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Mao X, Li J, Meng E, Jin W, Han W. Responses of physiological, microbiome and lipid metabolism to lignocellulose wastes in gut of yellow mealworm (Tenebrio molitor). BIORESOURCE TECHNOLOGY 2024; 401:130731. [PMID: 38663637 DOI: 10.1016/j.biortech.2024.130731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 04/30/2024]
Abstract
There is limited research on physiological and degradation mechanisms of yellow mealworm, a novel organic waste converter, in processing lignocellulosic wastes. This study has selected two types of lignocellulosic wastes, distillers' grains (DG) and maize straw (MS), to feed yellow mealworms. This study investigated the effects of lignocellulosic wastes on the growth, antioxidant system, microbiome, and lipidome of yellow mealworms. The relative growth of lignocellulosic waste group was not significantly different from wheat bran. The antioxidant level was elevated in DG. MS was significantly enriched in cellulose-degrading bacteria in the gut and was accompanied by disturbances in lipid metabolism. The correlation coefficients were used to construct a network connecting diet, microbiota, and lipids. The correlation analysis indicated that two sphingolipids, hexylglyceramide and dihydroglyceramide, were strongly and positively linked with the dominating species. This study provides comprehensive information on physiological and mechanism of mealworms in process of treating lignocellulosic waste.
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Affiliation(s)
- Xinrui Mao
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen, Guangdong 518055, China
| | - Jiaming Li
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen Key Laboratory of Agricultural Synthetic Biology, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Enqing Meng
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen, Guangdong 518055, China
| | - Wenbiao Jin
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen, Guangdong 518055, China.
| | - Wei Han
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen, Guangdong 518055, China
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Heng S, Sutheeworapong S, Champreda V, Uke A, Kosugi A, Pason P, Waeonukul R, Ceballos RM, Ratanakhanokchai K, Tachaapaikoon C. Genomics and cellulolytic, hemicellulolytic, and amylolytic potential of Iocasia fonsfrigidae strain SP3-1 for polysaccharide degradation. PeerJ 2022; 10:e14211. [PMID: 36281362 PMCID: PMC9587714 DOI: 10.7717/peerj.14211] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 09/19/2022] [Indexed: 01/24/2023] Open
Abstract
Background Cellulolytic, hemicellulolytic, and amylolytic (CHA) enzyme-producing halophiles are understudied. The recently defined taxon Iocasia fonsfrigidae consists of one well-described anaerobic bacterial strain: NS-1T. Prior to characterization of strain NS-1T, an isolate designated Halocella sp. SP3-1 was isolated and its genome was published. Based on physiological and genetic comparisons, it was suggested that Halocella sp. SP3-1 may be another isolate of I. fronsfrigidae. Despite being geographic variants of the same species, data indicate that strain SP3-1 exhibits genetic, genomic, and physiological characteristics that distinguish it from strain NS-1T. In this study, we examine the halophilic and alkaliphilic nature of strain SP3-1 and the genetic substrates underlying phenotypic differences between strains SP3-1 and NS-1T with focus on sugar metabolism and CHA enzyme expression. Methods Standard methods in anaerobic cell culture were used to grow strains SP3-1 as well as other comparator species. Morphological characterization was done via electron microscopy and Schaeffer-Fulton staining. Data for sequence comparisons (e.g., 16S rRNA) were retrieved via BLAST and EzBioCloud. Alignments and phylogenetic trees were generated via CLUTAL_X and neighbor joining functions in MEGA (version 11). Genomes were assembled/annotated via the Prokka annotation pipeline. Clusters of Orthologous Groups (COGs) were defined by eegNOG 4.5. DNA-DNA hybridization calculations were performed by the ANI Calculator web service. Results Cells of strain SP3-1 are rods. SP3-1 cells grow at NaCl concentrations of 5-30% (w/v). Optimal growth occurs at 37 °C, pH 8.0, and 20% NaCl (w/v). Although phylogenetic analysis based on 16S rRNA gene indicates that strain SP3-1 belongs to the genus Iocasia with 99.58% average nucleotide sequence identity to Iocasia fonsfrigida NS-1T, strain SP3-1 is uniquely an extreme haloalkaliphile. Moreover, strain SP3-1 ferments D-glucose to acetate, butyrate, carbon dioxide, hydrogen, ethanol, and butanol and will grow on L-arabinose, D-fructose, D-galactose, D-glucose, D-mannose, D-raffinose, D-xylose, cellobiose, lactose, maltose, sucrose, starch, xylan and phosphoric acid swollen cellulose (PASC). D-rhamnose, alginate, and lignin do not serve as suitable culture substrates for strain SP3-1. Thus, the carbon utilization profile of strain SP3-1 differs from that of I. fronsfrigidae strain NS-1T. Differences between these two strains are also noted in their lipid composition. Genomic data reveal key differences between the genetic profiles of strain SP3-1 and NS-1T that likely account for differences in morphology, sugar metabolism, and CHA-enzyme potential. Important to this study, I. fonsfrigidae SP3-1 produces and extracellularly secretes CHA enzymes at different levels and composition than type strain NS-1T. The high salt tolerance and pH range of SP3-1 makes it an ideal candidate for salt and pH tolerant enzyme discovery.
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Affiliation(s)
- Sobroney Heng
- School of Bioresources and Technology, King Mongkut’s Institute of Technology Thonburi, Bangkok, Thailand
| | - Sawannee Sutheeworapong
- Pilot Plant Development and Training Institute, King Mongkut’s Institute of Technology Thonburi, Bangkok, Thailand
| | - Verawat Champreda
- National Center for Genetic Engineering and Biotechnology, Thailand Science Park, Klong Luang, Pathumthani, Thailand
| | - Ayaka Uke
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences, Ibaraki, Japan
| | - Akihiko Kosugi
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences, Ibaraki, Japan
| | - Patthra Pason
- School of Bioresources and Technology, King Mongkut’s Institute of Technology Thonburi, Bangkok, Thailand,Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute, King Mongkut’s Institute of Technology Thonburi, Bangkok, Thailand
| | - Rattiya Waeonukul
- School of Bioresources and Technology, King Mongkut’s Institute of Technology Thonburi, Bangkok, Thailand,Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute, King Mongkut’s Institute of Technology Thonburi, Bangkok, Thailand
| | - Ruben Michael Ceballos
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, United States of America,Arkansas Center for Space & Planetary Sciences, University of Arkansas, Fayetteville, AR, United States of America
| | - Khanok Ratanakhanokchai
- School of Bioresources and Technology, King Mongkut’s Institute of Technology Thonburi, Bangkok, Thailand,Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute, King Mongkut’s Institute of Technology Thonburi, Bangkok, Thailand
| | - Chakrit Tachaapaikoon
- School of Bioresources and Technology, King Mongkut’s Institute of Technology Thonburi, Bangkok, Thailand,Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute, King Mongkut’s Institute of Technology Thonburi, Bangkok, Thailand
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3
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Pisa JH, Hero JS, Romero HG, Martínez MA. A genome-proteome-based approach for xylan degradation by Cohnella sp. AR92. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:755-765. [PMID: 35940859 DOI: 10.1111/1758-2229.13113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
Several members of Cohnella genus have been reported as xylanolytic bacteria with significant capacity as carbohydrate-active enzyme producers (CAZymes), whose mechanisms involving xylan degradation are a key goal for suitable applications in bio-based industries. Using Cohnella sp. AR92 bacterium, we ensembled a genomic-proteomic approach to assess plant biomass conversion targeting its xylanolytic set of enzymes. Also, the genomic traits of the strain AR92 were compared to other Cohnella spp., showing a significant variability in terms of genome sizes and content of genes that code CAZymes. The AR92 strain genome harbours 209 CAZymes encoding sequences active on different polysaccharides, particularly directed towards xylans. Concurrent proteomic data recovered from cultures containing three kinds of lignocellulosic-derived substrates showed a broad set of xylan-degrading enzymes. The most abundant CAZymes expressed in the different conditions assayed were endo-β-1,4-xylanases belonging to the GH11 and GH10 families, enzymes that were previously proved to be useful in the biotransformation of lignocellulosic biomass derived from sugarcane as well as onto xylan-enriched substrates. Therefore, considering the large reserve of CAZymes of Cohnella sp. AR92, a xylan processing model for AR92 strain is proposed.
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Affiliation(s)
- José Horacio Pisa
- PROIMI - CONICET (National Scientific and Technical Research Council), Tucumán, Argentina
| | - Johan Sebastian Hero
- PROIMI - CONICET (National Scientific and Technical Research Council), Tucumán, Argentina
| | - Héctor Gabriel Romero
- Department of Ecology and Evolution, Faculty of Sciences/CURE, University of the Republic, Montevideo, Uruguay
| | - María Alejandra Martínez
- PROIMI - CONICET (National Scientific and Technical Research Council), Tucumán, Argentina
- Faculty of Exact Sciences and Technology, National University of Tucuman, Tucumán, Argentina
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Khosravi F, Khaleghi M, Naghavi H. Screening and identification of cellulose-degrading bacteria from soil and leaves at Kerman province, Iran. Arch Microbiol 2021; 204:88. [PMID: 34961888 DOI: 10.1007/s00203-021-02713-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 11/11/2021] [Accepted: 11/15/2021] [Indexed: 11/25/2022]
Abstract
Cellulosic biomass is considered one of the most promising sources for the production of alternative renewable bioenergy and other valuable products. Identification and optimization of strains with high enzymatic activity that can overcome constraints imposed by the cellulosic structure is an essential step in the development of new biotechnologies. The aim of this study was to isolate and identify thermophilic (50 °C) and mesophilic (37 °C) cellulolytic bacteria from soil and leaves samples at Kerman, Iran. Degrader bacteria were isolated using serial dilution and pour plate method. Media contained carboxymethylcellulose (CMC), and filter paper was used as sources of carbon. Totally 22 mesophilic and 17 thermophilic bacterial strains which produced clear zones were further identified by morphological and biochemical tests. Screening of purified bacteria was performed to identify cellulase-producing bacteria by Congo red test. These bacteria were compared to each other based on cellulase activity, the percentage of growth, and extracellular protein amounts. The strains with the highest enzymatic activity were determined by the DNS method. The isolated US5 and US7 grew rapidly, and produced cellulase. The US5 created the largest clear zones (7 mm). Besides, these strains were selected for analysis of 16S rRNA sequence. The results showed that selected bacteria strains belong to Brevibacillus borstelensis. The B. borstelensis strains isolated in this study showed a suitable cellulase enzyme activity.
