1
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Melo VSD, Gomes BM, Chambergo FS. Biochemical characterization of a xylose-tolerant GH43 β-xylosidase from Geobacillus thermodenitrificans. Carbohydr Res 2023; 532:108901. [PMID: 37487384 DOI: 10.1016/j.carres.2023.108901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 07/12/2023] [Accepted: 07/15/2023] [Indexed: 07/26/2023]
Abstract
Hemicelluloses are the second most abundant polysaccharide in plant biomass, in which xylan is the main constituent. Aiming at the total degradation of xylan and the obtention of fermentable sugars, several enzymes acting synergistically are required, especially β-xylosidases. In this study, β-xylosidase from Geobacillus thermodenitrificans (GtXyl) was expressed in E. coli BL21 and characterized. The enzyme GtXyl has been grouped within the family of glycoside hydrolases 43 (GH43). Results showed that GtXyl obtained the highest activity at pH 5.0 and temperature of 60 °C. In the additive's tests, the enzyme remained stable in the presence of metal ions and EDTA, and showed high tolerance to xylose, with a relative activity of 55.4% at 400 mM. The enzyme also presented bifunctional activity of β-xylosidase and α-l-arabinofuranosidase, with the highest activity on the substrate p-nitrophenyl-β-d-xylopyranoside. The specific activity on p-nitrophenyl-β-d-xylopyranoside was 18.33 U mg-1 and catalytic efficiency of 20.21 mM-1 s-1, which is comparable to other β-xylosidases reported in the literature. Putting together, the GtXyl enzyme presented interesting biochemical characteristics that are desirable for the application in the enzymatic hydrolysis of plant biomass, such as activity at higher temperatures, high thermostability and stability to metal ions.
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Affiliation(s)
- Vandierly Sampaio de Melo
- Laboratory of Biochemistry and Protein Biotechnology, School of Arts, Sciences and Humanities, University of São Paulo, Av. Arlindo Bettio, 1000, São Paulo, CEP: 03828000, Brazil
| | - Brisa Moreira Gomes
- Laboratory of Biochemistry and Protein Biotechnology, School of Arts, Sciences and Humanities, University of São Paulo, Av. Arlindo Bettio, 1000, São Paulo, CEP: 03828000, Brazil
| | - Felipe Santiago Chambergo
- Laboratory of Biochemistry and Protein Biotechnology, School of Arts, Sciences and Humanities, University of São Paulo, Av. Arlindo Bettio, 1000, São Paulo, CEP: 03828000, Brazil.
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2
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Wang F, Yao Z, Zhang X, Han Z, Chu X, Ge X, Lu F, Liu Y. High-level production of xylose from agricultural wastes using GH11 endo-xylanase and GH43 β-xylosidase from Bacillus sp. Bioprocess Biosyst Eng 2022; 45:1705-1717. [PMID: 36063213 DOI: 10.1007/s00449-022-02778-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 08/23/2022] [Indexed: 11/24/2022]
Abstract
As a promising feedstock, alkali-extracted xylan from lignocellulosic biomass is desired for producing xylose, which can be used for renewable biofuels production. In this study, an efficient pathway has been established for low-cost and high-yield production of xylose by hydrolysis of alkali-extracted xylan from agricultural wastes using an endo-1,4-xylanase (XYLA) from Bacillus safensis TCCC 111022 and a β-xylosidase (XYLO) from B. pumilus TCCC 11573. The optimum activities of recombinant XYLA (rXYLA) and XYLO (rXYLO) were 60 ℃ and pH 8.0, and 30 ℃ and pH 7.0, respectively. They were stable over a broad pH range (pH 6.0-11.0 and 7.0-10.0). rXYLO showed a relatively high xylose tolerance up to 100 mM. Furthermore, the yield of xylose from wheat straw, rice straw, corn stover, corncob and sugarcane bagasse by rXYLA and rXYLO was 63.77%, 71.76%, 68.55%, 53.81%, and 58.58%, respectively. This study demonstrated a strategy to produce xylose from agricultural wastes by integrating alkali-extracted xylan and enzymatic hydrolysis.
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Affiliation(s)
- Fenghua Wang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, No.29, 13th Avenue, Tianjin Economic and Technological Development Area, Tianjin, 300457, People's Republic of China
| | - Zhiming Yao
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, No.29, 13th Avenue, Tianjin Economic and Technological Development Area, Tianjin, 300457, People's Republic of China
| | - Xue Zhang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, No.29, 13th Avenue, Tianjin Economic and Technological Development Area, Tianjin, 300457, People's Republic of China
| | - Zhuoxuan Han
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, No.29, 13th Avenue, Tianjin Economic and Technological Development Area, Tianjin, 300457, People's Republic of China
| | - Xiuxiu Chu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, No.29, 13th Avenue, Tianjin Economic and Technological Development Area, Tianjin, 300457, People's Republic of China
| | - Xiuqi Ge
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, No.29, 13th Avenue, Tianjin Economic and Technological Development Area, Tianjin, 300457, People's Republic of China
| | - Fuping Lu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, No.29, 13th Avenue, Tianjin Economic and Technological Development Area, Tianjin, 300457, People's Republic of China.
| | - Yihan Liu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, No.29, 13th Avenue, Tianjin Economic and Technological Development Area, Tianjin, 300457, People's Republic of China.
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3
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Wang F, Ge X, Yuan Z, Zhang X, Chu X, Lu F, Liu Y. Insights into the mechanism for the high-alkaline activity of a novel GH43 β-xylosidase from Bacillus clausii with a promising application to produce xylose. Bioorg Chem 2022; 126:105887. [DOI: 10.1016/j.bioorg.2022.105887] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/09/2022] [Accepted: 05/18/2022] [Indexed: 11/28/2022]
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4
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Verma D, Satyanarayana T. Xylanolytic Extremozymes Retrieved From Environmental Metagenomes: Characteristics, Genetic Engineering, and Applications. Front Microbiol 2020; 11:551109. [PMID: 33042057 PMCID: PMC7527525 DOI: 10.3389/fmicb.2020.551109] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Accepted: 08/21/2020] [Indexed: 01/29/2023] Open
Abstract
Xylanolytic enzymes have extensive applications in paper, food, and feed, pharmaceutical, and biofuel industries. These industries demand xylanases that are functional under extreme conditions, such as high temperature, acidic/alkaline pH, and others, which are prevailing in bioprocessing industries. Despite the availability of several xylan-hydrolyzing enzymes from cultured microbes, there is a huge gap between what is available and what industries require. DNA manipulations as well as protein-engineering techniques are also not quite satisfactory in generating xylan-hydrolyzing extremozymes. With a compound annual growth rate of 6.6% of xylan-hydrolyzing enzymes in the global market, there is a need for xylanolytic extremozymes. Therefore, metagenomic approaches have been employed to uncover hidden xylanolytic genes that were earlier inaccessible in culture-dependent approaches. Appreciable success has been achieved in retrieving several unusual xylanolytic enzymes with novel and desirable characteristics from different extreme environments using functional and sequence-based metagenomic approaches. Moreover, the Carbohydrate Active Enzymes database includes approximately 400 GH-10 and GH-11 unclassified xylanases. This review discusses sources, characteristics, and applications of xylanolytic enzymes obtained through metagenomic approaches and their amelioration by genetic engineering techniques.
