteomes were characterized during the growth on plant biomass and on microcrystalline cellulose. Pedobacter and Mucilaginibacter showed complex enzymatic systems containing highly diverse carbohydrate-active enzymes for the degradation of cellulose and hemicellulose, which were functionally redundant for endoglucanases, β-glucosidases, endoxylanases, β-xylosidases, mannosidases and carbohydrate-binding modules. Luteibacter did not express any glycosyl hydrolases traditionally recognized as cellulases. Instead, cellulose decomposition was likely performed by an expressed GH23 family protein containing a cellulose-binding domain. Interestingly, the presence of plant lignocellulose as well as crystalline cellulose both trigger the production of a wide set of hydrolytic proteins including cellulases, hemicellulases and other glycosyl hydrolases. Our findings highlight the extensive and unexplored structural diversity of enzymatic systems in cellulolytic soil bacteria and indicate the roles of multiple abundant bacterial taxa in the decomposition of cellulose and other plant polysaccharides.
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33
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Song HT, Liu SH, Gao Y, Yang YM, Xiao WJ, Xia WC, Liu ZL, Li R, Ma XD, Jiang ZB. Simultaneous saccharification and fermentation of corncobs with genetically modified Saccharomyces cerevisiae and characterization of their microstructure during hydrolysis. Bioengineered 2016; 7:198-204. [PMID: 27116398 DOI: 10.1080/21655979.2016.1178424] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Cellulose is an abundant natural polysaccharide that is universally distributed. It can be extracted from corncobs, which are inexpensive, easily accessible, renewable, and environmentally friendly. A common strategy for effectively utilizing cellulose is efficient heterogeneous expression of cellulase genes in Saccharomyces cerevisiae. However, the improvement of cellulose utilization is a relevant issue. Based on our previous findings, we constructed an integrated secretion expression vector, pHBM368-pgk, containing a constitutive promoter sequence. Three genetically modified S. cerevisiae strains containing heterologous β-glucosidase, exoglucanase, and endoglucanase genes were constructed. The results of a 1-L bioreactor fermentation process revealed that the mixed recombinant S. cerevisiae could efficiently carry out simultaneous saccharification and fermentation (SSF) by using corncobs as the sole carbon source. The ethanol concentration reached 6.37 g/L after 96 hours of fermentation, which was about 3 times higher than that produced by genetically modified S. cerevisiae with the inducible promoter sequence. To investigate the microstructure characteristics of hydrolyzed corncobs during the fermentation process, corncob residues were detected by using a scanning electron microscope. This study provides a feasible method to improve the effect of SSF using corncobs as the sole carbon source.
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Affiliation(s)
- Hui-Ting Song
- a Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei University , Wuhan , P. R. China.,b Hubei Key Laboratory of Regional Development and Environmental Response , College of Resources and Environmental Science, Hubei University , Wuhan , P. R. China
| | - Shi-Hui Liu
- a Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei University , Wuhan , P. R. China
| | - Yuan Gao
- a Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei University , Wuhan , P. R. China
| | - Yi-Min Yang
- a Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei University , Wuhan , P. R. China
| | - Wen-Jing Xiao
- a Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei University , Wuhan , P. R. China
| | - Wu-Cheng Xia
- a Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei University , Wuhan , P. R. China
| | - Zi-Lu Liu
- a Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei University , Wuhan , P. R. China
| | - Rong Li
- a Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei University , Wuhan , P. R. China
| | - Xiang-Dong Ma
- a Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei University , Wuhan , P. R. China
| | - Zheng-Bing Jiang
- a Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei University , Wuhan , P. R. China.,c Hubei Key Laboratory of Industrial Biotechnology , College of Life Science, Hubei University , Wuhan , P. R. China
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34
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Velmurugan R, Incharoensakdi A. Proper ultrasound treatment increases ethanol production from simultaneous saccharification and fermentation of sugarcane bagasse. RSC Adv 2016. [DOI: 10.1039/c6ra17792a] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
To improve the saccharification and fermentation processes, proper ultrasound was applied which resulted in the presence of cellulase complex with improved β-glucosidase ratio leading to enhanced overall ethanol yield.
