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Liu J, Liu D, Sun T, Fan TP, Cai Y. Construction and characterization of a promoter library with varying strengths to enhance acetoin production from xylose in Serratia marcescens. Biotechnol Appl Biochem 2024; 71:553-564. [PMID: 38225826 DOI: 10.1002/bab.2558] [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: 08/18/2023] [Accepted: 12/30/2023] [Indexed: 01/17/2024]
Abstract
Serratia marcescens is utilized as a significant enterobacteria in the production of various high-value secondary metabolites. Acetoin serves as a crucial foundational compound of development and finds application in a broad range of fields. Furthermore, S. marcescens HBQA-7 is capable of utilizing xylose as its exclusive carbon source for acetoin production. The objective of this study was to utilize a constitutive promoter screening strategy to enhance both xylose utilization and acetoin production in S. marcescens HBQA-7. By utilizing RNA-seq, we identified the endogenous constitutive promoter P6 that is the most robust, which facilitated the overexpression of the sugar transporter protein GlfL445I, α-acetyl lactate synthase, and α-acetyl lactate decarboxylase, respectively. The resultant recombinant strains exhibited enhanced xylose utilization rates and acetoin yields. Subsequently, a recombinant plasmid, denoted as pBBR1MCS-P6-glfL445IalsSalsD, was constructed, simultaneously expressing the aforementioned three genes. The resulting recombinant strain, designated as S3, demonstrated a 1.89-fold boost in xylose consumption rate compared with the original strain during shake flask fermentation. resulting in the accumulation of 7.14 g/L acetoin in the final fermentation medium. Subsequently, in a 5 L fermenter setup, the acetoin yield reached 48.75 g/L, corresponding to a xylose-to-acetoin conversion yield of 0.375 g/g.
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Affiliation(s)
- Jie Liu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Di Liu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Tingting Sun
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Tai-Ping Fan
- Department of Pharmacology, University of Cambridge, Cambridge, UK
| | - Yujie Cai
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
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2
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Liu H, Chen Y, Wang S, Liu Y, Zhao W, Huo K, Guo H, Xiong W, Wang S, Yang C, Liu R. Metabolic engineering of genome-streamlined strain Pseudomonas putida KTU-U27 for medium-chain-length polyhydroxyalkanoate production from xylose and cellobiose. Int J Biol Macromol 2023; 253:126732. [PMID: 37678685 DOI: 10.1016/j.ijbiomac.2023.126732] [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: 07/03/2023] [Revised: 09/03/2023] [Accepted: 09/03/2023] [Indexed: 09/09/2023]
Abstract
Bio-based plastics polyhydroxyalkanoates (PHAs) are considered as a good substitutive to traditional fossil-based plastics because PHAs outcompete chemical plastics in several important properties, such as biodegradability, biocompatibility, and renewability. However, the industrial production of PHA (especially medium-chain-length PHA, mcl-PHA) is greatly restricted by the cost of carbon sources. Currently, xylose and cellobiose derived from lignocellulose are potential substrates for mcl-PHA production. In this study, Pseudomonas putida KTU-U27, a genome-streamlined strain derived from a mcl-PHA producer P. putida KT2440, was used as the optimal chassis for the construction of microbial cell factories with the capacity to efficiently produce mcl-PHA from xylose and cellobiose by introducing the xylose and cellobiose metabolism modules and enhancing the transport of xylose and cellobiose. The lag phases of the xylose- and cellobiose-grown engineered strains were almost completely eliminated and the xylose- and cellobiose-utilizing performance was greatly improved via adaptive laboratory evolution. In shake-flask fermentation, the engineered strain 27A-P13-xylABE-Ptac-tt and 27A-P13-bglC-P13-gts had a mcl-PHA content of 41.67 wt% and 45.18 wt%, respectively, and were able to efficiently utilize xylose or cellobiose as the sole carbon source for cell growth. Herein, microbial production of mcl-PHA using xylose as the sole carbon source has been demonstrated for the first time. Meanwhile, the highest yield of mcl-PHA produced from cellobiose has been obtained in this study. Interestingly, the engineered strains derived from genome-reduced P. putida strains showed higher xylose- and cellobiose-utilizing performance and higher PHA yield than those derived from P. putida KT2440. This study highlights enormous potential of the engineered strains as promising platforms for low-cost production of mcl-PHA from xylose- and cellobiose-rich substrates.