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Affiliation(s)
- Digvijay Verma
- Department of Microbiology, Babasaheb Bhimrao Ambedkar (Central) University, Lucknow, India
| | - Tulasi Satyanarayana
- Department of Biological Sciences and Engineering, Netaji Subhas University of Technology, Dwarka, New Delhi, India
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5
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Isolation, Expression and Characterization of the Thermophilic Recombinant Esterase from Geobacillus thermodenitrificans PS01. Appl Biochem Biotechnol 2020; 191:112-124. [DOI: 10.1007/s12010-020-03225-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 01/08/2020] [Indexed: 10/25/2022]
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6
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Liu Y, Huang L, Zheng D, Xu Z, Li Y, Shao S, Zhang Y, Ge X, Lu F. Biochemical characterization of a novel GH43 family β-xylosidase from Bacillus pumilus. Food Chem 2019; 295:653-661. [DOI: 10.1016/j.foodchem.2019.05.163] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 05/15/2019] [Accepted: 05/23/2019] [Indexed: 10/26/2022]
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7
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Parageobacillus thermantarcticus, an Antarctic Cell Factory: From Crop Residue Valorization by Green Chemistry to Astrobiology Studies. DIVERSITY 2019. [DOI: 10.3390/d11080128] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Knowledge of Antarctic habitat biodiversity, both marine and terrestrial, has increased considerably in recent years, causing considerable development in the studies of life science related to Antarctica. In the Austral summer 1986–1987, a new thermophilic bacterium, Parageobacillus thermantarcticus strain M1 was isolated from geothermal soil of the crater of Mount Melbourne (74°22′ S, 164°40′ E) during the Italian Antarctic Expedition. In addition to the biotechnological potential due to the production of exopolysaccharides and thermostable enzymes, successful studies have demonstrated its use in the green chemistry for the transformation and valorization of residual biomass and its employment as a suitable microbial model for astrobiology studies. The recent acquisition of its genome sequence opens up new opportunities for the use of this versatile bacterium in still unexplored biotechnology sectors.
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8
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Singh DN, Sood U, Singh AK, Gupta V, Shakarad M, Rawat CD, Lal R. Genome Sequencing Revealed the Biotechnological Potential of an Obligate Thermophile Geobacillus thermoleovorans Strain RL Isolated from Hot Water Spring. Indian J Microbiol 2019; 59:351-355. [PMID: 31388213 DOI: 10.1007/s12088-019-00809-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 06/04/2019] [Indexed: 01/11/2023] Open
Abstract
In the present study, we report the draft genome sequence of an obligate thermophile Geobacillus thermoleovorans strain RL isolated from Manikaran hot water spring located atop the Himalayan ranges, India. Strain RL grew optimally at 70 °C but not below 45 °C. The draft genome (3.39 Mb) obtained by Illumina sequencing contains 138 contigs with an average G + C content of 52.30%. RAST annotation showed that amino acid metabolism pathways were most dominant followed by carbohydrate metabolism. Genome-wide analysis using NCBI's Prokaryotic Genome Annotation Pipeline revealed that strain RL encodes for a cocktail of industrially important hydrolytic enzymes glycoside hydrolase, α-and β-glucosidase, xylanase, amylase, neopullulanase, pullulanase and lipases required for white biotechnology. In addition, the presence of genes encoding green biocatalyst multicopper polyphenol oxidase (laccase) and an anticancer enzyme l-glutaminase reflects the significance of strain RL in gray and red biotechnology, respectively. Strain RL is a thermophilic multi-enzyme encoding bacterium which could be the source for the recombinant production of biotechnologically significant enzymes. In, addition whole cells of strain RL may be used in bioremediation studies.
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Affiliation(s)
| | - Utkarsh Sood
- 1Department of Zoology, University of Delhi, Delhi, 110007 India.,Present Address: PhiXGen Private Limited, Gurugram, Haryana 122001 India
| | - Amit Kumar Singh
- 3Department of Biotechnology, Jamia Millia Islamia, New Delhi, Delhi 110025 India
| | - Vipin Gupta
- 1Department of Zoology, University of Delhi, Delhi, 110007 India.,Present Address: PhiXGen Private Limited, Gurugram, Haryana 122001 India
| | | | - Charu Dogra Rawat
- 4Department of Zoology, Ramjas College, University of Delhi, Delhi, 110007 India
| | - Rup Lal
- 1Department of Zoology, University of Delhi, Delhi, 110007 India.,Present Address: PhiXGen Private Limited, Gurugram, Haryana 122001 India
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9
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Bibi Z, Ansari A, Zohra RR, Aman A, Ul Qader SA. Production of xylan degrading endo-1, 4-β-xylanase from thermophilicGeobacillus stearothermophilusKIBGE-IB29. JOURNAL OF RADIATION RESEARCH AND APPLIED SCIENCES 2019. [DOI: 10.1016/j.jrras.2014.08.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Zainab Bibi
- The Karachi Institute of Biotechnology and Genetic Engineering (KIBGE), University of Karachi, Karachi, 75270, Pakistan
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10
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Bhardwaj N, Kumar B, Agarwal K, Chaturvedi V, Verma P. Purification and characterization of a thermo-acid/alkali stable xylanases from Aspergillus oryzae LC1 and its application in Xylo-oligosaccharides production from lignocellulosic agricultural wastes. Int J Biol Macromol 2019; 122:1191-1202. [DOI: 10.1016/j.ijbiomac.2018.09.070] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 08/24/2018] [Accepted: 09/12/2018] [Indexed: 01/17/2023]
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11
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Bibi Z, Ul Qader SA, Aman A, Ur Rehman H, Nawaz MA, Karim A, Us Salam I, Waqas M, Kamran A. Xylan deterioration approach: Purification and catalytic behavior optimization of a novel β-1,4-d-xylanohydrolase from Geobacillus stearothermophilus KIBGE-IB29. ACTA ACUST UNITED AC 2019; 21:e00299. [PMID: 30619731 PMCID: PMC6312829 DOI: 10.1016/j.btre.2018.e00299] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Revised: 12/16/2018] [Accepted: 12/17/2018] [Indexed: 12/05/2022]
Abstract
β-1,4-d-Xylanohydrolase from Geobacillus stearothermophilus KIBGE-IB29 was purified and characterized. The catalytic properties revealed significant stability over broad pH and temperature range. Native-PAGE and In-gel activity assay were carried out. Various organic solvents and detergents significantly improved the enzyme activity. β-1,4-d-Xylanohydrolase showed excellent storage stability for prospective industrial use.
