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Paredes-Barrada M, Kopsiaftis P, Claassens NJ, van Kranenburg R. Parageobacillus thermoglucosidasius as an emerging thermophilic cell factory. Metab Eng 2024; 83:39-51. [PMID: 38490636 DOI: 10.1016/j.ymben.2024.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 02/21/2024] [Accepted: 03/05/2024] [Indexed: 03/17/2024]
Abstract
Parageobacillus thermoglucosidasius is a thermophilic and facultatively anaerobic microbe, which is emerging as one of the most promising thermophilic model organisms for metabolic engineering. The use of thermophilic microorganisms for industrial bioprocesses provides the advantages of increased reaction rates and reduced cooling costs for bioreactors compared to their mesophilic counterparts. Moreover, it enables starch or lignocellulose degradation and fermentation to occur at the same temperature in a Simultaneous Saccharification and Fermentation (SSF) or Consolidated Bioprocessing (CBP) approach. Its natural hemicellulolytic capabilities and its ability to convert CO to metabolic energy make P. thermoglucosidasius a potentially attractive host for bio-based processes. It can effectively degrade hemicellulose due to a number of hydrolytic enzymes, carbohydrate transporters, and regulatory elements coded from a genomic cluster named Hemicellulose Utilization (HUS) locus. The growing availability of effective genetic engineering tools in P. thermoglucosidasius further starts to open up its potential as a versatile thermophilic cell factory. A number of strain engineering examples showcasing the potential of P. thermoglucosidasius as a microbial chassis for the production of bulk and fine chemicals are presented along with current research bottlenecks. Ultimately, this review provides a holistic overview of the distinct metabolic characteristics of P. thermoglucosidasius and discusses research focused on expanding the native metabolic boundaries for the development of industrially relevant strains.
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Affiliation(s)
- Miguel Paredes-Barrada
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | | | - Nico J Claassens
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.
| | - Richard van Kranenburg
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands; Corbion, Arkelsedijk 46, 4206 AC, Gorinchem, The Netherlands.
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Liang X, Wan D, Tan L, Liu H. Dynamic changes of endophytic bacteria in the bark and leaves of medicinal plant Eucommia ulmoides in different seasons. Microbiol Res 2024; 280:127567. [PMID: 38103467 DOI: 10.1016/j.micres.2023.127567] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 11/28/2023] [Accepted: 12/04/2023] [Indexed: 12/19/2023]
Abstract
The bark and leaves of the Eucommia ulmoides Oliv. (E. ulmoides) have good medicinal value. Studies show endophytes play important roles in host medicinal plant secondary metabolite synthesis, with season being a key influencing factor. Therefore, we used 16 S rRNA to detect endophytic bacteria (EB) in E. ulmoides bark and leaves collected in winter, spring, summer, and autumn, and analyzed the contents of major active components respectively. The results showed that the species diversity and richness of EB of the E. ulmoides bark were higher than those of leaves in all seasons except fall. Among them, the higher species diversity and richness were found in the E. ulmoides bark in winter and spring. EB community structure differed significantly between medicinal tissues and seasons. Concurrently, the bark and leaves of E. ulmoides showed abundant characteristic EB across seasons. For active components, geniposidic acid showed a significant positive correlation with EB diversity and richness, while the opposite was true for aucubin. Additionally, some dominant EB exhibited close correlations with the accumulation of active components. Delftia, enriched in autumn, correlated significantly positively with aucubin. Notably, the impact of the same EB genera on active components differed across medicinal tissues. For example, Sphingomonas, enriched in summer, correlated significantly positively with pinoresinol diglucoside (PDG) in the bark, but with aucubin in the leaves. In summary, EB of E. ulmoides was demonstrated high seasonal dynamics and tissue specificity, with seasonal characteristic EB like Delftia and Sphingomonas correlating with the accumulation of active components in medicinal tissues.
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Affiliation(s)
- Xuejuan Liang
- Institute of Innovative Traditional Chinese Medications, Hunan Academy of Chinese Medicine, Changsha 410013, China
| | - Dan Wan
- Institute of Innovative Traditional Chinese Medications, Hunan Academy of Chinese Medicine, Changsha 410013, China
| | - Lei Tan
- Cili Meteorological Bureau, Zhangjiajie 410013, China
| | - Hao Liu
- Institute of Traditional Chinese Medicine Resources, Hunan Academy of Chinese Medicine, Changsha 410013, China.
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3
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Nithimethachoke T, Boonmak C, Morikawa M. A novel alkane monooxygenase evolved from a broken piece of ribonucleotide reductase in Geobacillus kaustophilus HTA426 isolated from Mariana Trench. Extremophiles 2024; 28:18. [PMID: 38353731 PMCID: PMC10867098 DOI: 10.1007/s00792-024-01332-8] [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: 11/04/2023] [Accepted: 12/30/2023] [Indexed: 02/16/2024]
Abstract
We have accidentally found that a thermophilic Geobacillus kaustophilus HTA426 is capable of degrading alkanes although it has no alkane oxygenating enzyme genes. Our experimental results revealed that a putative ribonucleotide reductase small subunit GkR2loxI (GK2771) gene encodes a novel heterodinuclear Mn-Fe alkane monooxygenase/hydroxylase. GkR2loxI protein can perform two-electron oxidations similar to homonuclear diiron bacterial multicomponent soluble methane monooxygenases. This finding not only answers a long-standing question about the substrate of the R2lox protein clade, but also expands our understanding of the vast diversity and new evolutionary lineage of the bacterial alkane monooxygenase/hydroxylase family.
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Affiliation(s)
- Tanasap Nithimethachoke
- Graduate School of Environmental Science, Hokkaido University, Kita-10 Nishi-5, Kita-ku, Sapporo, 060-0810, Japan
| | - Chanita Boonmak
- Department of Microbiology, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Rd., Lat Yao, Chatuchak, Bangkok, 10900, Thailand
| | - Masaaki Morikawa
- Graduate School of Environmental Science, Hokkaido University, Kita-10 Nishi-5, Kita-ku, Sapporo, 060-0810, Japan.
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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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Millgaard M, Bidart GN, Pogrebnyakov I, Nielsen AT, Welner DH. An improved integrative GFP-based vector for genetic engineering of Parageobacillus thermoglucosidasius facilitates the identification of a key sporulation regulator. AMB Express 2023; 13:44. [PMID: 37154828 PMCID: PMC10167077 DOI: 10.1186/s13568-023-01544-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 04/05/2023] [Indexed: 05/10/2023] Open
Abstract
Parageobacillus thermoglucosidasius is a thermophilic Gram-positive bacterium, which is a promising host organism for sustainable bio-based production processes. However, to take full advantage of the potential of P. thermoglucosidasius, more efficient tools for genetic engineering are required. The present study describes an improved shuttle vector, which speeds up recombination-based genomic modification by incorporating a thermostable sfGFP variant into the vector backbone. This additional selection marker allows for easier identification of recombinants, thereby removing the need for several culturing steps. The novel GFP-based shuttle is therefore capable of facilitating faster metabolic engineering of P. thermoglucosidasius through genomic deletion, integration, or exchange. To demonstrate the efficiency of the new system, the GFP-based vector was utilised for deletion of the spo0A gene in P. thermoglucosidasius DSM2542. This gene is known to be a key regulator of sporulation in Bacillus subtilis, and it was therefore hypothesised that the deletion of spo0A in P. thermoglucosiadius would produce an analogous sporulation-inhibited phenotype. Subsequent analyses of cell morphology and culture heat resistance suggests that the P. thermoglucosidasius ∆spo0A strain is sporulation-deficient. This strain may be an excellent starting point for future cell factory engineering of P. thermoglucosidasius, as the formation of endospores is normally not a desired trait in large-scale production.