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Affiliation(s)
- Honglu Liu
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Yaping Chen
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Siqi Wang
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Yujie Liu
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Wanwan Zhao
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Kaiyue Huo
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Hongfu Guo
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Weini Xiong
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Shufang Wang
- Key Laboratory of Bioactive Materials for Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China.
| | - Chao Yang
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China.
| | - Ruihua Liu
- Tianjin Key Laboratory of Protein Science, College of Life Sciences, Nankai University, Tianjin 300071, China.
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3
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Akinsemolu A, Onyeaka H. Exploring the Role of Green Microbes in Sustainable Bioproduction of Biodegradable Polymers. Polymers (Basel) 2023; 15:4617. [PMID: 38232039 PMCID: PMC10708544 DOI: 10.3390/polym15234617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 11/23/2023] [Accepted: 12/02/2023] [Indexed: 01/19/2024] Open
Abstract
Research efforts have shifted to creating biodegradable polymers to offset the harmful environmental impacts associated with the accumulation of non-degradable synthetic polymers in the environment. This review presents a comprehensive examination of the role of green microbes in fostering sustainable bioproduction of these environment-friendly polymers. Green microbes, primarily algae and cyanobacteria, have emerged as promising bio-factories due to their ability to capture carbon dioxide and utilize solar energy efficiently. It further discusses the metabolic pathways harnessed for the synthesis of biopolymers such as polyhydroxyalkanoates (PHAs) and the potential for genetic engineering to augment their production yields. Additionally, the techno-economic feasibility of using green microbes, challenges associated with the up-scaling of biopolymer production, and potential solutions are elaborated upon. With the twin goals of environmental protection and economic viability, green microbes pave the way for a sustainable polymer industry.
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Affiliation(s)
- Adenike Akinsemolu
- Institute of Advanced Studies, University of Birmingham, Birmingham B15 2TT, UK
- Department of Integrated Science, Adeyemi Federal University of Education, Ondo 351101, Nigeria
| | - Helen Onyeaka
- School of Chemical Engineering, University of Birmingham, Birmingham B15 2TT, UK
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4
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Li HF, Tian L, Lian G, Fan LH, Li ZJ. Engineering Vibrio alginolyticus as a novel chassis for PHB production from starch. Front Bioeng Biotechnol 2023; 11:1130368. [PMID: 36824353 PMCID: PMC9941669 DOI: 10.3389/fbioe.2023.1130368] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 01/30/2023] [Indexed: 02/09/2023] Open
Abstract
Vibrio alginolyticus LHF01 was engineered to efficiently produce poly-3-hydroxybutyrate (PHB) from starch in this study. Firstly, the ability of Vibrio alginolyticus LHF01 to directly accumulate PHB using soluble starch as the carbon source was explored, and the highest PHB titer of 2.06 g/L was obtained in 18 h shake flask cultivation. Then, with the analysis of genomic information of V. alginolyticus LHF01, the PHB synthesis operon and amylase genes were identified. Subsequently, the effects of overexpressing PHB synthesis operon and amylase on PHB production were studied. Especially, with the co-expression of PHB synthesis operon and amylase, the starch consumption rate was improved and the PHB titer was more than doubled. The addition of 20 g/L insoluble corn starch could be exhausted in 6-7 h cultivation, and the PHB titer was 4.32 g/L. To the best of our knowledge, V. alginolyticus was firstly engineered to produce PHB with the direct utilization of starch, and this stain can be considered as a novel host to produce PHB using starch as the raw material.