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Wang C, Dong D, Wang H, Müller K, Qin Y, Wang H, Wu W. Metagenomic analysis of microbial consortia enriched from compost: new insights into the role of Actinobacteria in lignocellulose decomposition. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:22. [PMID: 26834834 PMCID: PMC4731972 DOI: 10.1186/s13068-016-0440-2] [Citation(s) in RCA: 155] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 01/14/2016] [Indexed: 05/18/2023]
Abstract
BACKGROUND Compost habitats sustain a vast ensemble of microbes specializing in the degradation of lignocellulosic plant materials and are thus important both for their roles in the global carbon cycle and as potential sources of biochemical catalysts for advanced biofuels production. Studies have revealed substantial diversity in compost microbiomes, yet how this diversity relates to functions and even to the genes encoding lignocellulolytic enzymes remains obscure. Here, we used a metagenomic analysis of the rice straw-adapted (RSA) microbial consortia enriched from compost ecosystems to decipher the systematic and functional contexts within such a distinctive microbiome. RESULTS Analyses of the 16S pyrotag library and 5 Gbp of metagenomic sequence showed that the phylum Actinobacteria was the predominant group among the Bacteria in the RSA consortia, followed by Proteobacteria, Firmicutes, Chloroflexi, and Bacteroidetes. The CAZymes profile revealed that CAZyme genes in the RSA consortia were also widely distributed within these bacterial phyla. Strikingly, about 46.1 % of CAZyme genes were from actinomycetal communities, which harbored a substantially expanded catalog of the cellobiohydrolase, β-glucosidase, acetyl xylan esterase, arabinofuranosidase, pectin lyase, and ligninase genes. Among these communities, a variety of previously unrecognized species was found, which reveals a greater ecological functional diversity of thermophilic Actinobacteria than previously assumed. CONCLUSION These data underline the pivotal role of thermophilic Actinobacteria in lignocellulose biodegradation processes in the compost habitat. Besides revealing a new benchmark for microbial enzymatic deconstruction of lignocelluloses, the results suggest that actinomycetes found in compost ecosystems are potential candidates for mining efficient lignocellulosic enzymes in the biofuel industry.
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Affiliation(s)
- Cheng Wang
- />Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety Technology, Institute of Environmental Science and Technology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058 China
| | - Da Dong
- />Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety Technology, Institute of Environmental Science and Technology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058 China
- />Key Laboratory of Soil Contamination Bioremediation of Zhejiang Province, School of Environmental and Resource Sciences, Zhejiang A & F University, Lin’an, Hangzhou, 311300 China
| | - Haoshu Wang
- />Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety Technology, Institute of Environmental Science and Technology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058 China
| | - Karin Müller
- />Ruakura Research Centre, The New Zealand Institute for Plant and Food Research Limited, Private Bag 3123, Hamilton, New Zealand
| | - Yong Qin
- />Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety Technology, Institute of Environmental Science and Technology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058 China
| | - Hailong Wang
- />Key Laboratory of Soil Contamination Bioremediation of Zhejiang Province, School of Environmental and Resource Sciences, Zhejiang A & F University, Lin’an, Hangzhou, 311300 China
| | - Weixiang Wu
- />Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety Technology, Institute of Environmental Science and Technology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058 China
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Martinez T, Texier H, Nahoum V, Lafitte C, Cioci G, Heux L, Dumas B, O’Donohue M, Gaulin E, Dumon C. Probing the Functions of Carbohydrate Binding Modules in the CBEL Protein from the Oomycete Phytophthora parasitica. PLoS One 2015; 10:e0137481. [PMID: 26390127 PMCID: PMC4577117 DOI: 10.1371/journal.pone.0137481] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 08/17/2015] [Indexed: 11/29/2022] Open
Abstract
Oomycetes are microorganisms that are distantly related to true fungi and many members of this phylum are major plant pathogens. Oomycetes express proteins that are able to interact with plant cell wall polysaccharides, such as cellulose. This interaction is thought to be mediated by carbohydrate-binding modules that are classified into CBM family 1 in the CAZy database. In this study, the two CBMs (1–1 and 1–2) that form part of the cell wall glycoprotein, CBEL, from Phytophthora parasitica have been submitted to detailed characterization, first to better quantify their interaction with cellulose and second to determine whether these CBMs can be useful for biotechnological applications, such as biomass hydrolysis. A variety of biophysical techniques were used to study the interaction of the CBMs with various substrates and the data obtained indicate that CBEL’s CBM1-1 exhibits much greater cellulose binding ability than CBM1-2. Engineering of the family 11 xylanase from Talaromyces versatilis (TvXynB), an enzyme that naturally bears a fungal family 1 CBM, has produced two variants. The first one lacks its native CBM, whereas the second contains the CBEL CBM1-1. The study of these enzymes has revealed that wild type TvXynB binds to cellulose, via its CBM1, and that the substitution of its CBM by oomycetal CBM1-1 does not affect its activity on wheat straw. However, intriguingly the addition of CBEL during the hydrolysis of wheat straw actually potentiates the action of TvXynB variant lacking a CBM1. This suggests that the potentiating effect of CBM1-1 might not require the formation of a covalent linkage to TvXynB.