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Affiliation(s)
- Marie Millgaard
- The Novo Nordisk Foundation Center for Biosustainability, Building 220, Kemitorvet, 2800, Kgs. Lyngby, Denmark
| | - Gonzalo Nahuel Bidart
- The Novo Nordisk Foundation Center for Biosustainability, Building 220, Kemitorvet, 2800, Kgs. Lyngby, Denmark
| | - Ivan Pogrebnyakov
- The Novo Nordisk Foundation Center for Biosustainability, Building 220, Kemitorvet, 2800, Kgs. Lyngby, Denmark
| | - Alex Toftgaard Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Building 220, Kemitorvet, 2800, Kgs. Lyngby, Denmark.
| | - Ditte Hededam Welner
- The Novo Nordisk Foundation Center for Biosustainability, Building 220, Kemitorvet, 2800, Kgs. Lyngby, Denmark.
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Li M, Yu J, Cao L, Yin Y, Su Z, Chen S, Li G, Ma T. Facultative anaerobic conversion of lignocellulose biomass to new bioemulsifier by thermophilic Geobacillus thermodenitrificans NG80-2. JOURNAL OF HAZARDOUS MATERIALS 2023; 443:130210. [PMID: 36308930 DOI: 10.1016/j.jhazmat.2022.130210] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 10/06/2022] [Accepted: 10/16/2022] [Indexed: 06/16/2023]
Abstract
Heavy oil has hindered crude oil exploitation and pollution remediation due to its high density and viscosity. Bioemulsifiers efficiently facilitate the formation and stabilization of oil-in-water emulsions in low concentrations thus eliminating the above bottleneck. Despite their potential benefits, various obstacles had still impeded the practical applications of bioemulsifiers, including high purification costs and poor adaptability to extreme environments such as high temperature and oxygen deficiency. Herein, thermophilic facultative anaerobic Geobacillus thermodenitrificans NG80-2 was proved capable of emulsifying heavy oils and reducing their viscosity. An exocelluar bioemulsifier could be produced by NG80-2 using low-cost lignocellulose components as carbon sources even under anaerobic condition. The purified bioemulsifier was proved to be polysaccharide-protein complexes, and both components contributed to its emulsifying capability. In addition, it displayed excellent stress tolerance over wide ranges of temperatures, salinities, and pHs. Meanwhile, the bioemulsifier significantly improved oil recovery and degradation efficiency. An eps gene cluster for polysaccharide biosynthesis and genes for the covalently bonded proteins was further certificated. Therefore, the bioemulsifier produced by G. thermodenitrificans NG80-2 has immense potential for applications in bioremediation and EOR, and its biosynthesis pathway revealed here provides a theoretical basis for increasing bioemulsifier output.
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Affiliation(s)
- Mingchang Li
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Jiaqi Yu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Lu Cao
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Yujun Yin
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Zhaoying Su
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Shuai Chen
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Guoqiang Li
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China; Tianjin Engineering Technology Center of Green Manufacturing Biobased Materials, Tianjin 300071, China
| | - Ting Ma
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China; Tianjin Engineering Technology Center of Green Manufacturing Biobased Materials, Tianjin 300071, China.
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7
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Genome-scale reconstruction and metabolic modelling of the fast-growing thermophile Geobacillus sp. LC300. Metab Eng Commun 2022; 15:e00212. [DOI: 10.1016/j.mec.2022.e00212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 10/31/2022] [Accepted: 11/01/2022] [Indexed: 11/09/2022] Open
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8
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Sun S, Song X, Bian Y, Wan X, Zhang J, Wang W. Multi-parameter optimization maximizes the performance of genetically engineered Geobacillus for degradation of high-concentration nitroalkanes in wastewater. BIORESOURCE TECHNOLOGY 2022; 347:126690. [PMID: 35007737 DOI: 10.1016/j.biortech.2022.126690] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 01/02/2022] [Accepted: 01/05/2022] [Indexed: 02/08/2023]
Abstract
Nitroalkanes are important toxic pollutants for which there is no effective removal method at present. Although genetic engineering bacteria have been developed as a promising bioremediation strategy for years, their actual performance is far lower than expected. In this study, important factors affecting the application of engineered Geobacillus for nitroalkanes degradation were comprehensively optimized. The deep-reconstructed engineered strains significantly raised the expression and activity level of catalytic enzymes, but failed to fully enhance the degradation efficiency. However, further debugging of a variety of key parameters effectively improved the performance of the engineering strains. The increased cell membrane permeability, trace supplementation of vital nutritional factors, synergy of multifunctional enzyme engineered bacteria, switch of oxygen-supply mode, and moderate initial biomass all effectively boosted the degradation efficiency. Finally, a low-cost and highly effective bioreactor test for high-concentration nitroalkanes degradation proved the multi-parameter optimization mode helps to maximize the performance of genetically engineered bacteria.
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Affiliation(s)
- Shenmei Sun
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin 300457, PR China
| | - Xiaoru Song
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin 300457, PR China
| | - Ya Bian
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin 300457, PR China
| | - Xuehua Wan
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin 300457, PR China
| | - Jingjing Zhang
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin 300457, PR China
| | - Wei Wang
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin 300457, PR China; Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin 300457, PR China.
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9
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Obruča S, Dvořák P, Sedláček P, Koller M, Sedlář K, Pernicová I, Šafránek D. Polyhydroxyalkanoates synthesis by halophiles and thermophiles: towards sustainable production of microbial bioplastics. Biotechnol Adv 2022; 58:107906. [DOI: 10.1016/j.biotechadv.2022.107906] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 12/15/2021] [Accepted: 01/07/2022] [Indexed: 01/10/2023]
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10
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Mol V, Bennett M, Sánchez BJ, Lisowska BK, Herrgård MJ, Nielsen AT, Leak DJ, Sonnenschein N. Genome-scale metabolic modeling of P. thermoglucosidasius NCIMB 11955 reveals metabolic bottlenecks in anaerobic metabolism. Metab Eng 2021; 65:123-134. [PMID: 33753231 DOI: 10.1016/j.ymben.2021.03.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 03/01/2021] [Indexed: 12/27/2022]
Abstract
Parageobacillus thermoglucosidasius represents a thermophilic, facultative anaerobic bacterial chassis, with several desirable traits for metabolic engineering and industrial production. To further optimize strain productivity, a systems level understanding of its metabolism is needed, which can be facilitated by a genome-scale metabolic model. Here, we present p-thermo, the most complete, curated and validated genome-scale model (to date) of Parageobacillus thermoglucosidasius NCIMB 11955. It spans a total of 890 metabolites, 1175 reactions and 917 metabolic genes, forming an extensive knowledge base for P. thermoglucosidasius NCIMB 11955 metabolism. The model accurately predicts aerobic utilization of 22 carbon sources, and the predictive quality of internal fluxes was validated with previously published 13C-fluxomics data. In an application case, p-thermo was used to facilitate more in-depth analysis of reported metabolic engineering efforts, giving additional insight into fermentative metabolism. Finally, p-thermo was used to resolve a previously uncharacterised bottleneck in anaerobic metabolism, by identifying the minimal required supplemented nutrients (thiamin, biotin and iron(III)) needed to sustain anaerobic growth. This highlights the usefulness of p-thermo for guiding the generation of experimental hypotheses and for facilitating data-driven metabolic engineering, expanding the use of P. thermoglucosidasius as a high yield production platform.
