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Hu HF, Zhou HY, Wang MX, Wang YS, Xue YP, Zheng YG. A rapid throughput assay for screening (R)-2-(4-hydroxyphenoxy)propionic acid producing microbes. J Microbiol Methods 2019; 158:44-51. [PMID: 30703447 DOI: 10.1016/j.mimet.2019.01.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 01/28/2019] [Indexed: 10/27/2022]
Abstract
(R)-2-(4-hydroxyphenoxy)propionic acid ((R)-HPOPA) is an important intermediate for the synthesis of optically pure aryloxyphenoxypropionic acid herbicides. Regioselective hydroxylation of (R)-2-phenoxypropionic acid ((R)-POPA) by microbes is one of the most useful methods for the industrial production of (R)-HPOPA. In this study, we designed and optimized a rapid throughput assay for screening (R)-HPOPA producing bacterial/fungal strains which can regioselectively hydroxylate (R)-POPA. (R)-HPOPA could react with 4-aminoantipyrine (4-AAP) in the presence of potassium hexacyanoferrate (K3[Fe(CN)6]) to form indoxyl antipyrine, an orange-red chromophore, that can easily spectrophotometrically be determined at 550 nm. During the verification of the assay we observed an average recovery rate of between 97.3% and 104.5%. Apart from the rapid throughput, no obvious differences in detection (R)-HPOPA in the culture broth samples were found between our rapid throughput multiplate assay and a high-performance liquid chromatography method. Our optimized assay method is simple, rapid and accurate with high repeatability. It has the potential for high throughput screening (about 3000-5000 samples/day) of the (R)-HPOPA producing strains.
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Affiliation(s)
- Hai-Feng Hu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China; Engineering Research Center of Bioconversion, Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou 310014, China
| | - Hai-Yan Zhou
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China; Engineering Research Center of Bioconversion, Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou 310014, China
| | - Mei-Xin Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China; Engineering Research Center of Bioconversion, Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou 310014, China
| | - Yuan-Shan Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China; Engineering Research Center of Bioconversion, Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou 310014, China
| | - Ya-Ping Xue
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China; Engineering Research Center of Bioconversion, Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou 310014, China.
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China; Engineering Research Center of Bioconversion, Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou 310014, China
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Bosma EF, Koehorst JJ, van Hijum SAFT, Renckens B, Vriesendorp B, van de Weijer AHP, Schaap PJ, de Vos WM, van der Oost J, van Kranenburg R. Complete genome sequence of thermophilic Bacillus smithii type strain DSM 4216(T). Stand Genomic Sci 2016; 11:52. [PMID: 27559429 PMCID: PMC4995803 DOI: 10.1186/s40793-016-0172-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 08/09/2016] [Indexed: 11/10/2022] Open
Abstract
Bacillus smithii is a facultatively anaerobic, thermophilic bacterium able to use a variety of sugars that can be derived from lignocellulosic feedstocks. Being genetically accessible, it is a potential new host for biotechnological production of green chemicals from renewable resources. We determined the complete genomic sequence of the B. smithii type strain DSM 4216(T), which consists of a 3,368,778 bp chromosome (GenBank accession number CP012024.1) and a 12,514 bp plasmid (GenBank accession number CP012025.1), together encoding 3880 genes. Genome annotation via RAST was complemented by a protein domain analysis. Some unique features of B. smithii central metabolism in comparison to related organisms included the lack of a standard acetate production pathway with no apparent pyruvate formate lyase, phosphotransacetylase, and acetate kinase genes, while acetate was the second fermentation product.