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Affiliation(s)
- Thomas Martinez
- Université Toulouse 3, UPS, Laboratoire de Recherche en Sciences Végétales, 24 chemin de Borde Rouge, BP42617, Auzeville, F-31326, Castanet-Tolosan, France
- CNRS, Laboratoire de Recherche en Sciences Végétales, 24 chemin de Borde Rouge, BP42617, Auzeville, F-31326, Castanet-Tolosan, France
- Université de Toulouse; INSA, UPS, INP, LISBP, 135 Avenue de Rangueil, F-31077 Toulouse, France
- CNRS, UMR5504, F-31400 Toulouse, France
- INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse, France
| | - Hélène Texier
- Université de Toulouse; INSA, UPS, INP, LISBP, 135 Avenue de Rangueil, F-31077 Toulouse, France
- CNRS, UMR5504, F-31400 Toulouse, France
- INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse, France
- Cinabio ADISSEO France SAS, Hall Gilbert Durand 3, 135 avenue de Rangueil, 31077 Toulouse, France
| | - Virginie Nahoum
- Université de Toulouse, UPS, IPBS, Toulouse, F-31077, France
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Centre National de la Recherche Scientifique (CNRS), Toulouse, F-31077, France
| | - Claude Lafitte
- Université Toulouse 3, UPS, Laboratoire de Recherche en Sciences Végétales, 24 chemin de Borde Rouge, BP42617, Auzeville, F-31326, Castanet-Tolosan, France
- CNRS, Laboratoire de Recherche en Sciences Végétales, 24 chemin de Borde Rouge, BP42617, Auzeville, F-31326, Castanet-Tolosan, France
| | - Gianluca Cioci
- Université de Toulouse; INSA, UPS, INP, LISBP, 135 Avenue de Rangueil, F-31077 Toulouse, France
- CNRS, UMR5504, F-31400 Toulouse, France
- INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse, France
| | | | - Bernard Dumas
- Université Toulouse 3, UPS, Laboratoire de Recherche en Sciences Végétales, 24 chemin de Borde Rouge, BP42617, Auzeville, F-31326, Castanet-Tolosan, France
- CNRS, Laboratoire de Recherche en Sciences Végétales, 24 chemin de Borde Rouge, BP42617, Auzeville, F-31326, Castanet-Tolosan, France
| | - Michael O’Donohue
- Université de Toulouse; INSA, UPS, INP, LISBP, 135 Avenue de Rangueil, F-31077 Toulouse, France
- CNRS, UMR5504, F-31400 Toulouse, France
- INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse, France
| | - Elodie Gaulin
- Université Toulouse 3, UPS, Laboratoire de Recherche en Sciences Végétales, 24 chemin de Borde Rouge, BP42617, Auzeville, F-31326, Castanet-Tolosan, France
- CNRS, Laboratoire de Recherche en Sciences Végétales, 24 chemin de Borde Rouge, BP42617, Auzeville, F-31326, Castanet-Tolosan, France
| | - Claire Dumon
- Université de Toulouse; INSA, UPS, INP, LISBP, 135 Avenue de Rangueil, F-31077 Toulouse, France
- CNRS, UMR5504, F-31400 Toulouse, France
- INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse, France
- * E-mail:
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de Oliveira HFN, Farès C, Rinaldi R. Beyond a solvent: the roles of 1-butyl-3-methylimidazolium chloride in the acid-catalysis for cellulose depolymerisation. Chem Sci 2015; 6:5215-5224. [PMID: 28717500 PMCID: PMC5500853 DOI: 10.1039/c5sc00393h] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 06/14/2015] [Indexed: 11/21/2022] Open
Abstract
In this report, 1-butyl-3-methylimidazolium chloride ([C4C1im]Cl) is demonstrated to enhance the kinetics of acid-catalysed hydrolysis of 1,4-β-glucans in binary solvent mixtures. [C4C1im]Cl plays other roles in the reaction beyond acting as a solvent for cellulose, as currently accepted. In fact, the presence of the IL increases the Hammett acidity of the catalyst dissolved in the reaction medium. The kinetic data from cellobiose and cellulose hydrolysis directly correlate with the acid strength found for p-toluenesulfonic acid in the different reaction media studied here. The current report identifies neglected, but yet very important phenomena occurring in cellulose depolymerisation.