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Affiliation(s)
- Viviënne Mol
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Martyn Bennett
- The Department of Biology & Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, United Kingdom; The Centre for Sustainable Chemical Technologies (CSCT), University of Bath, Claverton Down, Bath, BA2 7AY, United Kingdom
| | - Benjamín J Sánchez
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark; Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Beata K Lisowska
- The Department of Biology & Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, United Kingdom
| | - Markus J Herrgård
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark; BioInnovation Institute, Copenhagen N, Denmark
| | - Alex Toftgaard Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark.
| | - David J Leak
- The Department of Biology & Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, United Kingdom; The Centre for Sustainable Chemical Technologies (CSCT), University of Bath, Claverton Down, Bath, BA2 7AY, United Kingdom.
| | - Nikolaus Sonnenschein
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark.
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Zhang B, Sun L, Song X, Huang D, Li M, Peng C, Wang W. Genetically engineered thermotolerant facultative anaerobes for high-efficient degradation of multiple hazardous nitroalkanes. JOURNAL OF HAZARDOUS MATERIALS 2021; 405:124253. [PMID: 33144004 DOI: 10.1016/j.jhazmat.2020.124253] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 10/09/2020] [Accepted: 10/09/2020] [Indexed: 06/11/2023]
Abstract
Nitroalkanes are important industrial raw materials but also toxic pollutants, which are difficult to degrade once released into the environment. In this study, to significantly improve the degradation-efficiency of multiple nitroalkanes, a facultative anaerobe was genetically engineered, possible influencing factors and simulated application experiments of bioreactor were tested and evaluated. Among all engineered recombinants, the most effective strains NG-S1 (anaerobic) and NG-S2 (aerobic) displayed 2-fold and 2.8-fold final degradation rates higher than the wild type, respectively. Exogenous components, particularly those that enhance coenzyme synthesis, helped to increase the degradation rate, as the level of coenzymes affected full function of overexpressed nitroalkane oxidase. Importantly, simulated mixed-nitroalkane-wastewater bioreactor experiments proved excellent and sustainable degradation performance of the engineered strains for potential industrial applications. Collectively, these findings provide a promising thermophilic biological engineering platform and a new perspective for high-efficient and continuous environmental bioremediation of hazardous pollutants under aerobic and anaerobic conditions.
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Affiliation(s)
- Bingling Zhang
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin 300457, PR China
| | - Linbo Sun
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin 300457, PR China
| | - Xiaoru Song
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin 300457, PR China
| | - Di Huang
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin 300457, PR China
| | - Mingchang Li
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin 300457, PR China
| | - Chenchen Peng
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin 300457, PR China
| | - Wei Wang
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin 300457, PR China; Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin 300457, PR China.
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12
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Complete Genome Sequence of Geobacillus sp. Strain E55-1, Isolated from Mine Geyser in Japan. Microbiol Resour Announc 2020; 9:9/20/e00339-20. [PMID: 32409542 PMCID: PMC7225541 DOI: 10.1128/mra.00339-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We report here the complete genome sequence of Geobacillus sp. strain E55-1, isolated from the hot sediments of Mine Geyser in Japan. This strain exhibited ∼85% average nucleotide identity and ∼98.5% 16S rRNA sequence identity with the most closely related Geobacillus species. We report here the complete genome sequence of Geobacillus sp. strain E55-1, isolated from the hot sediments of Mine Geyser in Japan. This strain exhibited ∼85% average nucleotide identity and ∼98.5% 16S rRNA sequence identity with the most closely related Geobacillus species.
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13
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Puopolo R, Gallo G, Mormone A, Limauro D, Contursi P, Piochi M, Bartolucci S, Fiorentino G. Identification of a New Heavy-Metal-Resistant Strain of Geobacillus stearothermophilus Isolated from a Hydrothermally Active Volcanic Area in Southern Italy. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:E2678. [PMID: 32295125 PMCID: PMC7215868 DOI: 10.3390/ijerph17082678] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/09/2020] [Accepted: 04/13/2020] [Indexed: 01/08/2023]
Abstract
Microorganisms thriving in hot springs and hydrothermally active volcanic areas are dynamically involved in heavy-metal biogeochemical cycles; they have developed peculiar resistance systems to cope with such metals which nowadays can be considered among the most permanent and toxic pollutants for humans and the environment. For this reason, their exploitation is functional to unravel mechanisms of toxic-metal detoxification and to address bioremediation of heavy-metal pollution with eco-sustainable approaches. In this work, we isolated a novel strain of the thermophilic bacterium Geobacillus stearothermophilus from the solfataric mud pool in Pisciarelli, a well-known hydrothermally active zone of the Campi Flegrei volcano located near Naples in Italy, and characterized it by ribotyping, 16S rRNA sequencing and mass spectrometry analyses. The minimal inhibitory concentration (MIC) toward several heavy-metal ions indicated that the novel G. stearothermophilus isolate is particularly resistant to some of them. Functional and morphological analyses suggest that it is endowed with metal resistance systems for arsenic and cadmium detoxification.
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Affiliation(s)
- Rosanna Puopolo
- Dipartimento di Biologia, Università Degli Studi di Napoli Federico II, 80139 Napoli, Italy; (R.P.); (G.G.); (D.L.); (P.C.); (S.B.)
| | - Giovanni Gallo
- Dipartimento di Biologia, Università Degli Studi di Napoli Federico II, 80139 Napoli, Italy; (R.P.); (G.G.); (D.L.); (P.C.); (S.B.)
| | - Angela Mormone
- Istituto Nazionale di Geofisica e Vulcanologia, Sezione Osservatorio Vesuviano, 80125 Napoli, Italy; (A.M.); (M.P.)
| | - Danila Limauro
- Dipartimento di Biologia, Università Degli Studi di Napoli Federico II, 80139 Napoli, Italy; (R.P.); (G.G.); (D.L.); (P.C.); (S.B.)
| | - Patrizia Contursi
- Dipartimento di Biologia, Università Degli Studi di Napoli Federico II, 80139 Napoli, Italy; (R.P.); (G.G.); (D.L.); (P.C.); (S.B.)
| | - Monica Piochi
- Istituto Nazionale di Geofisica e Vulcanologia, Sezione Osservatorio Vesuviano, 80125 Napoli, Italy; (A.M.); (M.P.)
| | - Simonetta Bartolucci
- Dipartimento di Biologia, Università Degli Studi di Napoli Federico II, 80139 Napoli, Italy; (R.P.); (G.G.); (D.L.); (P.C.); (S.B.)
| | - Gabriella Fiorentino
- Dipartimento di Biologia, Università Degli Studi di Napoli Federico II, 80139 Napoli, Italy; (R.P.); (G.G.); (D.L.); (P.C.); (S.B.)