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Affiliation(s)
- Elleke F. Bosma
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands
- Present address: The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Kgs. Lyngby, 2800 Denmark
| | - Jasper J. Koehorst
- Laboratory of Systems and Synthetic Biology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands
| | | | - Bernadet Renckens
- CMBI, NCMLS, Geert-Grooteplein Zuid 26-28, 6525 GA Nijmegen, The Netherlands
| | | | | | - Peter J. Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands
| | - Willem M. de Vos
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands
| | - Richard van Kranenburg
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands
- Corbion, Arkelsedijk 46, 4206 AC Gorinchem, The Netherlands
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Lu ZY, Guo XJ, Li H, Huang ZZ, Lin KF, Liu YD. High-throughput screening for a moderately halophilic phenol-degrading strain and its salt tolerance response. Int J Mol Sci 2015; 16:11834-48. [PMID: 26020478 PMCID: PMC4490417 DOI: 10.3390/ijms160611834] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 05/06/2015] [Indexed: 11/24/2022] Open
Abstract
A high-throughput screening system for moderately halophilic phenol-degrading bacteria from various habitats was developed to replace the conventional strain screening owing to its high efficiency. Bacterial enrichments were cultivated in 48 deep well microplates instead of shake flasks or tubes. Measurement of phenol concentrations was performed in 96-well microplates instead of using the conventional spectrophotometric method or high-performance liquid chromatography (HPLC). The high-throughput screening system was used to cultivate forty-three bacterial enrichments and gained a halophilic bacterial community E3 with the best phenol-degrading capability. Halomonas sp. strain 4-5 was isolated from the E3 community. Strain 4-5 was able to degrade more than 94% of the phenol (500 mg·L−1 starting concentration) over a range of 3%–10% NaCl. Additionally, the strain accumulated the compatible solute, ectoine, with increasing salt concentrations. PCR detection of the functional genes suggested that the largest subunit of multicomponent phenol hydroxylase (LmPH) and catechol 1,2-dioxygenase (C12O) were active in the phenol degradation process.
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Affiliation(s)
- Zhi-Yan Lu
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China.
| | - Xiao-Jue Guo
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China.
| | - Hui Li
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China.
| | - Zhong-Zi Huang
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China.
- School of Chemical Engineering, Shanghai University of Engineering Science, Shanghai 201620, China.
| | - Kuang-Fei Lin
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China.
| | - Yong-Di Liu
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China.
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Hu G, Ji S, Yu Y, Wang S, Zhou G, Li F. Organisms for biofuel production: natural bioresources and methodologies for improving their biosynthetic potentials. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2015; 147:185-224. [PMID: 24085385 DOI: 10.1007/10_2013_245] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
In order to relieve the pressure of energy supply and environment contamination that humans are facing, there are now intensive worldwide efforts to explore natural bioresources for production of energy storage compounds, such as lipids, alcohols, hydrocarbons, and polysaccharides. Around the world, many plants have been evaluated and developed as feedstock for bioenergy production, among which several crops have successfully achieved industrialization. Microalgae are another group of photosynthetic autotroph of interest due to their superior growth rates, relatively high photosynthetic conversion efficiencies, and vast metabolic capabilities. Heterotrophic microorganisms, such as yeast and bacteria, can utilize carbohydrates from lignocellulosic biomass directly or after pretreatment and enzymatic hydrolysis to produce liquid biofuels such as ethanol and butanol. Although finding a suitable organism for biofuel production is not easy, many naturally occurring organisms with good traits have recently been obtained. This review mainly focuses on the new organism resources discovered in the last 5 years for production of transport fuels (biodiesel, gasoline, jet fuel, and alkanes) and hydrogen, and available methods to improve natural organisms as platforms for the production of biofuels.