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Affiliation(s)
| | - Christophe Farès
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1 , 45470 , Mülheim an der Ruhr , Germany
| | - Roberto Rinaldi
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1 , 45470 , Mülheim an der Ruhr , Germany
- Imperial College London , Department of Chemical Engineering , South Kensington Campus , SW7 AZ2 London , UK .
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Gregg KJ, Suits MDL, Deng L, Vocadlo DJ, Boraston AB. Structural Analysis of a Family 101 Glycoside Hydrolase in Complex with Carbohydrates Reveals Insights into Its Mechanism. J Biol Chem 2015; 290:25657-69. [PMID: 26304114 DOI: 10.1074/jbc.m115.680470] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Indexed: 11/06/2022] Open
Abstract
O-Linked glycosylation is one of the most abundant post-translational modifications of proteins. Within the secretory pathway of higher eukaryotes, the core of these glycans is frequently an N-acetylgalactosamine residue that is α-linked to serine or threonine residues. Glycoside hydrolases in family 101 are presently the only known enzymes to be able to hydrolyze this glycosidic linkage. Here we determine the high-resolution structures of the catalytic domain comprising a fragment of GH101 from Streptococcus pneumoniae TIGR4, SpGH101, in the absence of carbohydrate, and in complex with reaction products, inhibitor, and substrate analogues. Upon substrate binding, a tryptophan lid (residues 724-WNW-726) closes on the substrate. The closing of this lid fully engages the substrate in the active site with Asp-764 positioned directly beneath C1 of the sugar residue bound within the -1 subsite, consistent with its proposed role as the catalytic nucleophile. In all of the bound forms of the enzyme, however, the proposed catalytic acid/base residue was found to be too distant from the glycosidic oxygen (>4.3 Å) to serve directly as a general catalytic acid/base residue and thereby facilitate cleavage of the glycosidic bond. These same complexes, however, revealed a structurally conserved water molecule positioned between the catalytic acid/base and the glycosidic oxygen. On the basis of these structural observations we propose a new variation of the retaining glycoside hydrolase mechanism wherein the intervening water molecule enables a Grotthuss proton shuttle between Glu-796 and the glycosidic oxygen, permitting this residue to serve as the general acid/base catalytic residue.
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Affiliation(s)
- Katie J Gregg
- From the Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, V8W 3P6 and
| | - Michael D L Suits
- From the Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, V8W 3P6 and
| | - Lehua Deng
- the Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - David J Vocadlo
- the Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Alisdair B Boraston
- From the Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, V8W 3P6 and
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Georgelis N, Nikolaidis N, Cosgrove DJ. Bacterial expansins and related proteins from the world of microbes. Appl Microbiol Biotechnol 2015; 99:3807-23. [PMID: 25833181 PMCID: PMC4427351 DOI: 10.1007/s00253-015-6534-0] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Revised: 03/05/2015] [Accepted: 03/09/2015] [Indexed: 12/31/2022]
Abstract
The discovery of microbial expansins emerged from studies of the mechanism of plant cell growth and the molecular basis of plant cell wall extensibility. Expansins are wall-loosening proteins that are universal in the plant kingdom and are also found in a small set of phylogenetically diverse bacteria, fungi, and other organisms, most of which colonize plant surfaces. They loosen plant cell walls without detectable lytic activity. Bacterial expansins have attracted considerable attention recently for their potential use in cellulosic biomass conversion for biofuel production, as a means to disaggregate cellulosic structures by nonlytic means ("amorphogenesis"). Evolutionary analysis indicates that microbial expansins originated by multiple horizontal gene transfers from plants. Crystallographic analysis of BsEXLX1, the expansin from Bacillus subtilis, shows that microbial expansins consist of two tightly packed domains: the N-terminal domain D1 has a double-ψ β-barrel fold similar to glycosyl hydrolase family-45 enzymes but lacks catalytic residues usually required for hydrolysis; the C-terminal domain D2 has a unique β-sandwich fold with three co-linear aromatic residues that bind β-1,4-glucans by hydrophobic interactions. Genetic deletion of expansin in Bacillus and Clavibacter cripples their ability to colonize plant tissues. We assess reports that expansin addition enhances cellulose breakdown by cellulase and compare expansins with distantly related proteins named swollenin, cerato-platanin, and loosenin. We end in a speculative vein about the biological roles of microbial expansins and their potential applications. Advances in this field will be aided by a deeper understanding of how these proteins modify cellulosic structures.