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14
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Zhou J, Lian J, Rao CV. Metabolic engineering of Parageobacillus thermoglucosidasius for the efficient production of (2R, 3R)-butanediol. Appl Microbiol Biotechnol 2020; 104:4303-4311. [PMID: 32221689 DOI: 10.1007/s00253-020-10553-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 03/02/2020] [Accepted: 03/15/2020] [Indexed: 11/27/2022]
Abstract
High-temperature fermentation using thermophilic microorganisms may provide cost-effective processes for the industrial production of fuels and chemicals, due to decreased hygiene and cooling costs. In the present study, the genetically trackable thermophile Parageobacillus thermoglucosidasius DSM2542T was engineered to produce (2R, 3R)-butanediol (R-BDO), a valuable chemical with broad industrial applications. The R-BDO biosynthetic pathway was optimized by testing different combinations of pathway enzymes, with acetolactate synthase (AlsS) from Bacillus subtilis and acetolactate decarboxylase (AlsD) from Streptococcus thermophilus yielding the highest production in P. thermoglucosidasius DSM2542T. Following fermentation condition optimization, shake flask fermentation at 55 °C resulted in the production of 7.2 g/L R-BDO with ~ 72% theoretical yield. This study details the microbial production of R-BDO at the highest fermentation temperature reported to date and demonstrates that P. thermoglucosidasius DSM2542T is a promising cell factory for the production of fuels and chemicals using high-temperature fermentation.
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Affiliation(s)
- Jiewen Zhou
- Department of Chemical and Biomolecular Engineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Hangzhou Zhongmei Huadong Pharmaceutical Co., Ltd, 866 Moganshan Road, Hangzhou, 310011, China
| | - Jiazhang Lian
- Department of Chemical and Biomolecular Engineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Christopher V Rao
- Department of Chemical and Biomolecular Engineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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15
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Laurenceau R, Bliem C, Osburne MS, Becker JW, Biller SJ, Cubillos-Ruiz A, Chisholm SW. Toward a genetic system in the marine cyanobacterium Prochlorococcus. Access Microbiol 2020; 2:acmi000107. [PMID: 33005871 PMCID: PMC7523629 DOI: 10.1099/acmi.0.000107] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 01/30/2020] [Indexed: 11/26/2022] Open
Abstract
As the smallest and most abundant primary producer in the oceans, the cyanobacterium Prochlorococcus is of interest to diverse branches of science. For the past 30 years, research on this minimal phototroph has led to a growing understanding of biological organization across multiple scales, from the genome to the global ocean ecosystem. Progress in understanding drivers of its diversity and ecology, as well as molecular mechanisms underpinning its streamlined simplicity, has been hampered by the inability to manipulate these cells genetically. Multiple attempts have been made to develop an efficient genetic transformation method for Prochlorococcus over the years; all have been unsuccessful to date, despite some success with their close relative, Synechococcus. To avoid the pursuit of unproductive paths, we report here what has not worked in our hands, as well as our progress developing a method to screen the most efficient electroporation parameters for optimal DNA delivery into Prochlorococcus cells. We also report a novel protocol for obtaining axenic colonies and a new method for differentiating live and dead cells. The electroporation method can be used to optimize DNA delivery into any bacterium, making it a useful tool for advancing transformation systems in other genetically recalcitrant microorganisms.
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Affiliation(s)
- Raphaël Laurenceau
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Christina Bliem
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Marcia S Osburne
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Present address: Department of Molecular Biology and Microbiology Tufts University School of Medicine, Boston, MA, USA
| | - Jamie W Becker
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Present address: Department of Biology, Haverford College, Haverford, PA, USA
| | - Steven J Biller
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Present address: Department of Biological Sciences, Wellesley College, Wellesley, MA, USA
| | - Andres Cubillos-Ruiz
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Present address: Institute for Medical Engineering and Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA.,Present address: Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Present address: Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Sallie W Chisholm
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
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16
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Rational Engineering of the Substrate Specificity of a Thermostable D-Hydantoinase (Dihydropyrimidinase). High Throughput 2020; 9:ht9010005. [PMID: 32059545 PMCID: PMC7175128 DOI: 10.3390/ht9010005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 02/05/2020] [Accepted: 02/07/2020] [Indexed: 12/18/2022] Open
Abstract
D-hydantoinases catalyze an enantioselective opening of 5- and 6-membered cyclic structures and therefore can be used for the production of optically pure precursors for biomedical applications. The thermostable D-hydantoinase from Geobacillus stearothermophilus ATCC 31783 is a manganese-dependent enzyme and exhibits low activity towards bulky hydantoin derivatives. Homology modeling with a known 3D structure (PDB code: 1K1D) allowed us to identify the amino acids to be mutated at the substrate binding site and in its immediate vicinity to modulate the substrate specificity. Both single and double substituted mutants were generated by site-directed mutagenesis at appropriate sites located inside and outside of the stereochemistry gate loops (SGL) involved in the substrate binding. Substrate specificity and kinetic constant data demonstrate that the replacement of Phe159 and Trp287 with alanine leads to an increase in the enzyme activity towards D,L-5-benzyl and D,L-5-indolylmethyl hydantoins. The length of the side chain and the hydrophobicity of substrates are essential parameters to consider when designing the substrate binding pocket for bulky hydantoins. Our data highlight that D-hydantoinase is the authentic dihydropyrimidinase involved in the pyrimidine reductive catabolic pathway in moderate thermophiles.
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17
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Kurashiki R, Mizuno T, Murata K, Ohshiro T, Suzuki H. A plasmid vector that directs hyperproduction of recombinant proteins in the thermophiles Geobacillus species. Extremophiles 2019; 24:147-156. [PMID: 31701242 DOI: 10.1007/s00792-019-01142-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 10/23/2019] [Indexed: 11/24/2022]
Abstract
Geobacillus spp. are moderate thermophiles that have great potential for use in diverse applications. For effective utilization of the species, genetic tools have been extensively studied; however, an overexpression vector remains to be developed. Here we constructed a plasmid vector that can shuttle between Escherichia coli and Geobacillus spp., and which contained a maltose-inducible promoter from Geobacillus kaustophilus HTA426. Although the vector (termed pGKE119) was originally designed for basal gene expression, it surprisingly directed robust protein production in G. kaustophilus. Protein production essentially occurred in an auto-inducible manner without maltose; however, some proteins were produced more efficiently in the presence of maltose. Although the productivity was affected by culture conditions, three proteins were successfully produced with abundance ratios of 12-27% (on a total protein basis) and yields of 77-170 mg (per L culture). pGKE119 directed substantial protein production even in Geobacillus subterraneus, Geobacillus thermoglucosidasius, and Geobacillus thermoleovorans. This suggests that pGKE119 can use a range of Geobacillus spp. as hosts and widely expand their genetic toolbox. Because Geobacillus spp. are highly proliferative bacteria that are distinct from organisms used as protein production hosts, pGKE119 may also provide a novel platform for hyperproduction of recombinant proteins.
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Affiliation(s)
- Ryota Kurashiki
- Department of Engineering, Graduate School of Sustainability Science, Tottori University, 4-101 Koyama-Minami, Tottori, 680-8552, Japan
| | - Tatsuki Mizuno
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, 4-101 Koyama-Minami, Tottori, 680-8552, Japan
| | - Kurumi Murata
- Faculty of Engineering, Tottori University, 4-101 Koyama-Minami, Tottori, 680-8552, Japan
| | - Takashi Ohshiro
- Faculty of Engineering, Tottori University, 4-101 Koyama-Minami, Tottori, 680-8552, Japan.,Center for Research on Green Sustainable Chemistry, Tottori University, 4-101 Koyama-Minami, Tottori, 680-8552, Japan
| | - Hirokazu Suzuki
- Faculty of Engineering, Tottori University, 4-101 Koyama-Minami, Tottori, 680-8552, Japan. .,Center for Research on Green Sustainable Chemistry, Tottori University, 4-101 Koyama-Minami, Tottori, 680-8552, Japan.