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Affiliation(s)
- Farshid Khosravi
- Department of Biology, Faculty of Science, Shahid Bahonar University of Kerman, Kerman, Iran.
| | - Mouj Khaleghi
- Department of Biology, Faculty of Science, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Hormazd Naghavi
- Soil and Water Research, Kerman Agricultural and Natural Resources Research and Education Center, AREEO, Kerman, Iran
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5
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A Novel Multifunctional Arabinofuranosidase/Endoxylanase/β-Xylosidase GH43 Enzyme from Paenibacillus curdlanolyticus B-6 and Its Synergistic Action To Produce Arabinose and Xylose from Cereal Arabinoxylan. Appl Environ Microbiol 2021; 87:e0173021. [PMID: 34613758 DOI: 10.1128/aem.01730-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PcAxy43B is a modular protein comprising a catalytic domain of glycoside hydrolase family 43 (GH43), a family 6 carbohydrate-binding module (CBM6), and a family 36 carbohydrate-binding module (CBM36) and found to be a novel multifunctional xylanolytic enzyme from Paenibacillus curdlanolyticus B-6. This enzyme exhibited α-l-arabinofuranosidase, endoxylanase, and β-d-xylosidase activities. The α-l-arabinofuranosidase activity of PcAxy43B revealed a new property of GH43, via the release of both long-chain cereal arabinoxylan and short-chain arabinoxylooligosaccharide (AXOS), as well as release from both the C(O)2 and C(O)3 positions of AXOS, which is different from what has been seen for other arabinofuranosidases. PcAxy43B liberated a series of xylooligosaccharides (XOSs) from birchwood xylan and xylohexaose, indicating that PcAxy43B exhibited endoxylanase activity. PcAxy43B produced xylose from xylobiose and reacted with p-nitrophenyl-β-d-xylopyranoside as a result of β-xylosidase activity. PcAxy43B effectively released arabinose together with XOSs and xylose from the highly arabinosyl-substituted rye arabinoxylan. Moreover, PcAxy43B showed significant synergistic action with the trifunctional endoxylanase/β-xylosidase/α-l-arabinofuranosidase PcAxy43A and the endoxylanase Xyn10C from strain B-6, in which almost all products produced from rye arabinoxylan by these combined enzymes were arabinose and xylose. In addition, the presence of CBM36 was found to be necessary for the endoxylanase property of PcAxy43B. PcAxy43B is capable of hydrolyzing untreated cereal biomass, corn hull, and rice straw into XOSs and xylose. Hence, PcAxy43B, a significant accessory multifunctional xylanolytic enzyme, is a potential candidate for application in the saccharification of cereal biomass. IMPORTANCE Enzymatic saccharification of cereal biomass is a strategy for the production of fermented sugars from low-price raw materials. In the present study, PcAxy43B from P. curdlanolyticus B-6 was found to be a novel multifunctional α-l-arabinofuranosidase/endoxylanase/β-d-xylosidase enzyme of glycoside hydrolase family 43. It is effective in releasing arabinose, xylose, and XOSs from the highly arabinosyl-substituted rye arabinoxylan, which is usually resistant to hydrolysis by xylanolytic enzymes. Moreover, almost all products produced from rye arabinoxylan by the combination of PcAxy43B with the trifunctional xylanolytic enzyme PcAxy43A and the endoxylanase Xyn10C from strain B-6 were arabinose and xylose, which can be used to produce several value-added products. In addition, PcAxy43B is capable of hydrolyzing untreated cereal biomass into XOSs and xylose. Thus, PcAxy43B is an important multifunctional xylanolytic enzyme with high potential in biotechnology.
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Cheawchanlertfa P, Tongsuk P, Sutheeworapong S, Waeonukul R, Pason P, Poomputsa K, Ratanakhanokchai K, Kosugi A, Tachaapaikoon C. A novel amylolytic/xylanolytic/cellulolytic multienzyme complex from Clostridium manihotivorum that hydrolyzes polysaccharides in cassava pulp. Appl Microbiol Biotechnol 2021; 105:6719-6733. [PMID: 34436648 DOI: 10.1007/s00253-021-11521-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 07/26/2021] [Accepted: 08/03/2021] [Indexed: 11/30/2022]
Abstract
Some anaerobic bacteria, particularly Clostridium species, produce extracellular cellulolytic and xylanolytic enzymes as multienzyme complexes (MECs). However, an amylolytic/xylanolytic/cellulolytic multienzyme complex (AXC-MEC) from anaerobic bacteria is rarely found. In this work, the glycoprotein AXC-MEC, composed of subunits of amylolytic, xylanolytic, and cellulolytic enzymes, was isolated from crude extracellular enzyme of the mesophilic anaerobic bacterium Clostridium manihotivorum CT4, grown on cassava pulp, using a milled cassava pulp column and Sephacryl S-500 gel filtration chromatography. The isolated AXC-MEC showed a single band upon native-polyacrylamide gel electrophoresis (native-PAGE). Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) showed at least eight protein bands of the multienzyme complex which predominantly exhibited amylolytic enzyme activity, followed by xylanolytic and cellulolytic enzyme activities. The AXC-MEC is highly capable of degrading starch and non-starch polysaccharides present in cassava pulp into glucose and oligosaccharides, without conventional pretreatment. Base on the genomic analysis of C. manihotivorum CT4, we found no evidence of the known structural components of the well-known multienzyme complexes from Clostridium species, cellulosomes such as scaffoldin, cohesin, and dockerin, indicating that AXC-MEC from strain CT4 exhibit a different manner of assembly from the cellulosomes. These results suggest that AXC-MEC from C. manihotivorum CT4 is a new MEC capable of hydrolyzing cassava pulp into value-added products, which will benefit the starch industry. KEY POINTS: • Glycoprotein AXC-MEC was first reported in Clostridium manihotivorum. • Unlike cellulosomes, AXC-MEC consists of amylase, xylanase, and cellulase. • Glucose and oligosaccharides were hydrolysis products from cassava pulp by AXC-MEC.
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Affiliation(s)
- Pattsarun Cheawchanlertfa
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Pornpimon Tongsuk
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Sawannee Sutheeworapong
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Rattiya Waeonukul
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand.,Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Patthra Pason
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand.,Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Kanokwan Poomputsa
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Khanok Ratanakhanokchai
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand.,Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Akihiko Kosugi
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki, 305-8686, Japan
| | - Chakrit Tachaapaikoon
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand. .,Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand.
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Srivastava S, Dafale NA, Purohit HJ. Functional genomics assessment of lytic polysaccharide mono-oxygenase with glycoside hydrolases in Paenibacillus dendritiformis CRN18. Int J Biol Macromol 2020; 164:3729-3738. [PMID: 32835796 DOI: 10.1016/j.ijbiomac.2020.08.147] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 08/06/2020] [Accepted: 08/19/2020] [Indexed: 11/25/2022]
Abstract
Recently discovered Lytic Polysaccharide Mono-Oxygenase (LPMO) enhances the enzymatic deconstruction of complex polysaccharide by oxidation. The present study demonstrates the agricultural waste hydrolyzing capabilities of Paenibacillus dendritiformis CRN18, which exhibits the enzyme activity of exo-glucanase, β-glucosidase, β-glucuronidase, endo-1, 4 β-xylanases, arabinosidase, and α-galactosidase as 0.1U/ml, 0.3U/ml, 0.09U/ml, 0.1U/ml, 0.05U/ml, and 0.41U/ml, respectively. The genome analysis of strain reveals the presence of four LPMO genes, along with lignocellulolytic genes. The gene structure of LPMO and its phylogenetic analysis shows the evolutionary relatedness with the Bacillus LPMO gene. Gene position of LPMOs in the genome of strains shows the close association of two LPMOs with chitin active enzyme GH18, and the other two are associated with hemicellulases (GH39, GH23). Protein-protein interaction and gene networking of LPMO sheds light on the co-occurrence, neighborhood, and interaction of LPMOs with chitinase and xylanase enzymes. Structural prediction of LPMOs unravels the information of the LPMO's binding site. Although the LPMO has been explored for its oxidative mechanism, a little light has been shed on its gene structure. This study provides insights into the LPMO gene structure in P. dendritiformis CRN18 and its potential in lignocellulose hydrolysis.