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Affiliation(s)
| | - Nikolas Nikolaidis
- Department of Biological Science, California State University, Fullerton, CA 92831, USA
| | - Daniel J. Cosgrove
- Department of Biology, Penn State University, University Park, PA 16802, USA
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40
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Kapoor RK, Rajan K, Carrier DJ. Applications of Trametes versicolor crude culture filtrates in detoxification of biomass pretreatment hydrolyzates. BIORESOURCE TECHNOLOGY 2015; 189:99-106. [PMID: 25876229 DOI: 10.1016/j.biortech.2015.03.100] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Revised: 03/20/2015] [Accepted: 03/21/2015] [Indexed: 06/04/2023]
Abstract
Laccases have wide range of substrate specificity and find applications from pulp industry to waste water remediation. Laccases have also been used in combined pretreatment of biomass hydrolyzates to remove enzymatic and fermentation inhibitors. In this study, laccase production by Trametes versicolor strains isolated from different regions of the United States was induced using copper salts. T. versicolor crude culture filtrates (CCF), without any purification step, were tested for removal of model inhibitor compounds as well as in poplar and rice straw pretreatment hydrolyzates. Phenolic inhibitors were removed by 76% and 94% from the dilute acid hydrolyzates of rice straw and poplar, respectively, when incubated with the CCF for 12h, at room temperature. Xylo-oligosaccharide concentrations present in rice straw hydrolyzates were reduced by 64% when incubated with T. versicolor CCF. T. versicolor CCF could be a low cost technology for decreasing enzymatic and fermentation inhibitors.
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Affiliation(s)
- Rajeev Kumar Kapoor
- Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, India
| | - Kalavathy Rajan
- Department of Food Science, University of Arkansas, 2650 N Young Ave, Fayetteville, AR 72704, USA
| | - Danielle Julie Carrier
- Department of Biological and Agricultural Engineering, 203 White Engineering Hall, 1 University of Arkansas, Fayetteville, AR 72701, USA.
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Bornscheuer U, Buchholz K, Seibel J. Enzymatic degradation of (ligno)cellulose. Angew Chem Int Ed Engl 2014; 53:10876-93. [PMID: 25136976 DOI: 10.1002/anie.201309953] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Indexed: 11/06/2022]
Abstract
Glycoside-degrading enzymes play a dominant role in the biochemical conversion of cellulosic biomass into low-price biofuels and high-value-added chemicals. New insight into protein functions and substrate structures, the kinetics of recognition, and degradation events has resulted in a substantial improvement of our understanding of cellulose degradation.