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Affiliation(s)
- Guangrong Hu
- Shandong Provincial Key Laboratory of Energy Genetics, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
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Isolation and screening of thermophilic bacilli from compost for electrotransformation and fermentation: characterization of Bacillus smithii ET 138 as a new biocatalyst. Appl Environ Microbiol 2015; 81:1874-83. [PMID: 25556192 DOI: 10.1128/aem.03640-14] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Thermophilic bacteria are regarded as attractive production organisms for cost-efficient conversion of renewable resources to green chemicals, but their genetic accessibility is a major bottleneck in developing them into versatile platform organisms. In this study, we aimed to isolate thermophilic, facultatively anaerobic bacilli that are genetically accessible and have potential as platform organisms. From compost, we isolated 267 strains that produced acids from C5 and C6 sugars at temperatures of 55°C or 65°C. Subsequently, 44 strains that showed the highest production of acids were screened for genetic accessibility by electroporation. Two Geobacillus thermodenitrificans isolates and one Bacillus smithii isolate were found to be transformable with plasmid pNW33n. Of these, B. smithii ET 138 was the best-performing strain in laboratory-scale fermentations and was capable of producing organic acids from glucose as well as from xylose. It is an acidotolerant strain able to produce organic acids until a lower limit of approximately pH 4.5. As genetic accessibility of B. smithii had not been described previously, six other B. smithii strains from the DSMZ culture collection were tested for electroporation efficiencies, and we found the type strain DSM 4216(T) and strain DSM 460 to be transformable. The transformation protocol for B. smithii isolate ET 138 was optimized to obtain approximately 5 × 10(3) colonies per μg plasmid pNW33n. Genetic accessibility combined with robust acid production capacities on C5 and C6 sugars at a relatively broad pH range make B. smithii ET 138 an attractive biocatalyst for the production of lactic acid and potentially other green chemicals.
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Engineering biofuel tolerance in non-native producing microorganisms. Biotechnol Adv 2014; 32:541-8. [PMID: 24530635 DOI: 10.1016/j.biotechadv.2014.02.001] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Revised: 01/19/2014] [Accepted: 02/08/2014] [Indexed: 01/17/2023]
Abstract
Large-scale production of renewable biofuels through microbiological processes has drawn significant attention in recent years, mostly due to the increasing concerns on the petroleum fuel shortages and the environmental consequences of the over-utilization of petroleum-based fuels. In addition to native biofuel-producing microbes that have been employed for biofuel production for decades, recent advances in metabolic engineering and synthetic biology have made it possible to produce biofuels in several non-native biofuel-producing microorganisms. Compared to native producers, these non-native systems carry the advantages of fast growth, simple nutrient requirements, readiness for genetic modifications, and even the capability to assimilate CO2 and solar energy, making them competitive alternative systems to further decrease the biofuel production cost. However, the tolerance of these non-native microorganisms to toxic biofuels is naturally low, which has restricted the potentials of their application for high-efficiency biofuel production. To address the issues, researches have been recently conducted to explore the biofuel tolerance mechanisms and to construct robust high-tolerance strains for non-native biofuel-producing microorganisms. In this review, we critically summarize the recent progress in this area, focusing on three popular non-native biofuel-producing systems, i.e. Escherichia coli, Lactobacillus and photosynthetic cyanobacteria.