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Affiliation(s)
- Shweta Srivastava
- Environmental Biotechnology & Genomics Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nagpur 440 020, India; AcSIR-Academy for Scientific and Innovative Research, Ghaziabad 201 002, India
| | - Nishant A Dafale
- Environmental Biotechnology & Genomics Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nagpur 440 020, India; AcSIR-Academy for Scientific and Innovative Research, Ghaziabad 201 002, India.
| | - Hemant J Purohit
- Environmental Biotechnology & Genomics Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nagpur 440 020, India
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Draft genome sequence data of Paenbacillus curdlanolyticus B-6 possessing a unique xylanolytic-cellulolytic multienzyme system. Data Brief 2020; 32:106213. [PMID: 32923539 PMCID: PMC7476223 DOI: 10.1016/j.dib.2020.106213] [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: 07/12/2020] [Accepted: 08/18/2020] [Indexed: 11/23/2022] Open
Abstract
Paenibacillus curdlanolyticus B-6 is a facultative anaerobic bacterium that efficiently produces a lignocellulolytic multienzyme complex. The whole genome of P. curdlanolyticus B-6 was sequenced on an Ion GeneStudio S5 system, which yielded 74 contigs with a total size of 4,875,097 bp, 4,473 protein-coding sequences, and a G+C content of 49.7%. The genome data have been deposited in DDBJ/ENA/GenBank under accession numbers BLWM01000001–BLWM01000074. Analyses of average nucleotide identities and phylogenetic relationships of 16S rRNA sequences of Paenibacillus species revealed that strain B-6 is most closely related to Paenibacillus xylaniclasticus TW1. P. curdlanolyticus B-6 should thus be reclassified as a strain of P. xylaniclasticus.
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9
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Pason P, Tachaapaikoon C, Panichnumsin P, Ketbot P, Waeonukul R, Kosugi A, Ratanakhanokchai K. One-step biohydrogen production from cassava pulp using novel enrichment of anaerobic thermophilic bacteria community. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2020. [DOI: 10.1016/j.bcab.2020.101658] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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10
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Limsakul P, Phitsuwan P, Waeonukul R, Pason P, Tachaapaikoon C, Poomputsa K, Kosugi A, Sakka M, Sakka K, Ratanakhanokchai K. A novel AA10 from Paenibacillus curdlanolyticus and its synergistic action on crystalline and complex polysaccharides. Appl Microbiol Biotechnol 2020; 104:7533-7550. [PMID: 32651597 DOI: 10.1007/s00253-020-10758-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/18/2020] [Accepted: 06/24/2020] [Indexed: 02/08/2023]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) play an important role in the degradation of complex polysaccharides in lignocellulosic biomass. In the present study, we characterized a modular LPMO (PcAA10A), consisting of a family 10 auxiliary activity of LPMO (AA10) catalytic domain, and non-catalytic domains including a family 5 carbohydrate-binding module, two fibronectin type-3 domains, and a family 3 carbohydrate-binding module from Paenibacillus curdlanolyticus B-6, which was expressed in a recombinant Escherichia coli. Comparison of activities between full-length PcAA10A and the catalytic domain polypeptide (PcAA10A_CD) indicates that the non-catalytic domains are important for the deconstruction of crystalline cellulose and complex polysaccharides contained in untreated lignocellulosic biomass. Interestingly, PcAA10A_CD acted not only on cellulose and chitin, but also on xylan, mannan, and xylan and cellulose contained in lignocellulosic biomass, which has not been reported for the AA10 family. Mutation of the key residues, Trp51 located at subsite - 2 and Phe171 located at subsite +2, in the substrate-binding site of PcAA10A_CD revealed that these residues are substantially involved in broad substrate specificity toward cellulose, xylan, and mannan, albeit with a low effect toward chitin. Furthermore, PcAA10A had a boosting effect on untreated corn hull degradation by P. curdlanolyticus B-6 endo-xylanase Xyn10D and Clostridium thermocellum endo-glucanase Cel9A. These results suggest that PcAA10A is a unique LPMO capable of cleaving and enhancing lignocellulosic biomass degradation, making it a good candidate for biotechnological applications. KEY POINTS: • PcAA10A is a novel modular LPMO family 10 from Paenibacillus curdlanolyticus. • PcAA10A showed broad substrate specificity on β-1,4 glycosidic linkage substrates. • Non-catalytic domains are important for degrading complex polysaccharides. • PcAA10A is a unique LPMO capable of enhancing lignocellulosic biomass degradation.
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Affiliation(s)
- Puangpen Limsakul
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Paripok Phitsuwan
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Rattiya Waeonukul
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Patthra Pason
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Chakrit Tachaapaikoon
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Kanokwan Poomputsa
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Akihiko Kosugi
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences, Tsukuba, Ibaraki, 305-8686, Japan
| | - Makiko Sakka
- Graduated School of Bioresources, Mie University, Tsu, Mie, 514-8507, Japan
| | - Kazuo Sakka
- Graduated School of Bioresources, Mie University, Tsu, Mie, 514-8507, Japan.
| | - Khanok Ratanakhanokchai
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand.
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Isolation and subunit compositions of the xylanosome complexes produced by Cellulosimicrobium species. Enzyme Microb Technol 2020; 133:109445. [PMID: 31874683 DOI: 10.1016/j.enzmictec.2019.109445] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 09/28/2019] [Accepted: 10/06/2019] [Indexed: 01/10/2023]
Abstract
Cellulosimicrobium cellulans, which is type species of the genus Cellulosimicrobium, produces xylanase predominant nanoscale multienzyme complexes, i.e., xylanosomes, when grown on water-insoluble polysaccharides. Here, we report on the isolation of similar multienzyme complexes (MECs) produced by two other species in genus Cellulosimicrobium (Cellulosimicrobium funkei and Cellulosimicrobium terreum). Functional studies and subunit structure identifications using genomic sequencing and proteomic techniques were also performed. When compared with the xylanosomes produced by C. cellulans F16, the isolated MECs showed a larger particle size and shared at least three conserved multidomain proteins. In addition, they also exhibited different enzymatic activities and subunit compositions, which indicates diverse capability and strategies in degrading hemicelluloses.
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A novel multifunctional GH9 enzyme from Paenibacillus curdlanolyticus B-6 exhibiting endo/exo functions of cellulase, mannanase and xylanase activities. Appl Microbiol Biotechnol 2020; 104:2079-2096. [DOI: 10.1007/s00253-020-10388-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 01/07/2020] [Accepted: 01/16/2020] [Indexed: 12/13/2022]
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13
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Pason P, Sermsathanaswadi J, Waeonukul R, Tachaapaikoon C, Baramee S, Ratanakhanokchai K, Kosugi A. Molecular characterization of hypothetical scaffolding-like protein S1 in multienzyme complex produced by Paenibacillus curdlanolyticus B-6. AMB Express 2019; 9:171. [PMID: 31673804 PMCID: PMC6823336 DOI: 10.1186/s13568-019-0896-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 10/15/2019] [Indexed: 11/24/2022] Open
Abstract
Paenibacillus curdlanolyticus B-6 produces an extracellular multienzyme complex containing a hypothetical scaffolding-like protein and several xylanases and cellulases. The largest (280-kDa) component protein, called S1, has cellulose-binding ability and xylanase activity, thus was considered to function like the scaffolding proteins found in cellulosomes. S1 consists of 863 amino acid residues with predicted molecular mass 91,029 Da and includes two N-terminal surface layer homology (SLH) domains, but most of its sequence shows no homology with proteins of known function. Native S1 (nS1) was highly glycosylated. Purified nS1 and recombinant Xyn11A (rXyn11A) as a major xylanase subunit could assemble in a complex, but recombinant S1 (rS1) could not interact with rXyn11A, indicating that S1 glycosylation is necessary for assembly of the multienzyme complex. nS1 and rS1 showed weak, typical endo-xylanase activity, even though they have no homology with known glycosyl hydrolase family enzymes. S1 and its SLH domains bound tightly to the peptide-glycan layer of P. curdlanolyticus B-6, microcrystalline cellulose, and insoluble xylan, indicating that the SLHs of S1 bind to carbohydrate polymers and the cell surface. When nS1 and rXyn11A were co-incubated with birchwood xylan, the degradation ability was synergistically increased compared with that for each protein; however synergy was not observed for rS1 and rXynA. These results indicate that S1 may have a scaffolding protein-like function by interaction with enzyme subunits and polysaccharides through its glycosylated sites and SLH domains.
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Agrawal S, Kaur A, Varghese LM, Mahajan R. Development of novel economical methodologies for zymographic analysis of purified xylano-pectinolytic enzymes using agrowaste-based substrates. Biotechnol Prog 2019; 36:e2913. [PMID: 31531951 DOI: 10.1002/btpr.2913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 08/06/2019] [Accepted: 09/06/2019] [Indexed: 11/06/2022]
Abstract
In this study, zymographic analysis for xylanase and pectinase enzymes has been carried out using agrowaste residues, wheat bran and citrus peel as well as their extracts. Isozymic forms of xylanase as well as pectinase enzyme displayed comparable zymographic bands onto agar petriplates containing either commercial substrates (xylan and pectin), agrowaste-based substrates (wheat bran and citrus peel), or polysaccharides extracted from these agrowastes (crude xylan and pectin extracted from wheat bran and citrus peel, respectively), indicating the fact that agro residues and their extracts can be utilized as a substitute of cost-intensive commercial substrates, xylan and pectin for zymographic analysis. This is the first report revealing the zymographic analysis of xylano-pectinolytic enzymes using agro-based solid residues particles or polysaccharides extracted from agro-based residues.