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Affiliation(s)
- Uwe Bornscheuer
- Ernst-Moritz-Arndt-Universität Greifswald, Biotechnologie und Enzymkatalyse, Institut für Biochemie, Felix-Hausdorff-Strasse 4, 17487 Greifswald (Germany)
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Isolation, screening, and identification of cellulolytic bacteria from natural reserves in the subtropical region of China and optimization of cellulase production by Paenibacillus terrae ME27-1. BIOMED RESEARCH INTERNATIONAL 2014; 2014:512497. [PMID: 25050355 PMCID: PMC4090499 DOI: 10.1155/2014/512497] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 05/08/2014] [Indexed: 11/17/2022]
Abstract
From different natural reserves in the subtropical region of China, a total of 245 aerobic bacterial strains were isolated on agar plates containing sugarcane bagasse pulp as the sole carbon source. Of the 245 strains, 22 showed hydrolyzing zones on agar plates containing carboxymethyl cellulose after Congo-red staining. Molecular identification showed that the 22 strains belonged to 10 different genera, with the Burkholderia genus exhibiting the highest strain diversity and accounting for 36.36% of all the 22 strains. Three isolates among the 22 strains showed higher carboxymethyl cellulase (CMCase) activity, and isolate ME27-1 exhibited the highest CMCase activity in liquid culture. The strain ME27-1 was identified as Paenibacillus terrae on the basis of 16S rRNA gene sequence analysis as well as physiological and biochemical properties. The optimum pH and temperature for CMCase activity produced by the strain ME27-1 were 5.5 and 50°C, respectively, and the enzyme was stable at a wide pH range of 5.0–9.5. A 12-fold improvement in the CMCase activity (2.08 U/mL) of ME27-1 was obtained under optimal conditions for CMCase production. Thus, this study provided further information about the diversity of cellulose-degrading bacteria in the subtropical region of China and found P. terrae ME27-1 to be highly cellulolytic.
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Blumer-Schuette SE, Brown SD, Sander KB, Bayer EA, Kataeva I, Zurawski JV, Conway JM, Adams MWW, Kelly RM. Thermophilic lignocellulose deconstruction. FEMS Microbiol Rev 2014; 38:393-448. [DOI: 10.1111/1574-6976.12044] [Citation(s) in RCA: 128] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Revised: 08/20/2013] [Accepted: 08/28/2013] [Indexed: 11/28/2022] Open
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Wei H, Fu Y, Magnusson L, Baker JO, Maness PC, Xu Q, Yang S, Bowersox A, Bogorad I, Wang W, Tucker MP, Himmel ME, Ding SY. Comparison of transcriptional profiles of Clostridium thermocellum grown on cellobiose and pretreated yellow poplar using RNA-Seq. Front Microbiol 2014; 5:142. [PMID: 24782837 PMCID: PMC3990059 DOI: 10.3389/fmicb.2014.00142] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 03/19/2014] [Indexed: 01/01/2023] Open
Abstract
The anaerobic, thermophilic bacterium, Clostridium thermocellum, secretes multi-protein enzyme complexes, termed cellulosomes, which synergistically interact with the microbial cell surface and efficiently disassemble plant cell wall biomass. C. thermocellum has also been considered a potential consolidated bioprocessing (CBP) organism due to its ability to produce the biofuel products, hydrogen, and ethanol. We found that C. thermocellum fermentation of pretreated yellow poplar (PYP) produced 30 and 39% of ethanol and hydrogen product concentrations, respectively, compared to fermentation of cellobiose. RNA-seq was used to analyze the transcriptional profiles of these cells. The PYP-grown cells taken for analysis at the late stationary phase showed 1211 genes up-regulated and 314 down-regulated by more than two-fold compared to the cellobiose-grown cells. These affected genes cover a broad spectrum of specific functional categories. The transcriptional analysis was further validated by sub-proteomics data taken from the literature; as well as by quantitative reverse transcription-PCR (qRT-PCR) analyses of selected genes. Specifically, 47 cellulosomal protein-encoding genes, genes for 4 pairs of SigI-RsgI for polysaccharide sensing, 7 cellodextrin ABC transporter genes, and a set of NAD(P)H hydogenase and alcohol dehydrogenase genes were up-regulated for cells growing on PYP compared to cellobiose. These genes could be potential candidates for future studies aimed at gaining insight into the regulatory mechanism of this organism as well as for improvement of C. thermocellum in its role as a CBP organism.