The β-1,4-d-xylanohydrolase is an industry valuable catalytic protein and used to synthesize xylooligosaccharides and xylose. In the current study, β-1,4-d-xylanohydrolase from Geobacillus stearothermophilus KIBGE-IB29 was partially purified up to 9.5-fold with a recovery yield of 52%. It exhibited optimal catalytic activity at pH-7.0 and 50 °C within 5 min. Almost 50% activity retained at pH-4.0 to 9.0 however, 70% activity observed within the range of 40 °C to 70 °C. The β-1,4-d-xylanohydrolase showed a significant hydrolytic pattern with 48.7 kDa molecular mass. It was found that the enzymatic activity improved up to 160% with 1.0 mM ethanol. Moreover, the activity of enzyme drastically increased up to 2.3 and 1.5 fold when incubated with Tween 80 and Triton X-100 (1.0 mM), respectively. The β-1,4-d-xylanohydrolase also retained 72% activity at −80 °C after 180 days. Such a remarkable biochemical properties of β-1,4-d-xylanohydrolase make it possible to forecast its potential use in textile and food industries.
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Affiliation(s)
- Zainab Bibi
- Department of Biotechnology, Federal Urdu University of Arts, Science and Technology (FUUAST), Gulshan-e-Iqbal Campus, Karachi, 75300, Pakistan
| | - Shah Ali Ul Qader
- Department of Biochemistry, University of Karachi, Karachi, 75270, Pakistan
| | - Afsheen Aman
- The Karachi Institute of Biotechnology and Genetic Engineering (KIBGE), University of Karachi, Karachi, 75270, Pakistan
| | - Haneef Ur Rehman
- Department of Chemistry, University of Turbat, Kech, Balochistan, Pakistan
| | - Muhammad Asif Nawaz
- Department of Biotechnology, Shaheed Benazir Bhutto University, Sheringal, Dir Upper, KPK, Pakistan
| | - Asad Karim
- Jamil-Ur-Rahman Center for Genome Research, Dr. Punjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Science (ICCBS), University of Karachi, Karachi, 75270, Pakistan
| | - Irum Us Salam
- Department of Biotechnology, Federal Urdu University of Arts, Science and Technology (FUUAST), Gulshan-e-Iqbal Campus, Karachi, 75300, Pakistan
| | - Muhammad Waqas
- Department of Biotechnology, Federal Urdu University of Arts, Science and Technology (FUUAST), Gulshan-e-Iqbal Campus, Karachi, 75300, Pakistan
| | - Aysha Kamran
- Georg-August University School of Science (GAUSS), Georg-August-University Goettingen, Germany.,Department of Biotechnology, University of Karachi, Karachi-75270, Pakistan
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12
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Bibi Z, Nawaz MA, Irum-Us-Salam, Waqas M, Aman A, Qader SAU. Significance of metal ions, solvents and surfactants to improve the xylan degrading behavior of β-1,4-D-xylanohydrolase from Geobacillus stearothermophilus KIBGE-IB29. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2019. [DOI: 10.1016/j.bcab.2018.11.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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13
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Boyce A, Walsh G. Purification and Characterisation of a Thermostable β-Xylosidase from Aspergillus niger van Tieghem of Potential Application in Lignocellulosic Bioethanol Production. Appl Biochem Biotechnol 2018; 186:712-730. [DOI: 10.1007/s12010-018-2761-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 04/11/2018] [Indexed: 12/30/2022]
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14
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Purification and characterization of novel bi-functional GH3 family β-xylosidase/β-glucosidase from Aspergillus niger ADH-11. Int J Biol Macromol 2017; 109:1260-1269. [PMID: 29174354 DOI: 10.1016/j.ijbiomac.2017.11.132] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 11/18/2017] [Accepted: 11/20/2017] [Indexed: 11/22/2022]
Abstract
β-Xylosidase plays an important role in xylan degradation by relieving the end product inhibition of endo-xylanase caused by xylo-oligosaccharides. β-Xylosidase has a wide range of applications in food, feed, paper and pulp, pharmaceutical industries and in bioconversion of lignocellulosic biomass. Hence, in the present study focused on purification, biochemical characterization and partial sequencing of purified β-xylosidase from xylanolytic strain Aspergillus niger ADH-11. Acetone precipitation followed by GPC using Sephacryl S-200 yielded 20.59-fold purified β-xylosidase with 58.30% recovery. SDS-PAGE analysis of purified β-xylosidase relieved a monomeric subunit with a molecular weight 120.48kDa. Kinetic parameters of purified β-xylosidase viz Km, Vmax, Kcat and catalytic efficiency were assessed. Purified β-xylosidase was additionally active on p-nitrophenyl-β-d-glucopyranoside substrate also. Moreover, peptide mass fingerprinting analysis support our biochemical studies and showed that the purified protein is a novel β-xylosidase with β-glucosidase activity and belongs to the bi-functional GH3 superfamily. Besides, tolerance of purified β-xylosidase towards glucose and xylose was also assessed.
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15
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Ramanjaneyulu G, Sridevi A, Seshapani P, Ramya A, Dileep Kumar K, Praveen Kumar Reddy G, Rajasekhar Reddy B. Enhanced production of xylanase by Fusarium sp. BVKT R2 and evaluation of its biomass saccharification efficiency. 3 Biotech 2017; 7:351. [PMID: 28955648 PMCID: PMC5614900 DOI: 10.1007/s13205-017-0977-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 09/12/2017] [Indexed: 11/30/2022] Open
Abstract
Growth of Fusarium sp. BVKT R2, a potential isolate of forest soils of Eastern Ghats on birchwood xylan in mineral salts medium (MSM) under un-optimized conditions of 30 °C, pH of 5.0, 150 rpm and inoculum size of 5 agar plugs for 7 days, yielded titer of 1290 U/mL of xylanase (EC 3.2.1.8). The effect of various operating parameters such as different substrates and their concentration, additional carbon and nitrogen sources, incubation temperature, initial pH, agitation and inoculum size on the production of xylanase by Fusarium sp. BVKT R2 was studied in shake flask culture by one factor at a time approach. The same culture exhibited higher production of xylanase (4200 U/mL) when grown on birch wood xylan in MSM under optimized conditions with an additional carbon source-sorbitol (1.5%) nitrogen source-yeast extract (1.5%) temperature of 30 °C, pH of 5.0, agitation of 200 rpm and inoculum of 6 agar plugs for only 5 days. There was enhancement in xylanase production under optimized conditions by 3.2 folds over yields under un-optimized conditions. Growth of BVKT R2 culture on locally available lignocelluloses-sawdust, rice straw and cotton stalk-in MSM for 5 days released soluble sugars to the maximum extent of 52.76% with respect to sawdust indicating its greater importance in saccharification essential for biotechnological applications.