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Affiliation(s)
- Hong-Fei Li
- College of Chemical Engineering, Fujian Engineering Research Center of Advanced Manufacturing Technology for Fine Chemicals, Fuzhou University, Fuzhou, China,College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China,Qingyuan Innovation Laboratory, Quanzhou, China
| | - Linyue Tian
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Guoli Lian
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Li-Hai Fan
- College of Chemical Engineering, Fujian Engineering Research Center of Advanced Manufacturing Technology for Fine Chemicals, Fuzhou University, Fuzhou, China,Qingyuan Innovation Laboratory, Quanzhou, China,*Correspondence: Li-Hai Fan, ; Zheng-Jun Li,
| | - Zheng-Jun Li
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China,*Correspondence: Li-Hai Fan, ; Zheng-Jun Li,
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Pan X, Tang M, You J, Hao Y, Zhang X, Yang T, Rao Z. A Novel Method to Screen Strong Constitutive Promoters in Escherichia coli and Serratia marcescens for Industrial Applications. BIOLOGY 2022; 12:biology12010071. [PMID: 36671763 PMCID: PMC9855843 DOI: 10.3390/biology12010071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/18/2022] [Accepted: 12/28/2022] [Indexed: 01/04/2023]
Abstract
Promoters serve as the switch of gene transcription, playing an important role in regulating gene expression and metabolites production. However, the approach to screening strong constitutive promoters in microorganisms is still limited. In this study, a novel method was designed to identify strong constitutive promoters in E. coli and S. marcescens based on random genomic interruption and fluorescence-activated cell sorting (FACS) technology. First, genomes of E. coli, Bacillus subtilis, and Corynebacterium glutamicum were randomly interrupted and inserted into the upstream of reporter gene gfp to construct three promoter libraries, and a potential strong constitutive promoter (PBS) suitable for E. coli was screened via FACS technology. Second, the core promoter sequence (PBS76) of the screened promoter was identified by sequence truncation. Third, a promoter library of PBS76 was constructed by installing degenerate bases via chemical synthesis for further improving its strength, and the intensity of the produced promoter PBS76-100 was 59.56 times higher than that of the promoter PBBa_J23118. Subsequently, promoters PBBa_J23118, PBS76, PBS76-50, PBS76-75, PBS76-85, and PBS76-100 with different strengths were applied to enhance the metabolic flux of L-valine synthesis, and the L-valine yield was significantly improved. Finally, a strong constitutive promoter suitable for S. marcescens was screened by a similar method and applied to enhance prodigiosin production by 34.81%. Taken together, the construction of a promoter library based on random genomic interruption was effective to screen the strong constitutive promoters for fine-tuning gene expression and reprogramming metabolic flux in various microorganisms.
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Affiliation(s)
- Xuewei Pan
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Mi Tang
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Jiajia You
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Yanan Hao
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Xian Zhang
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Taowei Yang
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Correspondence: ; Tel.: +86-510-85916881
| | - Zhiming Rao
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
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Leadbeater DR, Bruce NC, Tonon T. In silico identification of bacterial seaweed-degrading bioplastic producers. Microb Genom 2022; 8:mgen000866. [PMID: 36125959 PMCID: PMC9676036 DOI: 10.1099/mgen.0.000866] [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: 01/18/2022] [Accepted: 06/21/2022] [Indexed: 11/18/2022] Open
Abstract
There is an urgent need to replace petroleum-based plastic with bio-based and biodegradable alternatives. Polyhydroxyalkanoates (PHAs) are attractive prospective replacements that exhibit desirable mechanical properties and are recyclable and biodegradable in terrestrial and marine environments. However, the production costs today still limit the economic sustainability of the PHA industry. Seaweed cultivation represents an opportunity for carbon capture, while also supplying a sustainable photosynthetic feedstock for PHA production. We mined existing gene and protein databases to identify bacteria able to grow and produce PHAs using seaweed-derived carbohydrates as substrates. There were no significant relationships between the genes involved in the deconstruction of algae polysaccharides and PHA production, with poor to negative correlations and diffused clustering suggesting evolutionary compartmentalism. We identified 2 987 bacterial candidates spanning 40 taxonomic families predominantly within Alphaproteobacteria, Gammaproteobacteria and Burkholderiales with enriched seaweed-degrading capacity that also harbour PHA synthesis potential. These included highly promising candidates with specialist and generalist specificities, including Alteromonas, Aquisphaera, Azotobacter, Bacillus, Caulobacter, Cellvibrionaceae, Duganella, Janthinobacterium, Massilia, Oxalobacteraceae, Parvularcula, Pirellulaceae, Pseudomonas, Rhizobacter, Rhodanobacter, Simiduia, Sphingobium, Sphingomonadaceae, Sphingomonas, Stieleria, Vibrio and Xanthomonas. In this enriched subset, the family-level densities of genes targeting green macroalgae polysaccharides were considerably higher (n=231.6±68.5) than enzymes targeting brown (n=65.34±13.12) and red (n=30.5±10.72) polysaccharides. Within these organisms, an abundance of FabG genes was observed, suggesting that the fatty acid de novo synthesis pathway supplies (R)-3-hydroxyacyl-CoA or 3-hydroxybutyryl-CoA from core metabolic processes and is the predominant mechanism of PHA production in these organisms. Our results facilitate extending seaweed biomass valorization in the context of consolidated biorefining for the production of bioplastics.