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Affiliation(s)
- Sharad Agrawal
- Department of Biotechnology, Kurukshetra University, Kurukshetra, India
| | - Amanjot Kaur
- Department of Biotechnology, Kurukshetra University, Kurukshetra, India
| | | | - Ritu Mahajan
- Department of Biotechnology, Kurukshetra University, Kurukshetra, India
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Zhang S, Xu Z, Wang T, Kong J. Endoglucanase improve the growth of homofermentative Lactobacillus spp. in ensilages. J Biotechnol 2019; 295:55-62. [PMID: 30853632 DOI: 10.1016/j.jbiotec.2019.02.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 01/25/2019] [Accepted: 02/05/2019] [Indexed: 10/27/2022]
Abstract
Endoglucanase, an important component of cellulases, is used as additives in ensiling of forage crops. However, its detailed role is unclear in ensilages. In the present study, two endoglucanases Cel5 and Cel9 produced by strain Paenibacillus panacisoli SDMCC050309, previously isolated from ensiled corn stover, were identified in the cultures by microcrystalline cellulose absorption coupled with zymogram analysis. After heterologously expressed in Escherichia coli DE3 and purified, these two proteins were biochemically characterized. Cel5 was 61 kDa and showed maximal activity at pH 7.0 and 45 °C, while the maximum activity was at pH 8.0 and 65 °C for Cel9 with 97 kDa in size. Both of them could degrade carboxymethyl cellulose into cellooligosaccharides, in which cellobiose and cellotriose could be used as substrates for the growth of homofermentative strains Lactobacillus plantarum CGMCC6888 and L. farciminis CCTCC AB2016237, but not for the heterofermentative strains L. brevis SDMCC050297 and L. parafarraginis SDMCC050300. Therefore, we concluded that the added endoglucanase contributed to enhance the growth of homofermentative lactic acid bacteria for high level of lactic acid production in ensilages.
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Affiliation(s)
- Susu Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, PR China
| | - Zhenshang Xu
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Science, Jinan, 250353, PR China
| | - Ting Wang
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Science, Jinan, 250353, PR China
| | - Jian Kong
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, PR China.
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16
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Yadav S, Dubey SK. Cellulose degradation potential of Paenibacillus lautus strain BHU3 and its whole genome sequence. BIORESOURCE TECHNOLOGY 2018; 262:124-131. [PMID: 29702421 DOI: 10.1016/j.biortech.2018.04.067] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 04/15/2018] [Accepted: 04/17/2018] [Indexed: 06/08/2023]
Abstract
The aim of this work was to study cellulose degradation and whole genome sequence of Paenibacillus lautus BHU3 isolate. The 16S rRNA gene sequence analysis revealed genetic relatedness (99%) of Iso 7 with Paenibacillus lautus, Iso 8 with Paenibacillus lactis, and Iso 9 with Bacillus amyloliquefaciens. Clear zone formation followed by CMCase and FPase assays exhibited cellulolytic potential in the order: P. lautus > P. lactis > B. amyloliquefaciens. The most potent isolate, Paenibacillus lautus strain BHU3 was subjected to whole genome analysis with reference to the genomic basis of cellulose degradation. Results showed that P. lautus strain BHU3 contains 6234 protein coding genes of which, 316 were associated with the carbohydrate metabolism. Further, genomic CAZymes analysis indicated that the P. lautus strain BHU3 comprising a range of glycoside hydrolase (GH) family genes (143), may play the vital role(s) in enhancing the cellulolytic attributes, and could be the useful tool for lignocellulosic biomass degradation and waste management.
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Affiliation(s)
- Suman Yadav
- Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Suresh Kumar Dubey
- Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India.
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17
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Jung BK, Hong SJ, Jo HW, Jung Y, Park YJ, Park CE, Kim MC, Ibal JC, Roh DH, Shin JH. Genome sequencing to develop Paenibacillus donghaensis strain JH8 T (KCTC 13049 T=LMG 23780 T) as a microbial fertilizer and correlation to its plant growth-promoting phenotype. Mar Genomics 2018; 37:39-42. [PMID: 33250125 DOI: 10.1016/j.margen.2017.11.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 11/16/2017] [Accepted: 11/18/2017] [Indexed: 11/29/2022]
Abstract
Paenibacillus donghaensis JH8T (KCTC 13049T=LMG 23780T) is a Gram-positive, mesophilic, endospore-forming bacterium isolated from East Sea sediment at depth of 500m in Korea. The strain exhibited plant cell wall hydrolytic and plant growth promoting abilities. The complete genome of P. donghaensis strain JH8T contains 7602 protein-coding sequences and an average GC content of 49.7% in its chromosome (8.54Mbp). Genes encoding proteins related to the degradation of plant cell wall, nitrogen-fixation, phosphate solubilization, and synthesis of siderophore were existed in the P. donghaensis strain JH8T genome, indicating that this strain can be used as an eco-friendly microbial agent for increasing agricultural productivity.
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Affiliation(s)
- Byung Kwon Jung
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Sung-Jun Hong
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Hyung Woo Jo
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - YeonGyun Jung
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Yeong-Jun Park
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Chang Eon Park
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Min-Chul Kim
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Jerald Conrad Ibal
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Dong-Hyun Roh
- Department of Microbiology, Chungbuk National Univeristy, Cheongju 28644, Republic of Korea
| | - Jae-Ho Shin
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu 41566, Republic of Korea; Institute of Agricultural Science & Technology, Kyungpook National University, Daegu 41566, Republic of Korea.
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18
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Kim ES, Kim BS, Kim KY, Woo HM, Lee SM, Um Y. Aerobic and anaerobic cellulose utilization by Paenibacillus sp. CAA11 and enhancement of its cellulolytic ability by expressing a heterologous endoglucanase. J Biotechnol 2018; 268:21-27. [PMID: 29339118 DOI: 10.1016/j.jbiotec.2018.01.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 01/09/2018] [Accepted: 01/12/2018] [Indexed: 12/21/2022]
Abstract
For cost-effective lignocellulosic biofuel/chemical production, consolidated bioprocessing (CBP)-enabling microorganisms utilizing cellulose as well as producing biofuel/chemical are required. A novel strain Paenibacillus sp. CAA11 isolated from sediment was found to be not only as a cellulose degrader under both aerobic and strict anaerobic conditions but also as a producer of cellulosic biofuel/chemicals. Paenibacillus sp. CAA11 secreted cellulolytic enzymes by its own secretion system and produced ethanol as well as short-chain organic acids (formic acid, acetic acid, lactic acid) from cellulose. Cellulolytic activity of the strain was significantly enhanced by expressing a heterologous endoglucanase 168Cel5 from Bacillus subtilis under both aerobic and anaerobic conditions. The strain harboring the 168cel5 gene revealed 2-fold bigger halo zone on Congo-red plate and 1.75-fold more aerobic cellulose utilization in liquid medium compared with the negative control. Notably, under anaerobic conditions, the recombinant strain expressing 168Cel5 consumed 1.83-fold more cellulose (5.10 g/L) and produced 5-fold more ethanol (0.65 g/L) along with 5-fold more total acids (1.6 g/L) compared with the control, resulting 2.73-fold higher yields. This result demonstrates the potential of Paenibacillus sp. CAA11 as a suitable aerobic and anaerobic CBP-enabling microbe with cellulolytic production of ethanol and short-chain organic acids.
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Affiliation(s)
- Eun Sook Kim
- Clean Energy Research Center, Korea Institute of Science and Technology, 5 Hwarang-ro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea
| | - Byeong-Soo Kim
- Clean Energy Research Center, Korea Institute of Science and Technology, 5 Hwarang-ro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea; Department of Chemical and Biological Engineering, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Ki-Yeon Kim
- Clean Energy Research Center, Korea Institute of Science and Technology, 5 Hwarang-ro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea; Clean Energy and Chemical Engineering, Korea University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, Republic of Korea
| | - Han-Min Woo
- Department of Food Science and Biotechnology, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
| | - Sun-Mi Lee
- Clean Energy Research Center, Korea Institute of Science and Technology, 5 Hwarang-ro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea; Green School (Graduate School of Energy and Environment), Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Youngsoon Um
- Clean Energy Research Center, Korea Institute of Science and Technology, 5 Hwarang-ro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea; Clean Energy and Chemical Engineering, Korea University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, Republic of Korea.
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19
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Sea Water as a Reaction Medium for Bioethanol Production. Microb Biotechnol 2018. [DOI: 10.1007/978-981-10-7140-9_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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20
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Pisa JH, Manfredi AP, Perotti NI, Romero HG, Breccia JD, Martínez MA. Agrowastes as Feedstock for the Production of Endo-β-Xylanase from Cohnella sp. Strain AR92. J Mol Microbiol Biotechnol 2017; 27:277-288. [DOI: 10.1159/000480541] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 08/17/2017] [Indexed: 11/19/2022] Open
Abstract
Members of <i>Cohnella </i>sp. isolated from a variety of environments have been shown to be glycoside hydrolase producers. Nevertheless, most evaluations of members of this genus are limited to their taxonomic description. The strain AR92, previously identified as belonging to the genus <i>Cohnella</i>, formed a well-supported cluster with <i>C. thailandensis</i> and <i>C. formosensis</i> (>80% bootstrap confidence). Its growth and xylanase production were approached by using a mineral-based medium containing alkali-pretreated sugarcane bagasse as the main carbon source, which was assayed as a convenient source to produce biocatalysts potentially fitting its degradation. By means of a two-step statistical approach, the production of endoxylanase was moderately improved (20%). However, a far more significant improvement was observed (145%), by increasing the inoculum size and lowering the fermentation temperature to 25°C, which is below the optimal growth temperature of the strain AR92 (37°C). The xylanolytic preparation produced by <i>Cohnella</i> sp. AR92 contained mild temperature-active endoxylanase (identified as redundant GH10 family) for the main activity which resulted in xylobiose and xylo-oligosaccharides as the main products from birchwood xylan.