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18
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Lin JH, Zhang KC, Tao WY, Wang D, Li S. Geobacillus strains that have potential value in microbial enhanced oil recovery. Appl Microbiol Biotechnol 2019; 103:8339-8350. [PMID: 31501940 DOI: 10.1007/s00253-019-10115-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 08/26/2019] [Accepted: 08/30/2019] [Indexed: 12/31/2022]
Abstract
Bacteria from the genus Geobacillus are generally obligately thermophilic, with a unique bioenergy production capacity and unique enzymes. Geobacillus species were isolated primarily from hot springs, oilfields, and associated soils. They often exhibit unique survival patterns in these extreme oligotrophic environments. With the development of the microbial resources found in oilfields, Geobacillus spp. have been proven as valuable bacteria in many reports related to oilfields. After the isolation of Geobacillus by culture methods, more evidence was found that they possess the abilities of hydrocarbon utilization and bioemulsifier production. This paper mainly summarizes some characteristics of the Geobacillus species found in the oilfield environment, focusing on the inference and analysis of hydrocarbon degradation and bioemulsifier synthesis based on existing research, which may reveal their potential value in microbial enhanced oil recovery. It also provides references for understanding microbes in extreme environments.
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Affiliation(s)
- Jia-Hui Lin
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu Road, Nanjing, 211800, China
| | - Kun-Cheng Zhang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu Road, Nanjing, 211800, China
| | - Wei-Yi Tao
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu Road, Nanjing, 211800, China
| | - Dan Wang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu Road, Nanjing, 211800, China
| | - Shuang Li
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu Road, Nanjing, 211800, China.
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19
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Singleton C, Gilman J, Rollit J, Zhang K, Parker DA, Love J. A design of experiments approach for the rapid formulation of a chemically defined medium for metabolic profiling of industrially important microbes. PLoS One 2019; 14:e0218208. [PMID: 31188885 PMCID: PMC6561596 DOI: 10.1371/journal.pone.0218208] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 05/28/2019] [Indexed: 12/30/2022] Open
Abstract
Geobacillus thermoglucosidans DSM2542 is an industrially important microbe, however the complex nutritional requirements of Geobacilli confound metabolic engineering efforts. Previous studies have utilised semi-defined media recipes that contain complex, undefined, biologically derived nutrients which have unknown ingredients that cannot be quantified during metabolic profiling. This study used design of experiments to investigate how individual nutrients and interactions between these nutrients contribute to growth. A mathematically derived defined medium has been formulated that has been shown to robustly support growth of G. thermoglucosidans in two different environmental conditions (96-well plate and shake flask) and with a variety of lignocellulose-based carbohydrates. This enabled the catabolism of industrially relevant carbohydrates to be investigated.
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Affiliation(s)
- Chloe Singleton
- The Exeter Microbial Biofuels Group, College of Life and Environmental Sciences, The University of Exeter, Exeter, Devon, United Kingdom
| | - James Gilman
- The Exeter Microbial Biofuels Group, College of Life and Environmental Sciences, The University of Exeter, Exeter, Devon, United Kingdom
| | - Jessica Rollit
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Kun Zhang
- Shell Technology Centre, Houston, Texas, United States of America
| | - David A. Parker
- The Exeter Microbial Biofuels Group, College of Life and Environmental Sciences, The University of Exeter, Exeter, Devon, United Kingdom
- Shell Technology Centre, Houston, Texas, United States of America
| | - John Love
- The Exeter Microbial Biofuels Group, College of Life and Environmental Sciences, The University of Exeter, Exeter, Devon, United Kingdom
- * E-mail:
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20
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Gilman J, Singleton C, Tennant RK, James P, Howard TP, Lux T, Parker DA, Love J. Rapid, Heuristic Discovery and Design of Promoter Collections in Non-Model Microbes for Industrial Applications. ACS Synth Biol 2019; 8:1175-1186. [PMID: 30995831 DOI: 10.1021/acssynbio.9b00061] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Well-characterized promoter collections for synthetic biology applications are not always available in industrially relevant hosts. We developed a broadly applicable method for promoter identification in atypical microbial hosts that requires no a priori understanding of cis-regulatory element structure. This novel approach combines bioinformatic filtering with rapid empirical characterization to expand the promoter toolkit and uses machine learning to improve the understanding of the relationship between DNA sequence and function. Here, we apply the method in Geobacillus thermoglucosidasius, a thermophilic organism with high potential as a synthetic biology chassis for industrial applications. Bioinformatic screening of G. kaustophilus, G. stearothermophilus, G. thermodenitrificans, and G. thermoglucosidasius resulted in the identification of 636 100 bp putative promoters, encompassing the genome-wide design space and lacking known transcription factor binding sites. Eighty of these sequences were characterized in vivo, and activities covered a 2-log range of predictable expression levels. Seven sequences were shown to function consistently regardless of the downstream coding sequence. Partition modeling identified sequence positions upstream of the canonical -35 and -10 consensus motifs that were predicted to strongly influence regulatory activity in Geobacillus, and artificial neural network and partial least squares regression models were derived to assess if there were a simple, forward, quantitative method for in silico prediction of promoter function. However, the models were insufficiently general to predict pre hoc promoter activity in vivo, most probably as a result of the relatively small size of the training data set compared to the size of the modeled design space.
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Affiliation(s)
- James Gilman
- The BioEconomy Centre, Biosciences, College of Life and Environmental Sciences, Stocker Road, University of Exeter, Exeter EX4 4QD, U.K
| | - Chloe Singleton
- The BioEconomy Centre, Biosciences, College of Life and Environmental Sciences, Stocker Road, University of Exeter, Exeter EX4 4QD, U.K
| | - Richard K. Tennant
- The BioEconomy Centre, Biosciences, College of Life and Environmental Sciences, Stocker Road, University of Exeter, Exeter EX4 4QD, U.K
| | - Paul James
- The BioEconomy Centre, Biosciences, College of Life and Environmental Sciences, Stocker Road, University of Exeter, Exeter EX4 4QD, U.K
| | - Thomas P. Howard
- School of Natural and Environmental Sciences, Newcastle University, Devonshire Building, Newcastle-upon-Tyne NE1 7RU, U.K
| | - Thomas Lux
- Plant Genome and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Munich 85764, Germany
| | - David A. Parker
- Biodomain, Shell Technology Center Houston, 3333 Highway 6 South, Houston, Texas 77082-3101, United States
| | - John Love
- The BioEconomy Centre, Biosciences, College of Life and Environmental Sciences, Stocker Road, University of Exeter, Exeter EX4 4QD, U.K
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21
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Peculiarities and biotechnological potential of environmental adaptation by Geobacillus species. Appl Microbiol Biotechnol 2018; 102:10425-10437. [PMID: 30310966 DOI: 10.1007/s00253-018-9422-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 09/25/2018] [Accepted: 09/26/2018] [Indexed: 12/21/2022]
Abstract
The genus Geobacillus comprises thermophilic bacilli capable of endospore formation. The members of this genus provide thermostable proteins and can be used in whole cell applications at elevated temperatures; therefore, these organisms are of biotechnological importance. While these applications have been described in previous reviews, the present paper highlights the environmental adaptations and genome diversifications of Geobacillus spp. and their applications in evolutionary-protein engineering. Despite their obligate thermophilic properties, Geobacillus spp. are widely distributed in nature. Because several isolates demonstrate remarkable properties for cell reproduction in their respective niches, they seem to exist not only as endospores but also as vegetative cells in diverse environments. This suggests their excellence in environmental adaptation via genome diversification; in fact, evidence suggests that Geobacillus spp. were derived from Bacillus spp. while diversifying their genomes via horizontal gene transfer. Moreover, when subjected to an environmental stressor, Geobacillus spp. diversify their genomes using inductive mutations and transposable elements to produce derivative cells that are adaptive to the stressor. Notably, inductive mutations in Geobacillus spp. occur more rapidly and frequently than the stress-induced mutagenesis observed in other microorganisms. Owing to this, Geobacillus spp. can efficiently generate mutant genes coding for thermostable enzyme variants from the thermolabile enzyme genes under appropriate selection pressures. This phenomenon provides a new approach to generate thermostable enzymes, termed as thermoadaptation-directed enzyme evolution, thereby expanding the biotechnological potentials of Geobacillus spp. In this review, we have discussed this approach using successful examples and major challenges yet to be addressed.