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Sun L, Zhang H, Yuan H, Tu R, Wang Q, Ma Y. A double-enzyme-coupled assay for high-throughput screening of succinic acid-producing strains. J Appl Microbiol 2013; 114:1696-701. [DOI: 10.1111/jam.12175] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Revised: 02/21/2013] [Accepted: 02/21/2013] [Indexed: 12/01/2022]
Affiliation(s)
- L. Sun
- Key Laboratory of Systems Microbial Biotechnology; Tianjin Institute of Industrial Biotechnology; Chinese Academy of Sciences; Tianjin China
- College of Life Sciences; University of Chinese Academy of Sciences; Beijing China
| | - H. Zhang
- Key Laboratory of Systems Microbial Biotechnology; Tianjin Institute of Industrial Biotechnology; Chinese Academy of Sciences; Tianjin China
| | - H. Yuan
- Key Laboratory of Systems Microbial Biotechnology; Tianjin Institute of Industrial Biotechnology; Chinese Academy of Sciences; Tianjin China
| | - R. Tu
- Key Laboratory of Systems Microbial Biotechnology; Tianjin Institute of Industrial Biotechnology; Chinese Academy of Sciences; Tianjin China
| | - Q. Wang
- Key Laboratory of Systems Microbial Biotechnology; Tianjin Institute of Industrial Biotechnology; Chinese Academy of Sciences; Tianjin China
| | - Y. Ma
- Key Laboratory of Systems Microbial Biotechnology; Tianjin Institute of Industrial Biotechnology; Chinese Academy of Sciences; Tianjin China
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Qiao J, Wang J, Chen L, Tian X, Huang S, Ren X, Zhang W. Quantitative iTRAQ LC-MS/MS proteomics reveals metabolic responses to biofuel ethanol in cyanobacterial Synechocystis sp. PCC 6803. J Proteome Res 2012; 11:5286-300. [PMID: 23062023 DOI: 10.1021/pr300504w] [Citation(s) in RCA: 114] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Recent progress in metabolic engineering has led to autotrophic production of ethanol in various cyanobacterial hosts. However, cyanobacteria are known to be sensitive to ethanol, which restricts further efforts to increase ethanol production levels in these renewable host systems. To understand the mechanisms of ethanol tolerance so that engineering more robust cyanobacterial hosts can be possible, in this study, the responses of model cyanobacterial Synechocystis sp. PCC 6803 to ethanol were determined using a quantitative proteomics approach with iTRAQ LC-MS/MS technologies. The resulting high-quality proteomic data set consisted of 24,887 unique peptides corresponding to 1509 identified proteins, a coverage of approximately 42% of the predicted proteins in the Synechocystis genome. Using a cutoff of 1.5-fold change and a p-value less than 0.05, 135 and 293 unique proteins with differential abundance levels were identified between control and ethanol-treated samples at 24 and 48 h, respectively. Functional analysis showed that the Synechocystis cells employed a combination of induced common stress response, modifications of cell membrane and envelope, and induction of multiple transporters and cell mobility-related proteins as protection mechanisms against ethanol toxicity. Interestingly, our proteomic analysis revealed that proteins related to multiple aspects of photosynthesis were up-regulated in the ethanol-treated Synechocystis cells, consistent with increased chlorophyll a concentration in the cells upon ethanol exposure. The study provided the first comprehensive view of the complicated molecular mechanisms against ethanol stress and also provided a list of potential gene targets for further engineering ethanol tolerance in Synechocystis PCC 6803.
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Affiliation(s)
- Jianjun Qiao
- School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, P.R. China
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Bae E, Patsekin V, Rajwa B, Bhunia AK, Holdman C, Davisson VJ, Hirleman ED, Robinson JP. Development of a microbial high-throughput screening instrument based on elastic light scatter patterns. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2012; 83:044304. [PMID: 22559555 PMCID: PMC3339897 DOI: 10.1063/1.3697853] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Accepted: 03/05/2012] [Indexed: 05/24/2023]
Abstract
A microbial high-throughput screening (HTS) system was developed that enabled high-speed combinatorial studies directly on bacterial colonies. The system consists of a forward scatterometer for elastic light scatter (ELS) detection, a plate transporter for sample handling, and a robotic incubator for automatic incubation. To minimize the ELS pattern-capturing time, a new calibration plate and correction algorithms were both designed, which dramatically reduced correction steps during acquisition of the circularly symmetric ELS patterns. Integration of three different control software programs was implemented, and the performance of the system was demonstrated with single-species detection for library generation and with time-resolved measurement for understanding ELS colony growth correlation, using Escherichia coli and Listeria. An in-house colony-tracking module enabled researchers to easily understand the time-dependent variation of the ELS from identical colony, which enabled further analysis in other biochemical experiments. The microbial HTS system provided an average scan time of 4.9 s per colony and the capability of automatically collecting more than 4000 ELS patterns within a 7-h time span.
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Affiliation(s)
- Euiwon Bae
- School of Mechanical Engineering, Purdue University, West Lafayette, Indiana 47907, USA
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