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Affiliation(s)
- Daniel R. Leadbeater
- Centre for Novel Agricultural Products, Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Neil C. Bruce
- Centre for Novel Agricultural Products, Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Thierry Tonon
- Centre for Novel Agricultural Products, Department of Biology, University of York, Heslington, York YO10 5DD, UK
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Liu H, Chen Y, Zhang Y, Zhao W, Guo H, Wang S, Xia W, Wang S, Liu R, Yang C. Enhanced production of polyhydroxyalkanoates in Pseudomonas putida KT2440 by a combination of genome streamlining and promoter engineering. Int J Biol Macromol 2022; 209:117-124. [PMID: 35395277 DOI: 10.1016/j.ijbiomac.2022.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/19/2022] [Accepted: 04/02/2022] [Indexed: 11/05/2022]
Abstract
Polyhydroxyalkanoates (PHAs), a class of bioplastics produced by a variety of microorganisms, have become the ideal alternatives for oil-derived plastics due to their superior physicochemical and material characteristics. Pseudomonas putida KT2440 can produce medium-chain-length PHA (mcl-PHA) from various substrates. In this study, a novel strategy of the large-scale deletion of genomic islands (GIs) coupling with promoter engineering was developed in P. putida KT2440 for constructing the minimal genome cell factories (MGF) capable of efficiently producing mcl-PHA. Firstly, P. putida KTU-U13, a 13 GIs- and upp-deleted mutant derived from the parental strain P. putida KT2440, was used as a starting strain for further deletion of GIs to generate a series of genome-reduced strains. Subsequently, the two minimal genome strains KTU-U24 and KTU-U27, which had a 7.19% and 8.35% reduction relative to the genome size of KT2440 and were advantageous over the strain KTU (KT2440∆upp) and KTU-U13 in several physiological traits such as the maximum specific growth rate, plasmid transformation efficiency, heterologous protein expression capacity and PHA production capacity, were selected as the chassis cells for PHA metabolic engineering. To prevent the formation of the by-product gluconic acid, the glucose dehydrogenase gene was deleted in KTU-U24 and KTU-U27, resulting in KTU-U24∆gcd and KTU-U27∆gcd. To enhance the transcriptional level of PHA synthase genes (phaC) and the supply of the precursor acetyl-CoA, a strong endogenous promoter P46 was inserted into upstream of the phaC operon and pyruvate dehydrogenase gene in the genome of KTU-U24∆gcd and KTU-U27∆gcd, to generate KTU-U24∆gcd-P46CA and KTU-U27∆gcd-P46CA, with the PHA yield of 50.5 wt% and 53.8 wt% (weight percent of PHA in cell dry weight). Finally, KTU-U27∆gcd-P46CA, the most minimal KT2440 chassis currently available, was able to accumulate the PHA to 55.82 wt% in a 5-l fermentor, which is the highest PHA yield obtained with P. putida KT2440 so far. This study suggests that genome streamlining in combination with promoter engineering may be a feasible strategy for the development of the MGF for the efficient production of high value products. Moreover, further streamlining of the P. putida KT2440 genome has great potential to create the optimal chassis for synthetic biology applications.
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Affiliation(s)
- Honglu Liu
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Yaping Chen
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Yiting Zhang
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Wanwan Zhao
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Hongfu Guo
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Siqi Wang
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Wenjie Xia
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Shufang Wang
- Key Laboratory of Bioactive Materials for Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Ruihua Liu
- Tianjin Key Laboratory of Protein Science, College of Life Sciences, Nankai University, Tianjin 300071, China.
| | - Chao Yang
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China.