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Affiliation(s)
- G. Ramanjaneyulu
- Department of Microbiology, Sri Krishnadevaraya University, Anantapuramu, Andhra Pradesh 515003 India
| | - A. Sridevi
- Department of Applied Microbiology, Sri Padmavati Mahila Visvavidyalayam, Tirupati, Andhra Pradesh India
| | - P. Seshapani
- Department of Microbiology, Sri Venkateswara University, Tirupati, Andhra Pradesh India
| | - A. Ramya
- Department of Microbiology, Sri Krishnadevaraya University, Anantapuramu, Andhra Pradesh 515003 India
| | - K. Dileep Kumar
- Department of Microbiology, Sri Krishnadevaraya University, Anantapuramu, Andhra Pradesh 515003 India
| | - G. Praveen Kumar Reddy
- Department of Microbiology, Sri Krishnadevaraya University, Anantapuramu, Andhra Pradesh 515003 India
| | - B. Rajasekhar Reddy
- Department of Microbiology, Sri Krishnadevaraya University, Anantapuramu, Andhra Pradesh 515003 India
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16
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Huang D, Liu J, Qi Y, Yang K, Xu Y, Feng L. Synergistic hydrolysis of xylan using novel xylanases, β-xylosidases, and an α-L-arabinofuranosidase from Geobacillus thermodenitrificans NG80-2. Appl Microbiol Biotechnol 2017; 101:6023-6037. [PMID: 28616644 DOI: 10.1007/s00253-017-8341-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 03/29/2017] [Accepted: 05/08/2017] [Indexed: 01/01/2023]
Abstract
Lignocellulosic biomass from various types of wood has become a renewable resource for production of biofuels and biobased chemicals. Because xylan is the major component of wood hemicelluloses, highly efficient enzymes to enhance xylan hydrolysis can improve the use of lignocellulosic biomass. In this study, a xylanolytic gene cluster was identified from the crude oil-degrading thermophilic strain Geobacillus thermodenitrificans NG80-2. The enzymes involved in xylan hydrolysis, which include two xylanases (XynA1, XynA2), three β-xylosidases (XynB1, XynB2, XynB3), and one α-L-arabinofuranosidase (AbfA), have many unique features, such as high pH tolerance, high thermostability, and a broad substrate range. The three β-xylosidases were highly resistant to inhibition by product (xylose) accumulation. Moreover, the combination of xylanase, β-xylosidase, and α-L-arabinofuranosidase exhibited the largest synergistic action on xylan degradation (XynA2, XynB1, and AbfA on oat spelt or beechwood xylan; XynA2, XynB3, and AbfA on birchwood xylan). We have demonstrated that the proposed enzymatic cocktail almost completely converts complex xylan to xylose and arabinofuranose and has great potential for use in the conversion of plant biomass into biofuels and biochemicals.
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Affiliation(s)
- Di Huang
- TEDA Institute of Biological Sciences and Biotechnology, Tianjin Economic-Technological Development Area (TEDA), Nankai University, 23 Hongda Street, Tianjin, 300457, People's Republic of China.
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin, 300071, People's Republic of China.
- Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin, 300457, People's Republic of China.
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Nankai University, Tianjin, 300071, People's Republic of China.
| | - Jia Liu
- TEDA Institute of Biological Sciences and Biotechnology, Tianjin Economic-Technological Development Area (TEDA), Nankai University, 23 Hongda Street, Tianjin, 300457, People's Republic of China
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin, 300071, People's Republic of China
| | - Yanfei Qi
- TEDA Institute of Biological Sciences and Biotechnology, Tianjin Economic-Technological Development Area (TEDA), Nankai University, 23 Hongda Street, Tianjin, 300457, People's Republic of China
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin, 300071, People's Republic of China
| | - Kexin Yang
- TEDA Institute of Biological Sciences and Biotechnology, Tianjin Economic-Technological Development Area (TEDA), Nankai University, 23 Hongda Street, Tianjin, 300457, People's Republic of China
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin, 300071, People's Republic of China
| | - Yingying Xu
- TEDA Institute of Biological Sciences and Biotechnology, Tianjin Economic-Technological Development Area (TEDA), Nankai University, 23 Hongda Street, Tianjin, 300457, People's Republic of China
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin, 300071, People's Republic of China
| | - Lu Feng
- TEDA Institute of Biological Sciences and Biotechnology, Tianjin Economic-Technological Development Area (TEDA), Nankai University, 23 Hongda Street, Tianjin, 300457, People's Republic of China.
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin, 300071, People's Republic of China.
- Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin, 300457, People's Republic of China.
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Nankai University, Tianjin, 300071, People's Republic of China.
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17
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Daas MJ, Martínez PM, van de Weijer AH, van der Oost J, de Vos WM, Kabel MA, van Kranenburg R. Biochemical characterization of the xylan hydrolysis profile of the extracellular endo-xylanase from Geobacillus thermodenitrificans T12. BMC Biotechnol 2017; 17:44. [PMID: 28521816 PMCID: PMC5437666 DOI: 10.1186/s12896-017-0357-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Accepted: 03/25/2017] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Endo-xylanases are essential in degrading hemicellulose of various lignocellulosic substrates. Hemicellulose degradation by Geobacillus spp. is facilitated by the hemicellulose utilization (HUS) locus that is present in most strains belonging to this genus. As part of the HUS locus, the xynA gene encoding an extracellular endo-xylanase is one of the few secreted enzymes and considered to be the key enzyme to initiate hemicellulose degradation. Several Geobacillus endo-xylanases have been characterized for their optimum temperature, optimum pH and generation of degradation products. However, these analyses provide limited details on the mode of action of the enzymes towards various substrates resulting in a lack of understanding about their hydrolytic potential. RESULTS A HUS-locus associated gene (GtxynA1) from the thermophile Geobacillus thermodenitrificans T12 encodes an extracellular endo-xylanase that belongs to the family 10 glycoside hydrolases (GH10). The GtxynA1 gene was cloned and expressed in Escherichia coli. The resulting endo-xylanase (termed GtXynA1) was purified to homogeneity and showed activity between 40 °C and 80 °C, with an optimum activity at 60 °C, while being active between pH 3.0 to 9.0 with an optimum at pH 6.0. Its thermal stability was high and GtXynA1 showed 85% residual activity after 1 h of incubation at 60 °C. Highest activity was towards wheat arabinoxylan (WAX), beechwood xylan (BeWX) and birchwood xylan (BiWX). GtXynA1 is able to degrade WAX and BeWX producing mainly xylobiose and xylotriose. To determine its mode of action, we compared the hydrolysis products generated by GtXynA1 with those from the well-characterized GH10 endo-xylanase produced from Aspergillus awamori (AaXynA). The main difference in the mode of action between GtXynA1 and AaXynA on WAX is that GtXynA1 is less hindered by arabinosyl substituents and can therefore release shorter oligosaccharides. CONCLUSIONS The G. thermodenitrificans T12 endo-xylanase, GtXynA1, shows temperature tolerance up to 80 °C and high activity to a variety of xylans. The mode of action of GtXynA1 reveals that arabinose substituents do not hamper substrate degradation by GtXynA1. The extensive hydrolysis of branched xylans makes this enzyme particularly suited for the conversion of a broad range of lignocellulosic substrates.