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Affiliation(s)
- Hui Wei
- Biosciences Center, National Renewable Energy Laboratory Golden, CO, USA
| | - Yan Fu
- Center for Plant Genomics, Iowa State University Ames, IA, USA
| | - Lauren Magnusson
- Biosciences Center, National Renewable Energy Laboratory Golden, CO, USA
| | - John O Baker
- Biosciences Center, National Renewable Energy Laboratory Golden, CO, USA
| | - Pin-Ching Maness
- Biosciences Center, National Renewable Energy Laboratory Golden, CO, USA
| | - Qi Xu
- Biosciences Center, National Renewable Energy Laboratory Golden, CO, USA
| | - Shihui Yang
- National Bioenergy Center, National Renewable Energy Laboratory Golden, CO, USA
| | - Andrew Bowersox
- Biosciences Center, National Renewable Energy Laboratory Golden, CO, USA ; National Bioenergy Center, National Renewable Energy Laboratory Golden, CO, USA
| | - Igor Bogorad
- Biosciences Center, National Renewable Energy Laboratory Golden, CO, USA
| | - Wei Wang
- Biosciences Center, National Renewable Energy Laboratory Golden, CO, USA
| | - Melvin P Tucker
- National Bioenergy Center, National Renewable Energy Laboratory Golden, CO, USA
| | - Michael E Himmel
- Biosciences Center, National Renewable Energy Laboratory Golden, CO, USA
| | - Shi-You Ding
- Biosciences Center, National Renewable Energy Laboratory Golden, CO, USA
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Li Q, Ng WT, Puah SM, Bhaskar RV, Soh LS, MacBeath C, Parakattil P, Green P, Wu JC. Efficient production of fermentable sugars from oil palm empty fruit bunch by combined use of acid and whole cell culture-catalyzed hydrolyses. Biotechnol Appl Biochem 2014; 61:426-31. [PMID: 24329860 DOI: 10.1002/bab.1188] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 12/02/2013] [Indexed: 11/08/2022]
Abstract
Empty fruit bunch (EFB) of oil palm trees was converted to fermentable sugars by the combined use of dilute acids and whole fungal cell culture-catalyzed hydrolyses. EFB (5%, w/v) was hydrolyzed in the presence of 0.5% H2 SO4 and 0.2% H3 PO4 at 160 °C for 10 Min. The solid fraction was separated from the acid hydrolysate by filtration and subjected to enzymatic hydrolysis at 50 °C using the whole cell culture of Trichoderma reesei RUT-C30 (2%, w/v), which was prepared by cultivation at 30 °C for 7 days to reach its maximal cellulase activity. The combined hydrolyses of EFB gave a total sugar yield of 82.0%. When used as carbon sources for cultivating Escherichia coli in M9 medium at 37 °C, the combined EFB hydrolysates were shown to be more favorable or at least as good as pure glucose for cell growth in terms of the higher (1.1 times) optical density of E. coli cells. The by-products generated during the acid-catalyzed hydrolysis did not seem to obviously affect cell growth. The combined use of acid and whole cell culture hydrolyses might be a commercially promising method for pretreatment of lignocellulose to get fermentable sugars.
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Affiliation(s)
- Qingxin Li
- Institute of Chemical & Engineering Sciences, Singapore
| | - Wei Ting Ng
- Institute of Chemical & Engineering Sciences, Singapore
| | - Sze Min Puah
- Institute of Chemical & Engineering Sciences, Singapore
| | | | - Loon Siong Soh
- Procter & Gamble International Operations, Biopolis, Singapore
| | - Calum MacBeath
- Procter & Gamble International Operations, Biopolis, Singapore
| | - Pius Parakattil
- Procter & Gamble International Operations, Biopolis, Singapore
| | - Phil Green
- Procter & Gamble Company, West Chester, OH, USA
| | - Jin Chuan Wu
- Institute of Chemical & Engineering Sciences, Singapore
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Scully ED, Hoover K, Carlson JE, Tien M, Geib SM. Midgut transcriptome profiling of Anoplophora glabripennis, a lignocellulose degrading cerambycid beetle. BMC Genomics 2013; 14:850. [PMID: 24304644 PMCID: PMC4046674 DOI: 10.1186/1471-2164-14-850] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Accepted: 11/22/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Wood-feeding insects often work in collaboration with microbial symbionts to degrade lignin biopolymers and release glucose and other fermentable sugars from recalcitrant plant cell wall carbohydrates, including cellulose and hemicellulose. Here, we present the midgut transcriptome of larval Anoplophora glabripennis, a wood-boring beetle with documented lignin-, cellulose-, and hemicellulose- degrading capabilities, which provides valuable insights into how this insect overcomes challenges associated with feeding in woody tissue. RESULTS Transcripts from putative protein coding regions of over 9,000 insect-derived genes were identified in the A. glabripennis midgut transcriptome using a combination of 454 shotgun and Illumina paired-end reads. The most highly-expressed genes predicted to encode digestive-related enzymes were