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Huo K, Liu Y, Huang R, Zhang Y, Liu H, Che Y, Yang C. Development of a novel promoter engineering-based strategy for creating an efficient para-nitrophenol-mineralizing bacterium. JOURNAL OF HAZARDOUS MATERIALS 2022; 424:127672. [PMID: 34753648 DOI: 10.1016/j.jhazmat.2021.127672] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 10/20/2021] [Accepted: 10/29/2021] [Indexed: 06/13/2023]
Abstract
A toxic and persistent pollutant para-nitrophenol (PNP) enters into the environment through improper industrial waste treatment and agricultural usage of chemical pesticides, leading to a potential risk to humans. Although a variety of PNP-degrading bacteria have been isolated, their application in bioremediation has been precluded due to unknown biosafety, poor PNP-mineralizing capacity, and lack of genome editing tools. In this study, a novel promoter engineering-based strategy is developed for creating efficient PNP-mineralizing bacteria. Initially, a complete PNP biodegradation pathway from Pseudomonas sp. strain WBC-3 was introduced into the genome of a biosafety and soil-dwelling bacterium Pseudomonas putida KT2440. Subsequently, five strong promoters were identified from P. putida KT2440 by transcriptome analysis and strength characterization, and each of the five promoters was independently inserted into upstream of the pnp operon in the KT2440 genome. Consequently, a P8 promoter-substituted mutant strain showed the highest PNP degradation rate and strong tolerance against high concentrations of PNP. Furthermore, when using P8 promoter to regulate the transcription of all PNP degradation genes pnpABCDEF, the complete and efficient PNP mineralization was demonstrated by stable isotope 13C-labeled PNP transformation assay. Additionally, the finally constructed KTU-P8pnp can be monitored using integrated GFP on chromosome. This strategy of a combination of pathway construction and promoter engineering should open new avenues for creating efficient degraders for bioremediation.
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Affiliation(s)
- Kaiyue Huo
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Yujie Liu
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Rui Huang
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Yiting Zhang
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Honglu Liu
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - You Che
- Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD 20892, USA.
| | - Chao Yang
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China.
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9
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Zhang Y, Liu H, Liu Y, Huo K, Wang S, Liu R, Yang C. A promoter engineering-based strategy enhances polyhydroxyalkanoate production in Pseudomonas putida KT2440. Int J Biol Macromol 2021; 191:608-617. [PMID: 34582907 DOI: 10.1016/j.ijbiomac.2021.09.142] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/18/2021] [Accepted: 09/20/2021] [Indexed: 11/24/2022]
Abstract
Polyhydroxyalkanoate (PHA), a class of biopolyester synthesized by various bacteria, is considered as an alternative to petroleum-based plastics because of its excellent physochemical and material properties. Pseudomonas putida KT2440 can produce medium-chain-length PHA (mcl-PHA) from glucose, fatty acid and glycerol, and its whole-genome sequences and cellular metabolic networks have been intensively researched. In this study, we aim to improve the PHA yield of P. putida KT2440 using a novel promoter engineering-based strategy. Unlike previous studies, endogenous strong promoters screening from P. putida KT2440 instead of synthetic or exogenous promoters was applied to the optimization of PHA biosynthesis pathway. Based on RNA-seq and promoter prediction, 30 putative strong promoters from P. putida KT2440 were identified. Subsequently, the strengths of these promoters were characterized by reporter gene assays. Furthermore, each of 10 strong promoters screened by transcriptional level and GFP fluorescence was independently inserted into upstream of PHA synthase gene (phaC1) on chromosome. As a result, the transcriptional levels of the phaC1 and phaC2 genes in almost all of the promoter-substituted strains were improved, and the relative PHA yields of the three promoter-substituted strains KTU-P1C1, KTU-P46C1 and KTU-P51C1 were improved obviously, reaching 30.62 wt%, 33.24 wt% and 33.29 wt% [the ratio of PHA weight to cell dry weight (CDW)], respectively. By further deletion of the glucose dehydrogenase gene in KTU-P1C1, KTU-P46C1 and KTU-P51C1, the relative PHA yield of the resulting mutant strain KTU-P46C1-∆gcd increased by 5.29% from 33.24% to 38.53%. Finally, by inserting P46 into upstream of pyruvate dehydrogenase gene in the genome of KTU-P46C1-∆gcd, the relative PHA yield and CDW of the resulting strain KTU-P46C1A-∆gcd reached nearly 42 wt% and 4.06 g/l, respectively, which increased by 90% and 40%, respectively, compared with the starting strain KTU. In particular, the absolute PHA yield of KTU-P46C1A-∆gcd reached 1.7 g/l, with a 165% improvement compared with the strain KTU. Herein, we report the highest PHA yield obtained by P. putida KT2440 in shake-flask fermentation to date. We demonstrate for the first time the effectiveness of endogenous strong promoters for improving the PHA yield and biomass of P. putida KT2440. More importantly, our findings highlight great potential of this strategy for enhanced production of secondary metabolites and heterologous proteins in P. putida KT2440.
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Affiliation(s)
- Yiting Zhang
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China.
| | - Honglu Liu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China.
| | - Yujie Liu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China.
| | - Kaiyue Huo
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China.
| | - Shufang Wang
- Key Laboratory of Bioactive Materials, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China.
| | - Ruihua Liu
- Tianjin Key Laboratory of Protein Science, College of Life Sciences, Nankai University, Tianjin 300071, China.
| | - Chao Yang
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China.