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21
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Mahmoudi N, Beaupré SR, Steen AD, Pearson A. Sequential bioavailability of sedimentary organic matter to heterotrophic bacteria. Environ Microbiol 2017; 19:2629-2644. [PMID: 28371310 DOI: 10.1111/1462-2920.13745] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 03/19/2017] [Indexed: 11/28/2022]
Abstract
Aquatic sediments harbour diverse microbial communities that mediate organic matter degradation and influence biogeochemical cycles. The pool of bioavailable carbon continuously changes as a result of abiotic processes and microbial activity. It remains unclear how microbial communities respond to heterogeneous organic matrices and how this ultimately affects heterotrophic respiration. To explore the relationships between the degradation of mixed carbon substrates and microbial activity, we incubated batches of organic-rich sediments in a novel bioreactor (IsoCaRB) that permitted continuous observations of CO2 production rates, as well as sequential sampling of isotopic signatures (δ13 C, Δ14 C), microbial community structure and diversity, and extracellular enzyme activity. Our results indicated that lower molecular weight (MW), labile, phytoplankton-derived compounds were degraded first, followed by petroleum-derived exogenous pollutants, and finally by higher MW polymeric plant material. This shift in utilization coincided with a community succession and increased extracellular enzyme activities. Thus, sequential utilization of different carbon pools induced changes at both the community and cellular level, shifting community composition, enzyme activity, respiration rates, and residual organic matter reactivity. Our results provide novel insight into the accessibility of sedimentary organic matter and demonstrate how bioavailability of natural organic substrates may affect the function and composition of heterotrophic bacterial populations.
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Affiliation(s)
- Nagissa Mahmoudi
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA, 02138, USA
| | - Steven R Beaupré
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, 11794-5000, USA
| | - Andrew D Steen
- Department of Earth and Planetary Sciences, University of Tennessee, Knoxville, TN, 37996, USA
| | - Ann Pearson
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA, 02138, USA
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22
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Jain A, Pelle HS, Baughman WH, Henson JM. Conversion of ammonia-pretreated switchgrass to biofuel precursors by bacterial-fungal consortia under solid-state and submerged-state cultivation. J Appl Microbiol 2017; 122:953-963. [PMID: 27626760 DOI: 10.1111/jam.13295] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 08/22/2016] [Accepted: 08/25/2016] [Indexed: 11/27/2022]
Abstract
AIM The aim of this study was to develop and evaluate bacterial-fungal communities to deconstruct switchgrass to biofuel precursors. METHODS AND RESULTS Bacterial-fungal consortia, mesophilic (25°C) and thermophilic (50°C), were enriched from switchgrass bales from which enzyme mixtures were used to deconstruct delignified switchgrass (DSG). The bacterial-fungal consortia were able to produce enzymes including endoglucanase, exoglucanase, β-glucosidase, xylanase, xylosidase and pectinase to convert DSG to soluble carbohydrates. 454 pyrosequencing revealed that Paenibacillus and Streptomyces were the dominant bacteria in the mesophilic and thermophilic consortia respectively. Penicillium and Acremonium were the dominant fungi in the mesophilic consortia, whereas Aspergillus and Penicillium were the dominant fungi present in the thermophilic consortia. CONCLUSIONS The results show that the state of cultivation, solid-state or submerged-state, affects the community structure as well as enzyme activities produced by these bacterial-fungal consortia. The enzyme mixture produced by the bacterial-fungal consortia released a higher amount of xylose than glucose during saccharification of DSG. SIGNIFICANCE AND IMPACT OF THE STUDY The study provides a novel approach to produce enzymes for conversion of lignocellulolytic feedstocks to soluble sugars which can be used to produce biofuel precursors.
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Affiliation(s)
- A Jain
- Biotechnology Institute, University of Minnesota, Twin Cities, Falcon Heights, MN, USA
| | - H S Pelle
- Department of Biology, Sacred Heart University, Fairfield, CT, USA
| | - W H Baughman
- University of South Carolina School of Law, Columbia, SC, USA
| | - J M Henson
- Department of Biological Sciences, Clemson University, Clemson, SC, USA
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Hero JS, Pisa JH, Perotti NI, Romero CM, Martínez MA. Endoglucanase and xylanase production by Bacillus sp. AR03 in co-culture. Prep Biochem Biotechnol 2017; 47:589-596. [PMID: 28106512 DOI: 10.1080/10826068.2017.1280826] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The behavior of three isolates retrieved from different cellulolytic consortia, Bacillus sp. AR03, Paenibacillus sp. AR247 and Achromobacter sp. AR476-2, were examined individually and as co-cultures in order to evaluate their ability to produce extracellular cellulases and xylanases. Utilizing a peptone-based medium supplemented with carboxymethyl cellulose (CMC), an increase estimation of 1.30 and 1.50 times was obtained by the co-culture containing the strains AR03 and AR247, with respect to enzyme titles registered by their individual cultivation. On the contrary, the extracellular enzymatic production decreased during the co-cultivation of strain AR03 with the non-cellulolytic Achromobacter sp. AR476-2. The synergistic behavior observed through the combined cultivation of the strains AR03 and AR247 might be a consequence of the consumption by Paenibacillus sp. AR247 of the products of the CMC hydrolysis (i.e., cellobiose and/or cello-oligosaccharides), which were mostly generated by the cellulase producer Bacillus sp. AR03. The effect observed could be driven by the requirement to fulfill the nutritional supply from both strains on the substrate evaluated. These results would contribute to a better description of the degradation of the cellulose fraction of the plant cell walls in nature, expected to an efficient utilization of renewable sources.
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Affiliation(s)
- Johan S Hero
- a PROIMI Planta Piloto de Procesos Industriales Microbiológicos , CONICET , Tucumán , Argentina
| | - José H Pisa
- a PROIMI Planta Piloto de Procesos Industriales Microbiológicos , CONICET , Tucumán , Argentina
| | - Nora I Perotti
- a PROIMI Planta Piloto de Procesos Industriales Microbiológicos , CONICET , Tucumán , Argentina.,b Facultad de Ciencias Exactas y Tecnología , Universidad Nacional de Tucumán , Tucumán , Argentina
| | - Cintia M Romero
- a PROIMI Planta Piloto de Procesos Industriales Microbiológicos , CONICET , Tucumán , Argentina.,c Facultad de Bioquímica, Química y Farmacia , Universidad Nacional de Tucumán , Tucumán , Argentina
| | - María A Martínez
- a PROIMI Planta Piloto de Procesos Industriales Microbiológicos , CONICET , Tucumán , Argentina.,b Facultad de Ciencias Exactas y Tecnología , Universidad Nacional de Tucumán , Tucumán , Argentina
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Sermsathanaswadi J, Baramee S, Tachaapaikoon C, Pason P, Ratanakhanokchai K, Kosugi A. The family 22 carbohydrate-binding module of bifunctional xylanase/β-glucanase Xyn10E from Paenibacillus curdlanolyticus B-6 has an important role in lignocellulose degradation. Enzyme Microb Technol 2017; 96:75-84. [DOI: 10.1016/j.enzmictec.2016.09.015] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 09/05/2016] [Accepted: 09/24/2016] [Indexed: 10/20/2022]
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25
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How to transform a recalcitrant Paenibacillus strain: From culture medium to restriction barrier. J Microbiol Methods 2016; 131:135-143. [PMID: 27780731 DOI: 10.1016/j.mimet.2016.10.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 10/11/2016] [Accepted: 10/21/2016] [Indexed: 11/20/2022]
Abstract
Paenibacillus riograndensis SBR5T is a plant growth-promoting bacterium isolated from the wheat rhizosphere. Its recalcitrance to genetic manipulation is a major bottleneck for molecular studies, as has been reported for other Paenibacillus environmental isolates. An efficient electroporation protocol was established by evaluating diverse parameters and optimizing the culture medium, culture growth phase, electroporation solution, recovery medium, DNA input, and electric field strength. Efficiencies of approximately 2.8×104transformantsμg-1 of plasmid DNA were obtained. The optimized protocol was tested with other Paenibacillus species, and the relevance of bypassing the restriction DNA defense system to transform Paenibacillus was highlighted. This protocol is the tool needed to deepen molecular studies with this strain and will aid in the manipulation of other new environmental isolates that also exhibit recalcitrant transformation difficulties.
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26
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Baramee S, Teeravivattanakit T, Phitsuwan P, Waeonukul R, Pason P, Tachaapaikoon C, Kosugi A, Sakka K, Ratanakhanokchai K. A novel GH6 cellobiohydrolase from Paenibacillus curdlanolyticus B-6 and its synergistic action on cellulose degradation. Appl Microbiol Biotechnol 2016; 101:1175-1188. [PMID: 27743043 DOI: 10.1007/s00253-016-7895-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Revised: 09/12/2016] [Accepted: 09/25/2016] [Indexed: 11/30/2022]
Abstract
We recently discovered a novel glycoside hydrolase family 6 (GH6) cellobiohydrolase from Paenibacillus curdlanolyticus B-6 (PcCel6A), which is rarely found in bacteria. This enzyme is a true exo-type cellobiohydrolase which exhibits high substrate specificity on amorphous cellulose and low substrate specificity on crystalline cellulose, while this showed no activity on substitution substrates, carboxymethyl cellulose and xylan, distinct from all other known GH6 cellobiohydrolases. Product profiles, HPLC analysis of the hydrolysis products and a schematic drawing of the substrate-binding subsites catalysing cellooligosaccharides can explain the new mode of action of this enzyme which prefers to hydrolyse cellopentaose. PcCel6A was not inhibited by glucose or cellobiose at concentrations up to 300 and 100 mM, respectively. A good synergistic effect for glucose production was found when PcCel6A acted together with processive endoglucanase Cel9R from Clostridium thermocellum and β-glucosidase CglT from Thermoanaerobacter brockii. These properties of PcCel6A make it a suitable candidate for industrial application in the cellulose degradation process.