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Affiliation(s)
- Martinus J.A. Daas
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, Wageningen, 6708 WE The Netherlands
| | - Patricia Murciano Martínez
- Laboratory of Food Chemistry, Wageningen University, Bornse Weilanden 9, Wageningen, 6708 WG The Netherlands
| | | | - John van der Oost
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, Wageningen, 6708 WE The Netherlands
| | - Willem M. de Vos
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, Wageningen, 6708 WE The Netherlands
| | - Mirjam A. Kabel
- Laboratory of Food Chemistry, Wageningen University, Bornse Weilanden 9, Wageningen, 6708 WG The Netherlands
| | - Richard van Kranenburg
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, Wageningen, 6708 WE The Netherlands
- Corbion, Arkelsedijk 46, Gorinchem, 4206 AC The Netherlands
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18
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Lemos LN, Pereira RV, Quaggio RB, Martins LF, Moura LMS, da Silva AR, Antunes LP, da Silva AM, Setubal JC. Genome-Centric Analysis of a Thermophilic and Cellulolytic Bacterial Consortium Derived from Composting. Front Microbiol 2017; 8:644. [PMID: 28469608 PMCID: PMC5395642 DOI: 10.3389/fmicb.2017.00644] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 03/29/2017] [Indexed: 11/22/2022] Open
Abstract
Microbial consortia selected from complex lignocellulolytic microbial communities are promising alternatives to deconstruct plant waste, since synergistic action of different enzymes is required for full degradation of plant biomass in biorefining applications. Culture enrichment also facilitates the study of interactions among consortium members, and can be a good source of novel microbial species. Here, we used a sample from a plant waste composting operation in the São Paulo Zoo (Brazil) as inoculum to obtain a thermophilic aerobic consortium enriched through multiple passages at 60°C in carboxymethylcellulose as sole carbon source. The microbial community composition of this consortium was investigated by shotgun metagenomics and genome-centric analysis. Six near-complete (over 90%) genomes were reconstructed. Similarity and phylogenetic analyses show that four of these six genomes are novel, with the following hypothesized identifications: a new Thermobacillus species; the first Bacillus thermozeamaize genome (for which currently only 16S sequences are available) or else the first representative of a new family in the Bacillales order; the first representative of a new genus in the Paenibacillaceae family; and the first representative of a new deep-branching family in the Clostridia class. The reconstructed genomes from known species were identified as Geobacillus thermoglucosidasius and Caldibacillus debilis. The metabolic potential of these recovered genomes based on COG and CAZy analyses show that these genomes encode several glycoside hydrolases (GHs) as well as other genes related to lignocellulose breakdown. The new Thermobacillus species stands out for being the richest in diversity and abundance of GHs, possessing the greatest potential for biomass degradation among the six recovered genomes. We also investigated the presence and activity of the organisms corresponding to these genomes in the composting operation from which the consortium was built, using compost metagenome and metatranscriptome datasets generated in a previous study. We obtained strong evidence that five of the six recovered genomes are indeed present and active in that composting process. We have thus discovered three (perhaps four) new thermophillic bacterial species that add to the increasing repertoire of known lignocellulose degraders, whose biotechnological potential can now be investigated in further studies.
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Affiliation(s)
- Leandro N Lemos
- Departamento de Bioquímica, Instituto de Química, Universidade de São PauloSão Paulo, Brazil.,Programa de Pós-Graduação Interunidades em Bioinformática, Universidade de São PauloSão Paulo, Brazil
| | - Roberta V Pereira
- Departamento de Bioquímica, Instituto de Química, Universidade de São PauloSão Paulo, Brazil
| | - Ronaldo B Quaggio
- Departamento de Bioquímica, Instituto de Química, Universidade de São PauloSão Paulo, Brazil
| | - Layla F Martins
- Departamento de Bioquímica, Instituto de Química, Universidade de São PauloSão Paulo, Brazil
| | - Livia M S Moura
- Departamento de Bioquímica, Instituto de Química, Universidade de São PauloSão Paulo, Brazil.,Programa de Pós-Graduação Interunidades em Bioinformática, Universidade de São PauloSão Paulo, Brazil
| | - Amanda R da Silva
- Departamento de Bioquímica, Instituto de Química, Universidade de São PauloSão Paulo, Brazil.,Programa de Pós-Graduação Interunidades em Bioinformática, Universidade de São PauloSão Paulo, Brazil
| | - Luciana P Antunes
- Departamento de Bioquímica, Instituto de Química, Universidade de São PauloSão Paulo, Brazil
| | - Aline M da Silva
- Departamento de Bioquímica, Instituto de Química, Universidade de São PauloSão Paulo, Brazil
| | - João C Setubal
- Departamento de Bioquímica, Instituto de Química, Universidade de São PauloSão Paulo, Brazil.,Biocomplexity Institute, Virginia TechBlacksburg, VA, USA
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19
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Galanopoulou AP, Moraïs S, Georgoulis A, Morag E, Bayer EA, Hatzinikolaou DG. Insights into the functionality and stability of designer cellulosomes at elevated temperatures. Appl Microbiol Biotechnol 2016; 100:8731-43. [PMID: 27207145 DOI: 10.1007/s00253-016-7594-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 04/23/2016] [Accepted: 04/28/2016] [Indexed: 01/21/2023]
Abstract
Enzymatic breakdown of lignocellulose is a major limiting step in second generation biorefineries. Assembly of the necessary activities into designer cellulosomes increases the productivity of this step by enhancing enzyme synergy through the proximity effect. However, most cellulosomal components are obtained from mesophilic microorganisms, limiting the applications to temperatures up to 50 °C. We hypothesized that a scaffoldin, comprising modular components of mainly mesophilic origin, can function at higher temperatures when combined with thermophilic enzymes, and the resulting designer cellulosomes could be employed in higher temperature reactions. For this purpose, we used a tetravalent scaffoldin constituted of three cohesins of mesophilic origin as well as a cohesin and cellulose-binding module derived from the thermophilic bacterium Clostridium thermocellum. The scaffoldin was combined with four thermophilic enzymes from Geobacillus and Caldicellulosiruptor species, each fused with a dockerin whose specificity matched one of the cohesins. We initially verified that the biochemical properties and thermal stability of the resulting chimeric enzymes were not affected by the presence of the mesophilic dockerins. Then we examined the stability of the individual single-enzyme-scaffoldin complexes and the full tetravalent cellulosome showing that all complexes are stable and functional for at least 6 h at 60 °C. Finally, within this time frame and conditions, the full complex appeared over 50 % more efficient in the hydrolysis of corn stover compared to the free enzymes. Overall, the results support the utilization of scaffoldin components of mesophilic origin at relatively high temperatures and provide a framework for the production of designer cellulosomes suitable for high temperature biorefinery applications.