trypsins, carboxylesterases, β-glucosidases, and cytochrome P450s. Furthermore, 180 unigenes predicted to encode glycoside hydrolases (GHs) were identified and included several GH 5, 45, and 48 cellulases, GH 1 xylanases, and GH 1 β-glucosidases. In addition, transcripts predicted to encode enzymes involved in detoxification were detected, including a substantial number of unigenes classified as cytochrome P450s (CYP6B) and carboxylesterases, which are hypothesized to play pivotal roles in detoxifying host tree defensive chemicals and could make important contributions to A. glabripennis' expansive host range. While a large diversity of insect-derived transcripts predicted to encode digestive and detoxification enzymes were detected, few transcripts predicted to encode enzymes required for lignin degradation or synthesis of essential nutrients were identified, suggesting that collaboration with microbial enzymes may be required for survival in woody tissue. CONCLUSIONS A. glabripennis produces a number of enzymes with putative roles in cell wall digestion, detoxification, and nutrient extraction, which likely contribute to its ability to thrive in a broad range of host trees. This system is quite different from the previously characterized termite fermentation system and provides new opportunities to discover enzymes that could be exploited for cellulosic ethanol biofuel production or the development of novel methods to control wood-boring pests.
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Affiliation(s)
| | | | | | | | - Scott M Geib
- Tropical Crop and Commodity Protection Research Unit, USDA-ARS Pacific Basin Agricultural Research Center, Hilo, HI 96720, USA.
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48
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Rogowski A, Baslé A, Farinas CS, Solovyova A, Mortimer JC, Dupree P, Gilbert HJ, Bolam DN. Evidence that GH115 α-glucuronidase activity, which is required to degrade plant biomass, is dependent on conformational flexibility. J Biol Chem 2013; 289:53-64. [PMID: 24214982 PMCID: PMC3879575 DOI: 10.1074/jbc.m113.525295] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The microbial degradation of the plant cell wall is an important biological process that is highly relevant to environmentally significant industries such as the bioenergy and biorefining sectors. A major component of the wall is glucuronoxylan, a β1,4-linked xylose polysaccharide that is decorated with α-linked glucuronic and/or methylglucuronic acid (GlcA/MeGlcA). Recently three members of a glycoside hydrolase family, GH115, were shown to hydrolyze MeGlcA side chains from the internal regions of xylan, an activity that has not previously been described. Here we show that a dominant member of the human microbiota, Bacteroides ovatus, contains a GH115 enzyme, BoAgu115A, which displays glucuronoxylan α-(4-O-methyl)-glucuronidase activity. The enzyme is significantly more active against substrates in which the xylose decorated with GlcA/MeGlcA is flanked by one or more xylose residues. The crystal structure of BoAgu115A revealed a four-domain protein in which the active site, comprising a pocket that abuts a cleft-like structure, is housed in the second domain that adopts a TIM barrel-fold. The third domain, a five-helical bundle, and the C-terminal β-sandwich domain make inter-chain contacts leading to protein dimerization. Informed by the structure of the enzyme in complex with GlcA in its open ring form, in conjunction with mutagenesis studies, the potential substrate binding and catalytically significant amino acids were identified. Based on the catalytic importance of residues located on a highly flexible loop, the enzyme is required to undergo a substantial conformational change to form a productive Michaelis complex with glucuronoxylan.
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Affiliation(s)
- Artur Rogowski
- From the Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH United Kingdom and
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49
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Gilbert HJ, Knox JP, Boraston AB. Advances in understanding the molecular basis of plant cell wall polysaccharide recognition by carbohydrate-binding modules. Curr Opin Struct Biol 2013; 23:669-77. [DOI: 10.1016/j.sbi.2013.05.005] [Citation(s) in RCA: 236] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 05/03/2013] [Accepted: 05/09/2013] [Indexed: 11/25/2022]
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50
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Souza FHM, Inocentes RF, Ward RJ, Jorge JA, Furriel RPM. Glucose and xylose stimulation of a β-glucosidase from the thermophilic fungus Humicola insolens: A kinetic and biophysical study. ACTA ACUST UNITED AC 2013. [DOI: 10.1016/j.molcatb.2013.05.012] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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