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Affiliation(s)
- Sirilak Baramee
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Thitiporn Teeravivattanakit
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Paripok Phitsuwan
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Rattiya Waeonukul
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Patthra Pason
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Chakrit Tachaapaikoon
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Akihiko Kosugi
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences, Tsukuba, Ibaraki, 305-8686, Japan
| | - Kazuo Sakka
- Graduated School of Bioresources, Mie University, Tsu, Mie, 514-8507, Japan
| | - Khanok Ratanakhanokchai
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand.
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Novel Trifunctional Xylanolytic Enzyme Axy43A from Paenibacillus curdlanolyticus Strain B-6 Exhibiting Endo-Xylanase, β-d-Xylosidase, and Arabinoxylan Arabinofuranohydrolase Activities. Appl Environ Microbiol 2016; 82:6942-6951. [PMID: 27663030 DOI: 10.1128/aem.02256-16] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 09/13/2016] [Indexed: 11/20/2022] Open
Abstract
The axy43A gene encoding the intracellular trifunctional xylanolytic enzyme from Paenibacillus curdlanolyticus B-6 was cloned and expressed in Escherichia coli Recombinant PcAxy43A consisting of a glycoside hydrolase family 43 and a family 6 carbohydrate-binding module exhibited endo-xylanase, β-xylosidase, and arabinoxylan arabinofuranohydrolase activities. PcAxy43A hydrolyzed xylohexaose and birch wood xylan to release a series of xylooligosaccharides, indicating that PcAxy43A contained endo-xylanase activity. PcAxy43A exhibited β-xylosidase activity toward a chromogenic substrate, p-nitrophenyl-β-d-xylopyranoside, and xylobiose, while it preferred to hydrolyze long-chain xylooligosaccharides rather than xylobiose. In addition, surprisingly, PcAxy43A showed arabinoxylan arabinofuranohydrolase activity; that is, it released arabinose from both singly and doubly arabinosylated xylose, α-l-Araf-(1→2)-d-Xylp or α-l-Araf-(1→3)-d-Xylp and α-l-Araf-(1→2)-[α-l-Araf-(1→3)]-β-d-Xylp Moreover, the combination of PcAxy43A and P. curdlanolyticus B-6 endo-xylanase Xyn10C greatly improved the efficiency of xylose and arabinose production from the highly substituted rye arabinoxylan, suggesting that these two enzymes function synergistically to depolymerize arabinoxylan. Therefore, PcAxy43A has the potential for the saccharification of arabinoxylan into simple sugars for many applications. IMPORTANCE In this study, the glycoside hydrolase 43 (GH43) intracellular multifunctional endo-xylanase, β-xylosidase, and arabinoxylan arabinofuranohydrolase (AXH) from P. curdlanolyticus B-6 were characterized. Interestingly, PcAxy43A AXH showed a new property that acted on both the C(O)-2 and C(O)-3 positions of xylose residues doubly substituted with arabinosyl, which usually obstruct the action of xylanolytic enzymes. Furthermore, the studies here show interesting properties for the processing of xylans from cereal grains, particularly rye arabinoxylan, and show a novel relationship between PcAxy43A and endo-xylanase Xyn10C from strain B-6, providing novel metabolic potential for processing arabinoxylans into xylose and arabinose.
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Nadaroglu H, Adiguzel G, Adiguzel A, Sonmez Z. A thermostable-endo-β-(1,4)-mannanase from Pediococcus acidilactici (M17): purification, characterization and its application in fruit juice clarification. Eur Food Res Technol 2016. [DOI: 10.1007/s00217-016-2735-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Ghio S, Insani EM, Piccinni FE, Talia PM, Grasso DH, Campos E. GH10 XynA is the main xylanase identified in the crude enzymatic extract of Paenibacillus sp. A59 when grown on xylan or lignocellulosic biomass. Microbiol Res 2016; 186-187:16-26. [DOI: 10.1016/j.micres.2016.02.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 02/23/2016] [Accepted: 02/29/2016] [Indexed: 12/15/2022]
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Adiguzel A, Nadaroglu H, Adiguzel G. Purification and characterization of [Formula: see text]-mannanase from Bacillus pumilus (M27) and its applications in some fruit juices. JOURNAL OF FOOD SCIENCE AND TECHNOLOGY 2015; 52:5292-5298. [PMID: 26243955 PMCID: PMC4519521 DOI: 10.1007/s13197-014-1609-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 09/08/2014] [Accepted: 10/13/2014] [Indexed: 10/24/2022]
Abstract
Thermo alkaline mannanase was purified from the bacteria of Bacillus pumilus (M27) using the techniques of ammonium sulphate precipitation, DEAE-Sephadex ion exchange chromatography and Sephacryl S200 gel filtration chromatography with 111-fold and 36 % yield. It was determined that the enzyme had 2 sub-units including 35 kDa and 55 kDa in gel filtration chromatography and SDS-PAGE electrophoresis systems. The optimum pH and temperature was determined as 8 and 60 °C, respectively. It was also noticed that the enzyme did not lose its activity at a wide interval such as pH 3-11 and at high temperatures such as 90 °C. Additionally, the effects of some metal ions on the mannanase enzyme activity. Moreover, the clarifying efficiency of purified mannanase enzyme with some fruit juices such as orange, apricot, grape and apple was also investigated. Enzymatic treatment was carried out with 1 mL L(-1) of purified mannanase for 1 h at 60 °C. It was determined that the highest pure enzyme was efficient upon clarifying the apple juice at 154 % rate.
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Affiliation(s)
- Ahmet Adiguzel
- />Faculty of Science, Department of Molecular Biology and Genetic, Ataturk University, 25240 Erzurum, Turkey
| | - Hayrunnisa Nadaroglu
- />Department of Food Technology, Erzurum Vocational Training School, Ataturk University, 25240 Erzurum, Turkey
| | - Gulsah Adiguzel
- />Department of Food Hygiene and Technology, Faculty of Veterinary, Ataturk University, 25240 Erzurum, Turkey
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Paenibacillus curdlanolyticus B-6 xylanase Xyn10C capable of producing a doubly arabinose-substituted xylose, α-l-Araf-(1→2)-[α-l-Araf-(1→3)]-d-Xylp, from rye arabinoxylan. Enzyme Microb Technol 2015; 72:1-9. [DOI: 10.1016/j.enzmictec.2015.02.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Revised: 01/31/2015] [Accepted: 02/05/2015] [Indexed: 11/18/2022]
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Baramee S, Phitsuwan P, Waeonukul R, Pason P, Tachaapaikoon C, Kosugi A, Ratanakhanokchai K. Alkaline xylanolytic–cellulolytic multienzyme complex from the novel anaerobic alkalithermophilic bacterium Cellulosibacter alkalithermophilus and its hydrolysis of insoluble polysaccharides under neutral and alkaline conditions. Process Biochem 2015. [DOI: 10.1016/j.procbio.2015.01.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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33
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Septiningrum K, Ohi H, Waeonukul R, Pason P, Tachaapaikoon C, Ratanakhanokchai K, Sermsathanaswadi J, Deng L, Prawitwong P, Kosugi A. The GH67 α-glucuronidase of Paenibacillus curdlanolyticus B-6 removes hexenuronic acid groups and facilitates biodegradation of the model xylooligosaccharide hexenuronosyl xylotriose. Enzyme Microb Technol 2015; 71:28-35. [PMID: 25765307 DOI: 10.1016/j.enzmictec.2015.01.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 11/25/2014] [Accepted: 01/19/2015] [Indexed: 10/24/2022]
Abstract
4-O-Methylglucuronic acid (MeGlcA) side groups attached to the xylan backbone through α-1,2 linkages are converted to hexenuronic acid (HexA) during alkaline pulping. α-Glucuronidase (EC 3.2.1.139) hydrolyzes 1,2-linked MeGlcA from xylooligosaccharides. To determine whether α-glucuronidase can also hydrolyze HexA-decorated xylooligosaccharides, a gene encoding α-glucuronidase (AguA) was cloned from Paenibacillus curdlanolyticus B-6. The purified protein degraded hexenuronosyl xylotriose (ΔX3), a model substrate prepared from kraft pulp. AguA released xylotriose and HexA from ΔX3, but the Vmax and kcat values for ΔX3 were lower than those for MeGlcA, indicating that HexA side groups may affect the hydrolytic activity. To explore the potential for biological bleaching, ΔX3 degradation was performed using intracellular extract from P. curdlanolyticus B-6. The intracellular extract, with synergistic α-glucuronidase and β-xylosidase activities, degraded ΔX3 to xylose and HexA. These results indicate that α-glucuronidase can be used to remove HexA from ΔX3 derived from pulp, reducing the need for chemical treatments in the pulping process.
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Affiliation(s)
- Krisna Septiningrum
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan; Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
| | - Hiroshi Ohi
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Rattiya Waeonukul
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkuntien, Bangkok 10150, Thailand
| | - Patthra Pason
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkuntien, Bangkok 10150, Thailand
| | - Chakrit Tachaapaikoon
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkuntien, Bangkok 10150, Thailand
| | - Khanok Ratanakhanokchai
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkuntien, Bangkok 10150, Thailand
| | - Junjarus Sermsathanaswadi
- Department of Chemical Technology, Faculty of Science and Technology, Suan Dusit Rajabhat University, 295 Rajasrima Road, Dusit, Bangkok 10300, Thailand
| | - Lan Deng
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
| | - Panida Prawitwong
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
| | - Akihiko Kosugi
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan; Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan.