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Affiliation(s)
- Anastasia P Galanopoulou
- Faculty of Biology, Microbiology Group, National and Kapodistrian University of Athens, Zografou Campus, 15784, Zografou, Attica, Greece
| | - Sarah Moraïs
- Department of Biomolecular Sciences, The Weizmann Institute of Science, 76100, Rehovot, Israel
| | - Anastasios Georgoulis
- Faculty of Biology, Microbiology Group, National and Kapodistrian University of Athens, Zografou Campus, 15784, Zografou, Attica, Greece
| | - Ely Morag
- Department of Biomolecular Sciences, The Weizmann Institute of Science, 76100, Rehovot, Israel
| | - Edward A Bayer
- Department of Biomolecular Sciences, The Weizmann Institute of Science, 76100, Rehovot, Israel
| | - Dimitris G Hatzinikolaou
- Faculty of Biology, Microbiology Group, National and Kapodistrian University of Athens, Zografou Campus, 15784, Zografou, Attica, Greece.
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20
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Suitability of the alkalistable carbonic anhydrase from a polyextremophilic bacterium Aeribacillus pallidus TSHB1 in biomimetic carbon sequestration. Bioprocess Biosyst Eng 2016; 39:1515-25. [PMID: 27215773 DOI: 10.1007/s00449-016-1627-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 05/15/2016] [Indexed: 10/21/2022]
Abstract
Carbonic anhydrase (CA) was produced from the polyextremophilic (halotolerant, moderately thermophilic and alkaliphilic) bacterium Aeribacillus pallidus TSHB1 isolated from water and sediment samples of Choti Anhoni hot spring of Pipariya, Madhya Pradesh (India), is being reported to be suitable for carbon sequestration. Growth and CA production were inhibited at higher CO2 concentration (5-10 %). Under optimized culture variables (tryptone 0.8 %, yeast extract 0.08 %, glucose 1 %, micronutrient solution 1 %, inoculums size 1.10 %, agitation 200 at pH 8, and temperature 55 °C), 3.7-fold higher CA production was attained than that under unoptimized conditions. The zymogram analysis of the partially purified CA revealed an activity band corresponding to 32 kDa. The enzyme is stable in the pH range between 8.0 and 11.0 with T 1/2 of 40, 15, and 8 min at 60, 70, and 80 °C, respectively. The CA of A. pallidus displayed a marked enhancement in the rate of CaCO3 precipitation from aqueous CO2. The CA-aided formation of CaCO3 was 42.5 mg mg(-1) protein. Scanning electron microscopy revealed the formation of rhomboid calcite crystals. This is the first report on the production and applicability of CA from the polyextremophilic A. pallidus in carbon sequestration.
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21
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Behera S, Sharma NK, Arora R, Kumar S. Effect of Evolutionary Adaption on Xylosidase Activity in Thermotolerant Yeast Isolates Kluyveromyces marxianus NIRE-K1 and NIRE-K3. Appl Biochem Biotechnol 2016; 179:1143-54. [DOI: 10.1007/s12010-016-2055-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 03/15/2016] [Indexed: 02/02/2023]
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22
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Biochemical and Thermodynamic Characterization of a Novel, Low Molecular Weight Xylanase from Bacillus Methylotrophicus CSB40 Isolated from Traditional Korean Food. Appl Biochem Biotechnol 2016; 179:126-42. [DOI: 10.1007/s12010-016-1983-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 01/06/2016] [Indexed: 10/22/2022]
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23
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Research Progress Concerning Fungal and Bacterial β-Xylosidases. Appl Biochem Biotechnol 2015; 178:766-95. [DOI: 10.1007/s12010-015-1908-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 10/22/2015] [Indexed: 01/08/2023]
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24
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Cordova LT, Long CP, Venkataramanan KP, Antoniewicz MR. Complete genome sequence, metabolic model construction and phenotypic characterization of Geobacillus LC300, an extremely thermophilic, fast growing, xylose-utilizing bacterium. Metab Eng 2015; 32:74-81. [PMID: 26391740 DOI: 10.1016/j.ymben.2015.09.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Revised: 08/26/2015] [Accepted: 09/11/2015] [Indexed: 02/07/2023]
Abstract
We have isolated a new extremely thermophilic fast-growing Geobacillus strain that can efficiently utilize xylose, glucose, mannose and galactose for cell growth. When grown aerobically at 72 °C, Geobacillus LC300 has a growth rate of 2.15 h(-1) on glucose and 1.52 h(-1) on xylose (doubling time less than 30 min). The corresponding specific glucose and xylose utilization rates are 5.55 g/g/h and 5.24 g/g/h, respectively. As such, Geobacillus LC300 grows 3-times faster than E. coli on glucose and xylose, and has a specific xylose utilization rate that is 3-times higher than the best metabolically engineered organism to date. To gain more insight into the metabolism of Geobacillus LC300 its genome was sequenced using PacBio's RS II single-molecule real-time (SMRT) sequencing platform and annotated using the RAST server. Based on the genome annotation and the measured biomass composition a core metabolic network model was constructed. To further demonstrate the biotechnological potential of this organism, Geobacillus LC300 was grown to high cell-densities in a fed-batch culture, where cells maintained a high xylose utilization rate under low dissolved oxygen concentrations. All of these characteristics make Geobacillus LC300 an attractive host for future metabolic engineering and biotechnology applications.
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Affiliation(s)
- Lauren T Cordova
- Department of Chemical and Biomolecular Engineering, Metabolic Engineering and Systems Biology Laboratory, University of Delaware, 150 Academy St, Newark, DE 19716, USA
| | - Christopher P Long
- Department of Chemical and Biomolecular Engineering, Metabolic Engineering and Systems Biology Laboratory, University of Delaware, 150 Academy St, Newark, DE 19716, USA
| | - Keerthi P Venkataramanan
- Department of Chemical and Biomolecular Engineering, Metabolic Engineering and Systems Biology Laboratory, University of Delaware, 150 Academy St, Newark, DE 19716, USA
| | - Maciek R Antoniewicz
- Department of Chemical and Biomolecular Engineering, Metabolic Engineering and Systems Biology Laboratory, University of Delaware, 150 Academy St, Newark, DE 19716, USA.
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25
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Brumm PJ, De Maayer P, Mead DA, Cowan DA. Genomic analysis of six new Geobacillus strains reveals highly conserved carbohydrate degradation architectures and strategies. Front Microbiol 2015; 6:430. [PMID: 26029180 PMCID: PMC4428132 DOI: 10.3389/fmicb.2015.00430] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 04/22/2015] [Indexed: 11/13/2022] Open
Abstract
In this work we report the whole genome sequences of six new Geobacillus xylanolytic strains along with the genomic analysis of their capability to degrade carbohydrates. The six sequenced Geobacillus strains described here have a range of GC contents from 43.9% to 52.5% and clade with named Geobacillus species throughout the entire genus. We have identified a ~200 kb unique super-cluster in all six strains, containing five to eight distinct carbohydrate degradation clusters in a single genomic region, a feature not seen in other genera. The Geobacillus strains rely on a small number of secreted enzymes located within distinct clusters for carbohydrate utilization, in contrast to most biomass-degrading organisms which contain numerous secreted enzymes located randomly throughout the genomes. All six strains are able to utilize fructose, arabinose, xylose, mannitol, gluconate, xylan, and α-1,6-glucosides. The gene clusters for utilization of these seven substrates have identical organization and the individual proteins have a high percent identity to their homologs. The strains show significant differences in their ability to utilize inositol, sucrose, lactose, α-mannosides, α-1,4-glucosides and arabinan.