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22
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Egan K, Field D, Ross RP, Cotter PD, Hill C. In silico Prediction and Exploration of Potential Bacteriocin Gene Clusters Within the Bacterial Genus Geobacillus. Front Microbiol 2018; 9:2116. [PMID: 30298056 PMCID: PMC6160750 DOI: 10.3389/fmicb.2018.02116] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 08/20/2018] [Indexed: 11/30/2022] Open
Abstract
The thermophilic, endospore-forming genus of Geobacillus has historically been associated with spoilage of canned food. However, in recent years it has become the subject of much attention due its biotechnological potential in areas such as enzyme and biofuel applications. One aspect of this genus that has not been fully explored or realized is its use as a source of novel forms of the ribosomally synthesized antimicrobial peptides known as bacteriocins. To date only two bacteriocins have been fully characterized within this genus, i.e., Geobacillin I and II, with only a small number of others partially characterized. Here we bioinformatically investigate the potential of this genus as a source of novel bacteriocins through the use of the in silico screening software BAGEL3, which scans publically available genomes for potential bacteriocin gene clusters. In this study we examined the association of bacteriocin gene presence with niche and phylogenetic position within the genus. We also identified a number of candidates from multiple bacteriocin classes which may be promising antimicrobial candidates when investigated in vitro in future studies.
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Affiliation(s)
- Kevin Egan
- School of Microbiology, University College, Cork, Ireland
| | - Des Field
- School of Microbiology, University College, Cork, Ireland.,APC Microbiome Institute, Cork, Cork, Ireland
| | - R Paul Ross
- School of Microbiology, University College, Cork, Ireland.,APC Microbiome Institute, Cork, Cork, Ireland
| | - Paul D Cotter
- APC Microbiome Institute, Cork, Cork, Ireland.,Teagasc Food Research Centre, Moorepark, Fermoy, Co., Cork, Ireland
| | - Colin Hill
- School of Microbiology, University College, Cork, Ireland.,APC Microbiome Institute, Cork, Cork, Ireland
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23
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Miyano M, Tanaka K, Ishikawa S, Mori K, Miguel-Arribas A, Meijer WJJ, Yoshida KI. A novel method for transforming the thermophilic bacterium Geobacillus kaustophilus. Microb Cell Fact 2018; 17:127. [PMID: 30119674 PMCID: PMC6098629 DOI: 10.1186/s12934-018-0969-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 07/28/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bacterial strains of the genus Geobacillus grow at high temperatures of 50-75 °C and could thus be useful for biotechnological applications. However, genetic manipulation of these species is difficult because the current techniques for transforming Geobacillus species are not efficient. In this study, we developed an easy and efficient method for transforming Geobacillus kaustophilus using the conjugative plasmid pLS20cat. RESULTS We constructed a transformation system comprising (i) a mobilizable Bacillus subtilis-G. kaustophilus shuttle plasmid named pGK1 that carries the elements for selection and replication in Geobacillus, and (ii) a pLS20cat-harboring B. subtilis donor strain expressing the dam methylase gene of Escherichia coli and the conjugation-stimulating rapLS20 gene of pLS20cat. This system can be used to efficiently introduce pGK1 into G. kaustophilus by mobilization in a pLS20cat-dependent way. Whereas the thermostable kanamycin marker and Geobacillus replication origin of pGK1 as well as expression of dam methylase in the donor were indispensable for mobilization, ectopic expression of rapLS20 increased its efficiency. In addition, the conditions of the recipient influenced mobilization efficiency: the highest mobilization efficiencies were obtained using recipient cells that were in the exponential growth phase. Furthermore, elimination of the origin of transfer from pLS20cat enhanced the mobilization. CONCLUSIONS We describe a novel method of plasmid mobilization into G. kaustophilus recipient from B. subtilis donor depending on the helper function of pLS20cat, which enables simple, rapid, and easy transformation of the thermophilic Gram-positive bacterium.
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Grants
- 17K19237 Ministry of Education, Culture, Sports, Science and Technology
- 18H02128 Ministry of Education, Culture, Sports, Science and Technology
- Bio2013-41489-P Ministerio de Economía, Industria y Competitividad, Gobierno de España
- BIO2016-77883-C2-1-P Ministerio de Economía, Industria y Competitividad, Gobierno de España
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Affiliation(s)
- Megumi Miyano
- Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657 8501 Japan
| | - Kosei Tanaka
- Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657 8501 Japan
| | - Shu Ishikawa
- Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657 8501 Japan
| | - Kotaro Mori
- Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657 8501 Japan
| | - Andrés Miguel-Arribas
- Centro de Biología Molecular ‘Severo Ochoa’ (CSIC-UAM), Instituto de Biología Molecular ‘Eladio Viñuela’ (CSIC), Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain
| | - Wilfried J. J. Meijer
- Centro de Biología Molecular ‘Severo Ochoa’ (CSIC-UAM), Instituto de Biología Molecular ‘Eladio Viñuela’ (CSIC), Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain
| | - Ken-ichi Yoshida
- Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657 8501 Japan
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24
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Drejer EB, Hakvåg S, Irla M, Brautaset T. Genetic Tools and Techniques for Recombinant Expression in Thermophilic Bacillaceae. Microorganisms 2018; 6:microorganisms6020042. [PMID: 29748477 PMCID: PMC6027425 DOI: 10.3390/microorganisms6020042] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 05/02/2018] [Accepted: 05/03/2018] [Indexed: 01/17/2023] Open
Abstract
Although Escherichia coli and Bacillus subtilis are the most prominent bacterial hosts for recombinant protein production by far, additional species are being explored as alternatives for production of difficult-to-express proteins. In particular, for thermostable proteins, there is a need for hosts able to properly synthesize, fold, and excrete these in high yields, and thermophilic Bacillaceae represent one potentially interesting group of microorganisms for such purposes. A number of thermophilic Bacillaceae including B.methanolicus, B.coagulans, B.smithii, B.licheniformis, Geobacillus thermoglucosidasius, G. kaustophilus, and G. stearothermophilus are investigated concerning physiology, genomics, genetic tools, and technologies, altogether paving the way for their utilization as hosts for recombinant production of thermostable and other difficult-to-express proteins. Moreover, recent successful deployments of CRISPR/Cas9 in several of these species have accelerated the progress in their metabolic engineering, which should increase their attractiveness for future industrial-scale production of proteins. This review describes the biology of thermophilic Bacillaceae and in particular focuses on genetic tools and methods enabling use of these organisms as hosts for recombinant protein production.