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Mathews SL, Pawlak J, Grunden AM. Bacterial biodegradation and bioconversion of industrial lignocellulosic streams. Appl Microbiol Biotechnol 2015; 99:2939-54. [PMID: 25722022 DOI: 10.1007/s00253-015-6471-y] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Revised: 02/05/2015] [Accepted: 02/08/2015] [Indexed: 01/10/2023]
Abstract
Lignocellulose is a term for plant materials that are composed of matrices of cellulose, hemicellulose, and lignin. Lignocellulose is a renewable feedstock for many industries. Lignocellulosic materials are used for the production of paper, fuels, and chemicals. Typically, industry focuses on transforming the polysaccharides present in lignocellulose into products resulting in the incomplete use of this resource. The materials that are not completely used make up the underutilized streams of materials that contain cellulose, hemicellulose, and lignin. These underutilized streams have potential for conversion into valuable products. Treatment of these lignocellulosic streams with bacteria, which specifically degrade lignocellulose through the action of enzymes, offers a low-energy and low-cost method for biodegradation and bioconversion. This review describes lignocellulosic streams and summarizes different aspects of biological treatments including the bacteria isolated from lignocellulose-containing environments and enzymes which may be used for bioconversion. The chemicals produced during bioconversion can be used for a variety of products including adhesives, plastics, resins, food additives, and petrochemical replacements.
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Affiliation(s)
- Stephanie L Mathews
- Department of Plant and Microbial Biology, North Carolina State University, 4550A Thomas Hall, Campus Box 7612, Raleigh, NC, 27695, USA,
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KURRATAA'YUN, YOPI, MERYANDINI ANJA. Characterization of Xylanase activity produced by Paenibacillus sp. XJ18 from TNBD Jambi, Indonesia. HAYATI JOURNAL OF BIOSCIENCES 2015. [DOI: 10.4308/hjb.22.1.20] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Tian JH, Pourcher AM, Bouchez T, Gelhaye E, Peu P. Occurrence of lignin degradation genotypes and phenotypes among prokaryotes. Appl Microbiol Biotechnol 2014; 98:9527-44. [PMID: 25343973 DOI: 10.1007/s00253-014-6142-4] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 10/06/2014] [Accepted: 10/07/2014] [Indexed: 11/24/2022]
Abstract
A number of prokaryotes actively contribute to lignin degradation in nature and their activity could be of interest for many applications including the production of biogas/biofuel from lignocellulosic biomass and biopulping. This review compares the reliability and efficiency of the culture-dependent screening methods currently used for the isolation of ligninolytic prokaryotes. Isolated prokaryotes exhibiting lignin-degrading potential are presented according to their phylogenetic groups. With the development of bioinformatics, culture-independent techniques are emerging that allow larger-scale data mining for ligninolytic prokaryotic functions but today, these techniques still have some limits. In this work, two phylogenetic affiliations of isolated prokaryotes exhibiting ligninolytic potential and laccase-encoding prokaryotes were determined on the basis of 16S rDNA sequences, providing a comparative view of results obtained by the two types of screening techniques. The combination of laboratory culture and bioinformatics approaches is a promising way to explore lignin-degrading prokaryotes.
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Affiliation(s)
- Jiang-Hao Tian
- IRSTEA, UR GERE, 17 avenue de Cucillé, CS 64427, 35044, Rennes, France
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37
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Gastelum-Arellanez A, Paredes-López O, Olalde-Portugal V. Extracellular endoglucanase activity from Paenibacillus polymyxa BEb-40: production, optimization and enzymatic characterization. World J Microbiol Biotechnol 2014; 30:2953-65. [DOI: 10.1007/s11274-014-1723-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Accepted: 08/14/2014] [Indexed: 10/24/2022]
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Singh S, Moholkar VS, Goyal A. Optimization of carboxymethylcellulase production from Bacillus amyloliquefaciens SS35. 3 Biotech 2014; 4:411-424. [PMID: 28324477 PMCID: PMC4145630 DOI: 10.1007/s13205-013-0169-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2013] [Accepted: 08/26/2013] [Indexed: 11/21/2022] Open
Abstract
In this paper, we have attempted optimization of production of enzyme carboxymethylcellulase or endoglucanase from the bacterium Bacillus amyloliquefaciens SS35. Optimization has been carried out in two stages using statistical experimental design, viz. medium optimization and optimization of fermentation parameters. For medium optimization, Plackett–Burman design followed by central composite design (CCD) was used, while for optimization of fermentation parameters one-variable-at-a-time method followed by CCD was used. Carbon and nitrogen sources in the medium have been revealed to be the significant factors for enzyme production (carboxymethylcellulose 18.05 g/L; yeast extract 8 g/L and peptone 2 g/L). The inorganic salts have been found to be insignificant components of medium. Optimum fermentation parameters for optimized medium were: initial medium pH 5.65, incubation temperature = 40 °C, shaking speed = 120 rpm, and inoculum size = 6.96 %, v/v. Interestingly, the influence of all four parameters was almost independent with no interlinks. Secondly, the overall effect of all parameters was also low, as indicated by linear, square and interaction regression coefficients that were at least one order of magnitude lower than the intercept in the model equation. These results essentially meant that medium components dominate overall enzyme production process in comparison to fermentation parameters.
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Mathews SL, Pawlak JJ, Grunden AM. Isolation of Paenibacillus glucanolyticus from pulp mill sources with potential to deconstruct pulping waste. BIORESOURCE TECHNOLOGY 2014; 164:100-5. [PMID: 24841577 DOI: 10.1016/j.biortech.2014.04.093] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 04/14/2014] [Accepted: 04/25/2014] [Indexed: 05/24/2023]
Abstract
Black liquor is a pulping waste generated by the kraft process that has potential for downstream bioconversion. A microorganism was isolated from a black liquor sample collected from the Department of Forest Biomaterials at North Carolina State University. The organism was identified as Paenibacillus glucanolyticus using 16S rRNA sequence analysis and was shown to be capable of growth on black liquor as the sole carbon source based on minimal media growth studies. Minimal media growth curves demonstrated that this facultative anaerobic microorganism can degrade black liquor as well as cellulose, hemicellulose, and lignin. Gas chromatography-mass spectrometry was used to identify products generated by P. glucanolyticus when it was grown anaerobically on black liquor. Fermentation products which could be converted into high-value chemicals such as succinic, propanoic, lactic, and malonic acids were detected.
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Affiliation(s)
- Stephanie L Mathews
- Department of Plant and Microbial Biology, 4550A Thomas Hall, Campus Box 7612, North Carolina State University, Raleigh, NC 27695, USA; Department of Forest Biomaterials, Biltmore Hall, Campus Box 8005, North Carolina State University, Raleigh, NC 27695, USA.
| | - Joel J Pawlak
- Department of Forest Biomaterials, Biltmore Hall, Campus Box 8005, North Carolina State University, Raleigh, NC 27695, USA.
| | - Amy M Grunden
- Department of Plant and Microbial Biology, 4550A Thomas Hall, Campus Box 7612, North Carolina State University, Raleigh, NC 27695, USA.
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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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Biodegradation of palm kernel cake by cellulolytic and hemicellulolytic bacterial cultures through solid state fermentation. ScientificWorldJournal 2014; 2014:729852. [PMID: 25019097 PMCID: PMC4082864 DOI: 10.1155/2014/729852] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 05/15/2014] [Accepted: 05/24/2014] [Indexed: 11/17/2022] Open
Abstract
Four cellulolytic and hemicellulolytic bacterial cultures were purchased from the Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Culture (DSMZ) and the American Type Culture Collection (ATCC). Two experiments were conducted; the objective of the first experiment was to determine the optimum time period required for solid state fermentation (SSF) of palm kernel cake (PKC), whereas the objective of the second experiment was to investigate the effect of combinations of these cellulolytic and hemicellulolytic bacteria on the nutritive quality of the PKC. In the first experiment, the SSF was lasted for 12 days with inoculum size of 10% (v/w) on different PKC to moisture ratios. In the second experiment, fifteen combinations were created among the four microbes with one untreated PKC as a control. The SSF lasted for 9 days, and the samples were autoclaved, dried, and analyzed for proximate analysis. Results showed that bacterial cultures produced high enzymes activities at the 4th day of SSF, whereas their abilities to produce enzymes tended to be decreased to reach zero at the 8th day of SSF. Findings in the second experiment showed that hemicellulose and cellulose was significantly (P < 0.05) decreased, whereas the amount of reducing sugars were significantly (P < 0.05) increased in the fermented PKC (FPKC) compared with untreated PKC.