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Affiliation(s)
- Phillip J. Brumm
- C5•6 TechnologiesMiddleton, WI, USA
- Great Lakes Bioenergy Research Center, University of WisconsinMadison, WI, USA
| | - Pieter De Maayer
- Centre for Microbial Ecology and Genomics, Genomics Research Institute, University of PretoriaPretoria, South Africa
- Department of Microbiology and Plant Pathology, University of PretoriaPretoria, South Africa
| | - David A. Mead
- C5•6 TechnologiesMiddleton, WI, USA
- Great Lakes Bioenergy Research Center, University of WisconsinMadison, WI, USA
- Lucigen CorporationMiddleton, WI, USA
| | - Don A. Cowan
- Centre for Microbial Ecology and Genomics, Genomics Research Institute, University of PretoriaPretoria, South Africa
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26
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Guerriero G, Hausman JF, Strauss J, Ertan H, Siddiqui KS. Destructuring plant biomass: focus on fungal and extremophilic cell wall hydrolases. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 234:180-93. [PMID: 25804821 PMCID: PMC4937988 DOI: 10.1016/j.plantsci.2015.02.010] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 02/17/2015] [Accepted: 02/18/2015] [Indexed: 05/05/2023]
Abstract
The use of plant biomass as feedstock for biomaterial and biofuel production is relevant in the current bio-based economy scenario of valorizing renewable resources. Fungi, which degrade complex and recalcitrant plant polymers, secrete different enzymes that hydrolyze plant cell wall polysaccharides. The present review discusses the current research trends on fungal, as well as extremophilic cell wall hydrolases that can withstand extreme physico-chemical conditions required in efficient industrial processes. Secretomes of fungi from the phyla Ascomycota, Basidiomycota, Zygomycota and Neocallimastigomycota are presented along with metabolic cues (nutrient sensing, coordination of carbon and nitrogen metabolism) affecting their composition. We conclude the review by suggesting further research avenues focused on the one hand on a comprehensive analysis of the physiology and epigenetics underlying cell wall degrading enzyme production in fungi and on the other hand on the analysis of proteins with unknown function and metagenomics of extremophilic consortia. The current advances in consolidated bioprocessing, altered secretory pathways and creation of designer plants are also examined. Furthermore, recent developments in enhancing the activity, stability and reusability of enzymes based on synergistic, proximity and entropic effects, fusion enzymes, structure-guided recombination between homologous enzymes and magnetic enzymes are considered with a view to improving saccharification.
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Affiliation(s)
- Gea Guerriero
- Environmental Research and Innovation (ERIN), Luxembourg Institute of Science and Technology (LIST), Esch/Alzette, Luxembourg.
| | - Jean-Francois Hausman
- Environmental Research and Innovation (ERIN), Luxembourg Institute of Science and Technology (LIST), Esch/Alzette, Luxembourg
| | - Joseph Strauss
- Department of Applied Genetics and Cell Biology, Fungal Genetics and Genomics Unit, University of Natural Resources and Life Sciences Vienna (BOKU), University and Research Center Campus Tulln-Technopol, Tulln/Donau, Austria; Health and Environment Department, Austrian Institute of Technology GmbH - AIT, University and Research Center Campus Tulln-Technopol, Tulln/Donau, Austria
| | - Haluk Ertan
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, Australia; Department of Molecular Biology and Genetics, Istanbul University, Turkey
| | - Khawar Sohail Siddiqui
- Biology Department, King Fahd University of Petroleum and Minerals (KFUPM), Dhahran, Saudi Arabia.
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27
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Production of xylooligosaccharides from garlic straw xylan by purified xylanase from Bacillus mojavensis UEB-FK and their in vitro evaluation as prebiotics. FOOD AND BIOPRODUCTS PROCESSING 2015. [DOI: 10.1016/j.fbp.2014.07.012] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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28
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Properties of an alkali-thermo stable xylanase from Geobacillus thermodenitrificans A333 and applicability in xylooligosaccharides generation. World J Microbiol Biotechnol 2015; 31:633-48. [DOI: 10.1007/s11274-015-1818-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 02/03/2015] [Indexed: 10/24/2022]
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29
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Bhalla A, Bischoff KM, Sani RK. Highly thermostable GH39 β-xylosidase from a Geobacillus sp. strain WSUCF1. BMC Biotechnol 2014; 14:963. [PMID: 25532585 PMCID: PMC4300165 DOI: 10.1186/s12896-014-0106-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 12/01/2014] [Indexed: 11/10/2022] Open
Abstract
Background Complete enzymatic hydrolysis of xylan to xylose requires the action of endoxylanase and β-xylosidase. β-xylosidases play an important part in hydrolyzing xylo-oligosaccharides to xylose. Thermostable β-xylosidases have been a focus of attention as industrially important enzymes due to their long shelf life and role in the relief of end-product inhibition of xylanases caused by xylo-oligosaccharides. Therefore, a highly thermostable β-xylosidase with high specific activity has significant potential in lignocellulose bioconversion. Results A gene encoding a highly thermostable GH39 β-xylosidase was cloned from Geobacillus sp. strain WSUCF1 and expressed in Escherichia coli. Recombinant β-xylosidase was active over a wide range of temperatures and pH with optimum temperature of 70°C and pH 6.5. It exhibited very high thermostability, retaining 50% activity at 70°C after 9 days. WSUCF1 β-xylosidase is more thermostable than β-xylosidases reported from other thermophiles (growth temperature ≤ 70°C). Specific activity was 133 U/mg when incubated with p-nitrophenyl xylopyranoside, with Km and Vmax values of 2.38 mM and 147 U/mg, respectively. SDS-PAGE analysis indicated that the recombinant enzyme had a mass of 58 kDa, but omitting heating prior to electrophoresis increased the apparent mass to 230 kDa, suggesting the enzyme exists as a tetramer. Enzyme exhibited high tolerance to xylose, retained approximately 70% of relative activity at 210 mM xylose concentration. Thin layer chromatography showed that the enzyme had potential to convert xylo-oligomers (xylobiose, triose, tetraose, and pentaose) into fermentable xylose. WSUCF1 β-xylosidase along with WSUCF1 endo-xylanase synergistically converted the xylan into fermentable xylose with more than 90% conversion. Conclusions Properties of the WSUCF1 β-xylosidase i.e. high tolerance to elevated temperatures, high specific activity, conversion of xylo-oligomers to xylose, and resistance to inhibition from xylose, make this enzyme potentially suitable for various biotechnological applications.