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Affiliation(s)
- Eivind B Drejer
- Department of Biotechnology and Food Science, NTNU: Norwegian University of Science and Technology, 7491 Trondheim, Norway.
| | - Sigrid Hakvåg
- Department of Biotechnology and Food Science, NTNU: Norwegian University of Science and Technology, 7491 Trondheim, Norway.
| | - Marta Irla
- Department of Biotechnology and Food Science, NTNU: Norwegian University of Science and Technology, 7491 Trondheim, Norway.
| | - Trygve Brautaset
- Department of Biotechnology and Food Science, NTNU: Norwegian University of Science and Technology, 7491 Trondheim, Norway.
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25
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Frenzel E, Legebeke J, van Stralen A, van Kranenburg R, Kuipers OP. In vivo selection of sfGFP variants with improved and reliable functionality in industrially important thermophilic bacteria. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:8. [PMID: 29371884 PMCID: PMC5771013 DOI: 10.1186/s13068-017-1008-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 12/29/2017] [Indexed: 05/03/2023]
Abstract
BACKGROUND Fluorescent reporter proteins (FP) have become an indispensable tool for the optimization of microbial cell factories and in synthetic biology per se. The applicability of the currently available FPs is, however, constrained by species-dependent performance and misfolding at elevated temperatures. To obtain functional reporters for thermophilic, biotechnologically important bacteria such as Parageobacillus thermoglucosidasius, an in vivo screening approach based on a mutational library of superfolder GFP was applied. RESULTS Flow cytometry-based benchmarking of a set of GFPs, sfGFPs and species-specific codon-optimized variants revealed that none of the proteins was satisfyingly detectable in P. thermoglucosidasius at its optimal growth temperature of 60 °C. An undirected mutagenesis approach coupled to fluorescence-activated cell sorting allowed the isolation of sfGFP variants that were extremely well expressed in the chassis background at 60 °C. Notably, a few nucleotide substitutions, including silent mutations, significantly improved the functionality and brightness. The best mutant sfGFP(N39D/A179A) showed an 885-fold enhanced mean fluorescence intensity (MFI) at 60 °C and is the most reliable reporter protein with respect to cell-to-cell variation and signal intensity reported so far. The in vitro spectral and thermostability properties were unaltered as compared to the parental sfGFP protein, strongly indicating that the combination of the amino acid exchange and an altered translation or folding speed, or protection from degradation, contribute to the strongly improved in vivo performance. Furthermore, sfGFP(N39D/A179A) and the newly developed cyan and yellow derivatives were successfully used for labeling several industrially relevant thermophilic bacilli, thus proving their broad applicability. CONCLUSIONS This study illustrates the power of in vivo isolation of thermostable proteins to obtain reporters for highly efficient fluorescence labeling. Successful expression in a variety of thermophilic bacteria proved that the novel FPs are highly suitable for imaging and flow cytometry-based studies. This enables a reliable cell tracking and single-cell-based real-time monitoring of biological processes that are of industrial and biotechnological interest.
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Affiliation(s)
- Elrike Frenzel
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic Biology, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Jelmer Legebeke
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic Biology, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Atze van Stralen
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic Biology, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Richard van Kranenburg
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
- Corbion, Arkselsedijk 46, 4206 AC Gorinchem, The Netherlands
| | - Oscar P. Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic Biology, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
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Complete Genome Sequence of Geobacillus thermodenitrificans T12, A Potential Host for Biotechnological Applications. Curr Microbiol 2017; 75:49-56. [PMID: 28900693 PMCID: PMC5765199 DOI: 10.1007/s00284-017-1349-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 08/28/2017] [Indexed: 01/12/2023]
Abstract
In attempt to obtain a thermophilic host for the conversion of lignocellulose derived substrates into lactic acid, Geobacillus thermodenitrificans T12 was isolated from a compost heap. It was selected from over 500 isolates as a genetically tractable hemicellulolytic lactic acid producer, requiring little nutrients. The strain is able to ferment glucose and xylose simultaneously and can produce lactic acid from xylan, making it a potential host for biotechnological applications. The genome of strain T12 consists of a 3.64 Mb chromosome and two plasmids of 59 and 56 kb. It has a total of 3.676 genes with an average genomic GC content of 48.7%. The T12 genome encodes a denitrification pathway, allowing for anaerobic respiration. The identity and localization of the responsible genes are similar to those of the denitrification pathways found in strain NG80-2. The hemicellulose utilization (HUS) locus was identified based on sequence homology against G. stearothermophilus T-6. It appeared that T12 has all the genes that are present in strain T-6 except for the arabinan degradation cluster. Instead, the HUS locus of strain T12 contains genes for both an inositol and a pectate degradation pathway. Strain T12 has complete pathways for the synthesis of purine and pyrimidine, all 20 amino acids and several vitamins except D-biotin. The host-defense systems present comprise a Type II and a Type III restriction-modification system, as well as a CRISPR-Cas Type II system. It is concluded that G. thermodenitrificans T12 is a potentially interesting candidate for industrial applications.
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Pogrebnyakov I, Jendresen CB, Nielsen AT. Genetic toolbox for controlled expression of functional proteins in Geobacillus spp. PLoS One 2017; 12:e0171313. [PMID: 28152017 PMCID: PMC5289569 DOI: 10.1371/journal.pone.0171313] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 01/19/2017] [Indexed: 11/20/2022] Open
Abstract
Species of genus Geobacillus are thermophilic bacteria and play an ever increasing role as hosts for biotechnological applications both in academia and industry. Here we screened a number of Geobacillus strains to determine which industrially relevant carbon sources they can utilize. One of the strains, G. thermoglucosidasius C56-YS93, was then chosen to develop a toolbox for controlled gene expression over a wide range of levels. It includes a library of semi-synthetic constitutive promoters (76-fold difference in expression levels) and an inducible promoter from the xylA gene. A library of synthetic in silico designed ribosome binding sites was also created for further tuning of translation. The PxylA was further used to successfully express native and heterologous xylanases in G. thermoglucosidasius. This toolbox enables fine-tuning of gene expression in Geobacillus species for metabolic engineering approaches in production of biochemicals and heterologous proteins.