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Purification and Partial Characterization of an Acidic α-Glucan–Protein Complex from the Fruiting Body ofPleurotus sajor-cajuand Its Effect on Macrophage Activation. Biosci Biotechnol Biochem 2014; 76:1884-90. [DOI: 10.1271/bbb.120371] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Sermsathanaswadi J, Pianwanit S, Pason P, Waeonukul R, Tachaapaikoon C, Ratanakhanokchai K, Septiningrum K, Kosugi A. The C-terminal region of xylanase domain in Xyn11A from Paenibacillus curdlanolyticus B-6 plays an important role in structural stability. Appl Microbiol Biotechnol 2014; 98:8223-33. [DOI: 10.1007/s00253-014-5748-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 03/31/2014] [Accepted: 04/02/2014] [Indexed: 02/02/2023]
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Li YF, Calley JN, Ebert PJ, Helmes EB. Paenibacillus lentus sp. nov., a β-mannanolytic bacterium isolated from mixed soil samples in a selective enrichment using guar gum as the sole carbon source. Int J Syst Evol Microbiol 2014; 64:1166-1172. [DOI: 10.1099/ijs.0.054726-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel bacterial strain, CMG1240T, was isolated in 1988 from mixed soil samples collected from the United States and South America in a selective enrichment medium with guar gum as the sole carbon source. This microbial isolate showed β-mannanolytic activity to hydrolyse the galactomannans present in guar gum. Strain CMG1240T was aerobic, Gram-stain-variable, non-motile, rod-shaped and endospore-forming. It was further examined based on a combination of phenotypic, physiological and genetic characterization. On the basis of 16S rRNA gene sequence similarity, cellular lipid profile and fatty acid composition, strain CMG1240T was shown to belong unequivocally to the genus
Paenibacillus
. Quinone analysis showed that MK-7 was the only menaquinone detected. The main cell-wall sugar was xylose with trace amounts of mannose and glucose. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and unknown glycolipids, phospholipids, phosphoglycolipids and other lipids. The peptidoglycan structure was A1γ (meso-diaminopimelic acid-direct). The major fatty acids were anteiso-C15 : 0 and C16 : 0. The DNA G+C content was 46 mol% as determined experimentally and by analysis of the genomic sequence. The 16S rRNA gene sequence of strain CMG1240T shared highest similarity with that of
Paenibacillus fonticola
ZLT (97.6 %) while all other tested
Paenibacillus
strains showed lower sequence similarities (≤95.3 %). The results of DNA–DNA hybridization and chemotaxonomic tests enabled the genotypic and phenotypic differentiation of strain CMG1240T from
P. fonticola
. Based on these results, strain CMG1240T ( = ATCC BAA-2594T = DSM 25539T) should be designated the type strain of a novel species within the genus
Paenibacillus
, for which the name Paenibacillus lentus sp. nov. is proposed.
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Affiliation(s)
- Yong-Fu Li
- Elanco Animal Health, A Division of Eli Lilly and Company, 211 Perry Parkway, Gaithersburg, MD 20877, USA
| | - John N. Calley
- Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN 46285, USA
| | - Philip J. Ebert
- Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN 46285, USA
| | - Emily Bulian Helmes
- Elanco Animal Health, A Division of Eli Lilly and Company, 211 Perry Parkway, Gaithersburg, MD 20877, USA
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Affiliation(s)
- Hisashi Kimoto
- Department of Bioscience, Faculty of Biotechnology, Fukui Prefectural University
| | - Takafumi Itoh
- Department of Bioscience, Faculty of Biotechnology, Fukui Prefectural University
| | - Takao Hibi
- Department of Bioscience, Faculty of Biotechnology, Fukui Prefectural University
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Raddadi N, Cherif A, Daffonchio D, Fava F. Halo-alkalitolerant and thermostable cellulases with improved tolerance to ionic liquids and organic solvents from Paenibacillus tarimensis isolated from the Chott El Fejej, Sahara desert, Tunisia. BIORESOURCE TECHNOLOGY 2013; 150:121-128. [PMID: 24161550 DOI: 10.1016/j.biortech.2013.09.089] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Revised: 09/19/2013] [Accepted: 09/21/2013] [Indexed: 06/02/2023]
Abstract
The wide number of industrial processes applying cellulases highlights the importance of discovering robust enzymes able to work under harsh conditions. In this study, carboxymethyl cellulase (CMCase) activity of Paenibacillus tarimensis was characterized. A high activity was observed in pH range 3.0-10.5 and 9 mM-5 M NaCl. In high salt buffer at 80°C, >80% and >76% of relative activity was retained at 20% of the ionic liquids (ILs) [EMIM]Ac and [BMIM]Cl; while >40% was detected with 40% [BMIM]Cl. Five CMCases were detected by renaturing SDS-PAGE. Their activity was retained in presence of 1.7 up to 5 M NaCl (for CMC1) or 4.6 M KCl; 5% organic solvents or 10 mM bivalent ions, EDTA and heavy metals; under neutral and halo-alkaline conditions. These cellulases stabile and highly functional under harsh conditions are promising candidates for application in detergents, textiles, paper/pulp industry; and simultaneous ILs treatment-saccharification of lignocellulose.
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Affiliation(s)
- Noura Raddadi
- Dipartimento di Ingegneria Civile, Chimica, Ambientale e dei Materiali (DICAM), Università di Bologna, I-40131 Bologna, Italy.
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Characterization of cellulolytic bacterial cultures grown in different substrates. ScientificWorldJournal 2013; 2013:689235. [PMID: 24319380 PMCID: PMC3844246 DOI: 10.1155/2013/689235] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 09/26/2013] [Indexed: 11/17/2022] Open
Abstract
Nine aerobic cellulolytic bacterial cultures were obtained from the Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Culture (DSMZ) and the American Type Culture Collection (ATCC). The objectives of this study were to characterize the cellulolytic bacteria and to determine the optimum moisture ratio required for solid state fermentation (SSF) of palm kernel cake (PKC). The bacteria cultures were grown on reconstituted nutrient broth, incubated at 30°C and agitated at 200 rpm. Carboxymethyl cellulase, xylanase, and mannanase activities were determined using different substrates and after SSF of PKC. The SSF was conducted for 4 and 7 days with inoculum size of 10% (v/w) on different PKC concentration-to-moisture ratios: 1 : 0.2, 1 : 0.3, 1 : 0.4, and 1 : 0.5. Results showed that Bacillus amyloliquefaciens 1067 DSMZ, Bacillus megaterium 9885 ATCC, Paenibacillus curdlanolyticus 10248 DSMZ, and Paenibacillus polymyxa 842 ATCC produced higher enzyme activities as compared to other bacterial cultures grown on different substrates. The cultures mentioned above also produced higher enzyme activities when they were incubated under SSF using PKC as a substrate in different PKC-to-moisture ratios after 4 days of incubation, indicating that these cellulolytic bacteria can be used to degrade and improve the nutrient quality of PKC.
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Cooperative degradation of chitin by extracellular and cell surface-expressed chitinases from Paenibacillus sp. strain FPU-7. Appl Environ Microbiol 2013; 79:7482-90. [PMID: 24077704 DOI: 10.1128/aem.02483-13] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Chitin, a major component of fungal cell walls and invertebrate cuticles, is an exceedingly abundant polysaccharide, ranking next to cellulose. Industrial demand for chitin and its degradation products as raw materials for fine chemical products is increasing. A bacterium with high chitin-decomposing activity, Paenibacillus sp. strain FPU-7, was isolated from soil by using a screening medium containing α-chitin powder. Although FPU-7 secreted several extracellular chitinases and thoroughly digested the powder, the extracellular fluid alone broke them down incompletely. Based on expression cloning and phylogenetic analysis, at least seven family 18 chitinase genes were found in the FPU-7 genome. Interestingly, the product of only one gene (chiW) was identified as possessing three S-layer homology (SLH) domains and two glycosyl hydrolase family 18 catalytic domains. Since SLH domains are known to function as anchors to the Gram-positive bacterial cell surface, ChiW was suggested to be a novel multimodular surface-expressed enzyme and to play an important role in the complete degradation of chitin. Indeed, the ChiW protein was localized on the cell surface. Each of the seven chitinase genes (chiA to chiF and chiW) was cloned and expressed in Escherichia coli cells for biochemical characterization of their products. In particular, ChiE and ChiW showed high activity for insoluble chitin. The high chitinolytic activity of strain FPU-7 and the chitinases may be useful for environmentally friendly processing of chitin in the manufacture of food and/or medicine.
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Vijayalaxmi S, Anu Appaiah KA, Jayalakshmi SK, Mulimani VH, Sreeramulu K. Production of bioethanol from fermented sugars of sugarcane bagasse produced by lignocellulolytic enzymes of Exiguobacterium sp. VSG-1. Appl Biochem Biotechnol 2013; 171:246-60. [PMID: 23832861 DOI: 10.1007/s12010-013-0366-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2013] [Accepted: 06/23/2013] [Indexed: 11/26/2022]
Abstract
Exiguobacterium sp. VSG-1 was isolated from the soil sample and characterized for the production of lignocellulolytic enzymes. Production of these enzymes by the strain VSG-1 was carried out using steam-exploded sugarcane bagasse (SCB) and found to secrete cellulase, pectinase, mannanase, xylanase, and tannase. The growth and enzyme production were found to be optimum at pH 9.0 and 37 °C. Upon steam explosion of SCB, the cellulose increased by 42 %, whereas hemicelluloses and lignin decreased by 40 and 62 %, respectively. Enzymatic hydrolysis of steam-exploded SCB yielded 640 g/l of total sugars. Fermentation of sugars produced from pretreated SCB was carried out by using Saccharomyces cerevisiae at pH 5.0 and 30 °C. The alcohol produced was calculated and found to be 62.24 g/l corresponding to 78 % of the theoretical yield of ethanol. Hence, the strain VSG-1 has an industrial importance for the production of fermentable sugars for biofuels.
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Affiliation(s)
- S Vijayalaxmi
- Department of Biochemistry, Gulbarga University, Gulbarga, 585106, Karnataka, India
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Eichorst SA, Varanasi P, Stavila V, Zemla M, Auer M, Singh S, Simmons BA, Singer SW. Community dynamics of cellulose-adapted thermophilic bacterial consortia. Environ Microbiol 2013; 15:2573-87. [DOI: 10.1111/1462-2920.12159] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Revised: 04/29/2013] [Accepted: 05/15/2013] [Indexed: 12/01/2022]
Affiliation(s)
| | | | - Vatalie Stavila
- Biological and Materials Sciences Center; Sandia National Laboratories; Livermore; CA; 94551; USA
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