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Affiliation(s)
- Aditya Bhalla
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD, 57701, USA. .,Present address: Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA.
| | - Kenneth M Bischoff
- Renewable Product Technology Research Unit, Agricultural Research Service, National Center for Agricultural Utilization Research, U.S. Department of Agriculture, Peoria, IL, 61604, USA.
| | - Rajesh K Sani
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD, 57701, USA.
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Secretion of recombinant thermo-alkali-stable endoxylanase of polyextremophilic Bacillus halodurans TSEV1 and its utility in generating xylooligosaccharides from renewable agro-residues. Process Biochem 2014. [DOI: 10.1016/j.procbio.2014.08.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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31
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Kallel F, Driss D, Chaabouni SE, Ghorbel R. Biological Activities of Xylooligosaccharides Generated from Garlic Straw Xylan by Purified Xylanase from Bacillus mojavensis UEB-FK. Appl Biochem Biotechnol 2014; 175:950-64. [DOI: 10.1007/s12010-014-1308-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Accepted: 10/15/2014] [Indexed: 10/24/2022]
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32
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Jain I, Kumar V, Satyanarayana T. Applicability of recombinant β-xylosidase from the extremely thermophilic bacterium Geobacillus thermodenitrificans in synthesizing alkylxylosides. BIORESOURCE TECHNOLOGY 2014; 170:462-469. [PMID: 25164338 DOI: 10.1016/j.biortech.2014.07.113] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2014] [Revised: 07/26/2014] [Accepted: 07/28/2014] [Indexed: 06/03/2023]
Abstract
The β-xylosidase encoding gene (XsidB) of the extremely thermophilic bacterium Geobacillus thermodenitrificans has been cloned and expressed in Escherichia coli. The homotrimeric recombinant XsidB is of 204.0kDa, which is optimally active at 60°C and pH 7.0 with T1/2 of 58min at 70°C. The β-xylosidase remains unaffected in the presence of most metal ions and organic solvents. The Km [p-nitrophenyl β-xyloside (pNPX)], Vmax and kcat values of the enzyme are 2×10(-3)M, 1250μmolesmg(-1)min(-1) and 13.20×10(5)min(-1), respectively. The enzyme catalyzes transxylosylation reactions in the presence of alcohols as acceptors. The pharmaceutically important β-methyl-d-xylosides could be produced using pNPX as the donor and methanol as acceptor. The products of transxylosylation were identified by TLC and HPLC, and the structure was confirmed by (1)H NMR analysis. The enzyme is also useful in synthesizing transxylosylation products from the wheat bran hydrolysate.
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Affiliation(s)
- Ira Jain
- Department of Microbiology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India.
| | - Vikash Kumar
- Department of Microbiology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India.
| | - T Satyanarayana
- Department of Microbiology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India.
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Zhang S, Wang H, Shi P, Xu B, Bai Y, Luo H, Yao B. Cloning, expression, and characterization of a thermostable β-xylosidase from thermoacidophilic Alicyclobacillus sp. A4. Process Biochem 2014. [DOI: 10.1016/j.procbio.2014.05.020] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Kumar L, Kumar D, Nagar S, Gupta R, Garg N, Kuhad RC, Gupta VK. Modulation of xylanase production from alkaliphilic Bacillus pumilus VLK-1 through process optimization and temperature shift operation. 3 Biotech 2014; 4:345-356. [PMID: 28324471 PMCID: PMC4145618 DOI: 10.1007/s13205-013-0160-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2013] [Accepted: 07/29/2013] [Indexed: 11/16/2022] Open
Abstract
This study was aimed at enhancing the production of xylanase from an alkaliphilic Bacillus pumilus VLK-1 in submerged fermentation using wheat bran, a cheap and abundantly available agro-residue, through process optimization and to monitor the effect of temperature shift operation on it. The potential of xylanase in saccharification of wheat straw was also investigated. The results showed that optimization of the fermentation process by one variable approach increased the enzyme yield from 402 to 4,986 IU/ml. Subsequently, optimization of nitrogen and carbon sources through response surface methodology led to high level xylanase production (7,295 IU/ml) which was 1.46-fold greater than one variable approach after 56 h of cultivation at 30 °C. Temperature shift operation during fermentation resulted in maximum xylanase production in lesser duration (48 h instead of 56 h). Enzymatic hydrolysis of the alkali pre-treated wheat straw with 500 IU xylanase alone released 173 ± 8 mg sugars/g whereas in combination with cellulase and β-glucosidase released 553 ± 12 mg sugars/g dry substrate in 6 h, indicating its potential in saccharification of the lignocellulosic substrate. Temperature shift operation is likely to be attractive for large scale industrial fermentation due to significant reduction in the operating cost. To our knowledge, this is the first report which showed the effect of temperature shift operation on xylanase production from bacteria. The xylanase production from Bacillus sp. in the present study is close to the highest titre reported in the literature. An enhanced xylanase production using wheat bran, a cheap and abundantly available agro-residue, will apparently reduce the enzyme cost, which would be beneficial for industry.
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Affiliation(s)
- Lalit Kumar
- Department of Biochemistry, Kurukshetra University, Kurukshetra, 136119, Haryana, India
| | - Davender Kumar
- Department of Biochemistry, Kurukshetra University, Kurukshetra, 136119, Haryana, India
| | - Sushil Nagar
- Department of Biochemistry, Kurukshetra University, Kurukshetra, 136119, Haryana, India
| | - Rishi Gupta
- Lignocellulose Biotechnology Laboratory, Department of Microbiology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - Neelam Garg
- Department of Microbiology, Kurukshetra University, Kurukshetra, 136119, Haryana, India
| | - Ramesh Chander Kuhad
- Lignocellulose Biotechnology Laboratory, Department of Microbiology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - Vijay Kumar Gupta
- Department of Biochemistry, Kurukshetra University, Kurukshetra, 136119, Haryana, India.
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Discovery and characterization of endo-xylanase and β-xylosidase from a highly xylanolytic bacterium in the hindgut of Holotrichia parallela larvae. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.molcatb.2014.03.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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36
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Production and in vitro evaluation of xylooligosaccharides generated from corncobs using immobilized Penicillium occitanis xylanase. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.molcatb.2014.02.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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37
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Kumar V, Satyanarayana T. Production of endoxylanase with enhanced thermostability by a novel polyextremophilic Bacillus halodurans TSEV1 and its applicability in waste paper deinking. Process Biochem 2014. [DOI: 10.1016/j.procbio.2013.12.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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38
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Kumar V, Satyanarayana T. Production of thermo-alkali-stable xylanase by a novel polyextremophilic Bacillus halodurans TSEV1 in cane molasses medium and its applicability in making whole wheat bread. Bioprocess Biosyst Eng 2013; 37:1043-53. [DOI: 10.1007/s00449-013-1075-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Accepted: 10/06/2013] [Indexed: 11/24/2022]
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Biochemical and thermodynamic characteristics of thermo-alkali-stable xylanase from a novel polyextremophilic Bacillus halodurans TSEV1. Extremophiles 2013; 17:797-808. [DOI: 10.1007/s00792-013-0565-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 07/08/2013] [Indexed: 10/26/2022]
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