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Affiliation(s)
- Ivan Pogrebnyakov
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Christian Bille Jendresen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Alex Toftgaard Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
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Wang Y, Zhao C, Zhang D, Zhao M, Zheng D, Lyu Y, Cheng W, Guo P, Cui Z. Effective degradation of aflatoxin B 1 using a novel thermophilic microbial consortium TADC7. BIORESOURCE TECHNOLOGY 2017; 224:166-173. [PMID: 27866802 DOI: 10.1016/j.biortech.2016.11.033] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 11/06/2016] [Accepted: 11/07/2016] [Indexed: 06/06/2023]
Abstract
We constructed a novel thermophilic microbial consortium, TADC7, with stable and efficient aflatoxin B1 (AFB1) degradation activity. The microbial consortium degraded more than 95% of the toxin within 72h when cultured with AFB1, and the optimum temperature was 55-60°C. TADC7 tolerated high doses of AFB1, with no inhibitory effects up to 5000μgL-1 AFB1; moreover, the degradation kinetics fit well with the Monod model. The proteins or enzymes in the TADC7 cell-free supernatant played a major role in AFB1 degradation. AFB1 degradation by the cell-free supernatant was stable up to 90°C, with an optimal pH of 8-10. We performed 16S rRNA sequencing to determine TADC7 community structure dynamics; the results indicated that Geobacillus and Tepidimicrobium played major roles in AFB1 degradation.
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Affiliation(s)
- Yi Wang
- Institute of Agricultural Products Processing and Nuclear Agriculture Technology Research, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; College of Biology and Pharmacy, Three Gorges University, Yichang 443002, China
| | - Chunxia Zhao
- Institute of Agricultural Products Processing and Nuclear Agriculture Technology Research, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; College of Biology and Pharmacy, Three Gorges University, Yichang 443002, China
| | - Dongdong Zhang
- Institute of Marine Biology, Ocean College, Zhejiang University, Zhoushan 316021, Zhejiang, China
| | - Mingming Zhao
- Institute of Agricultural Products Processing and Nuclear Agriculture Technology Research, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Dan Zheng
- Institute of Agricultural Products Processing and Nuclear Agriculture Technology Research, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Yucai Lyu
- College of Biology and Pharmacy, Three Gorges University, Yichang 443002, China
| | - Wei Cheng
- Institute of Agricultural Products Processing and Nuclear Agriculture Technology Research, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Peng Guo
- Institute of Agricultural Products Processing and Nuclear Agriculture Technology Research, Hubei Academy of Agricultural Sciences, Wuhan 430064, China.
| | - Zongjun Cui
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
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Zhou J, Wu K, Rao CV. Evolutionary engineering of Geobacillus thermoglucosidasius
for improved ethanol production. Biotechnol Bioeng 2016; 113:2156-67. [DOI: 10.1002/bit.25983] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 02/12/2016] [Accepted: 03/18/2016] [Indexed: 01/30/2023]
Affiliation(s)
- Jiewen Zhou
- Department of Chemical and Biomolecular Engineering; University of Illinois at Urbana-Champaign; 600 S. Mathews Ave Urbana Illinois 61801
| | - Kang Wu
- Department of Chemical Engineering; University of New Hampshire; Durham New Hampshire
| | - Christopher V. Rao
- Department of Chemical and Biomolecular Engineering; University of Illinois at Urbana-Champaign; 600 S. Mathews Ave Urbana Illinois 61801
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Tominaga Y, Ohshiro T, Suzuki H. Conjugative plasmid transfer from Escherichia coli is a versatile approach for genetic transformation of thermophilic Bacillus and Geobacillus species. Extremophiles 2016; 20:375-81. [DOI: 10.1007/s00792-016-0819-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 02/14/2016] [Indexed: 10/22/2022]
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Daas MJA, van de Weijer AHP, de Vos WM, van der Oost J, van Kranenburg R. Isolation of a genetically accessible thermophilic xylan degrading bacterium from compost. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:210. [PMID: 27752284 PMCID: PMC5053077 DOI: 10.1186/s13068-016-0618-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 09/20/2016] [Indexed: 05/20/2023]
Abstract
BACKGROUND Due to the finite nature of global oil resources we are now faced with the challenge of finding renewable resources to produce fuels and chemicals in the future. Lactic acid has great potential as a precursor for the production of bioplastics alternatives to conventional plastics. Efficient lactic acid fermentation from non-food lignocellulosic substrates requires pretreatment and saccharification to generate fermentable sugars. A fermentation process that requires little to no enzyme additions, i.e. consolidated bioprocessing would be preferred and requires lactic acid-producing organisms that have cellulolytic and/or hemicellulolytic activity. RESULTS To obtain candidate production strains we have enriched and isolated facultative anaerobic (hemi) cellulolytic bacterial strains from compost samples. By selecting for growth on both cellulose and xylan, 94 Geobacillus strains were isolated. Subsequent screening for lactic acid production was carried out from C6 and C5 sugar fermentations and a selection of the best lactic acid producers was made. The denitrifying Geobacillus thermodenitrificans T12 was selected for further research and was rendered genetically accessible. In fermentations on a mixture of glucose and xylose, a total of 20.3 g of lactic acid was produced with a yield of 0.94 g product/g sugar consumed. In addition, strain T12 is capable of direct conversion of beech wood xylan to mainly lactic acid in minimal media. CONCLUSIONS We have demonstrated that G. thermodenitrificans T12 is genetically accessible and produces lactic acid as its main fermentation product on glucose, xylose and a mixture thereof. Strain T12 was additionally used for the direct conversion of xylan to lactic acid. The genetic accessibility of the T12 strain provides a solid basis for the development of this strain into a host for consolidated bioprocessing of biomass to lactic acid.
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Affiliation(s)
- Martinus J. A. Daas
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | | | - Willem M. de Vos
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Richard van Kranenburg
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
- Corbion, Arkselsedijk 46, 4206 AC Gorinchem, The Netherlands
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Belduz AO, Canakci S, Chan KG, Kahar UM, Chan CS, Yaakop AS, Goh KM. Genome sequence of Anoxybacillus ayderensis AB04(T) isolated from the Ayder hot spring in Turkey. Stand Genomic Sci 2015; 10:70. [PMID: 26413199 PMCID: PMC4584021 DOI: 10.1186/s40793-015-0065-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 09/04/2015] [Indexed: 11/20/2022] Open
Abstract
Species of Anoxybacillus are thermophiles and, therefore, their enzymes are suitable for many biotechnological applications. Anoxybacillus ayderensis AB04T (= NCIMB 13972T = NCCB 100050T) was isolated from the Ayder hot spring in Rize, Turkey, and is one of the earliest described Anoxybacillus type strains. The present work reports the cellular features of A. ayderensis AB04T, together with a high-quality draft genome sequence and its annotation. The genome is 2,832,347 bp long (74 contigs) and contains 2,895 protein-coding sequences and 103 RNA genes including 14 rRNAs, 88 tRNAs, and 1 tmRNA. Based on the genome annotation of strain AB04T, we identified genes encoding various glycoside hydrolases that are important for carbohydrate-related industries, which we compared with those of other, sequenced Anoxybacillus spp. Insights into under-explored industrially applicable enzymes and the possible applications of strain AB04T were also described.
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Affiliation(s)
- Ali Osman Belduz
- Faculty of Sciences, Department of Biology, Karadeniz Technical University, 61080 Trabzon, Turkey
| | - Sabriye Canakci
- Faculty of Sciences, Department of Biology, Karadeniz Technical University, 61080 Trabzon, Turkey
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Ummirul Mukminin Kahar
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, 81310 Skudai, Johor Malaysia
| | - Chia Sing Chan
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, 81310 Skudai, Johor Malaysia
| | - Amira Suriaty Yaakop
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, 81310 Skudai, Johor Malaysia
| | - Kian Mau Goh
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, 81310 Skudai, Johor Malaysia
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