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10
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Jaffur N, Jeetah P, Kumar G. A review on enzymes and pathways for manufacturing polyhydroxybutyrate from lignocellulosic materials. 3 Biotech 2021; 11:483. [PMID: 34790507 DOI: 10.1007/s13205-021-03009-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 09/28/2021] [Indexed: 11/26/2022] Open
Abstract
Currently, major focus in the biopolymer field is being drawn on the exploitation of plant-based resources grounded on holistic sustainability trends to produce novel, affordable, biocompatible and environmentally safe polyhydroxyalkanoate biopolymers. The global PHA market, estimated at USD 62 Million in 2020, is predicted to grow by 11.2 and 14.2% between 2020-2024 and 2020-2025 correspondingly based on market research reports. The market is primarily driven by the growing demand for PHA products by the food packaging, biomedical, pharmaceutical, biofuel and agricultural sectors. One of the key limitations in the growth of the PHA market is the significantly higher production costs associated with pure carbon raw materials as compared to traditional polymers. Nonetheless, considerations such as consumer awareness on the toxicity of petroleum-based plastics and strict government regulations towards the prohibition of the use and trade of synthetic plastics are expected to boost the market growth rate. This study throws light on the production of polyhydroxybutyrate from lignocellulosic biomass using environmentally benign techniques via enzyme and microbial activities to assess its feasibility as a green substitute to conventional plastics. The novelty of the present study is to highlight the recent advances, pretreatment techniques to reduce the recalcitrance of lignocellulosic biomass such as dilute and concentrated acidic pretreatment, alkaline pretreatment, steam explosion, ammonia fibre explosion (AFEX), ball milling, biological pretreatment as well as novel emerging pretreatment techniques notably, high-pressure homogenizer, electron beam, high hydrostatic pressure, co-solvent enhanced lignocellulosic fractionation (CELF) pulsed-electric field, low temperature steep delignification (LTSD), microwave and ultrasound technologies. Additionally, inhibitory compounds and detoxification routes, fermentation downstream processes, life cycle and environmental impacts of recovered natural biopolymers, review green procurement policies in various countries, PHA strategies in line with the United Nations Sustainable Development Goals (SDGs) along with the fate of the spent polyhydroxybutyrate are outlined.
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Affiliation(s)
- Nausheen Jaffur
- Department of Chemical and Environmental Engineering, Faculty of Engineering, University of Mauritius, Réduit, 80837 Mauritius
| | - Pratima Jeetah
- Department of Chemical and Environmental Engineering, Faculty of Engineering, University of Mauritius, Réduit, 80837 Mauritius
| | - Gopalakrishnan Kumar
- Institute of Chemistry, Bioscience and Environmental Engineering, Faculty of Science and Technology, University of Stavanger, Stavanger, Norway
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11
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Ma J, Ji Q, Wang S, Qiu J, Liu Q. Identification and evaluation of a panel of strong constitutive promoters in Listeria monocytogenes for improving the expression of foreign antigens. Appl Microbiol Biotechnol 2021; 105:5135-5145. [PMID: 34086117 PMCID: PMC8175932 DOI: 10.1007/s00253-021-11374-z] [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: 02/12/2021] [Revised: 05/10/2021] [Accepted: 05/27/2021] [Indexed: 12/19/2022]
Abstract
Attenuated Listeria monocytogenes could be a potential vaccine vector for the immunotherapy of tumors or pathogens. However, the lack of reliable promoters has limited its ability to express foreign antigens. In the present study, 21 promoters were identified from Listeria monocytogenes through RNA-seq analysis under two pH conditions of pH 7.4 and pH 5.5. Based on the constructed fluorescence report system, 7 constitutive promoters exhibited higher strength than Phelp (1.8-fold to 5.4-fold), a previously reported strong promoter. Furthermore, the selected 5 constitutive promoters exhibited higher UreB production activity than Phelp (1.1-fold to 8.3-fold). Notably, a well-characterized constitutive promoter P18 was found with the highest activity of fluorescence intensity and UreB production. In summary, the study provides a panel of strong constitutive promoters for Listeria monocytogenes and offers a theoretical basis for mining constitutive promoters in other organisms. KEY POINTS: • Twenty-one promoters were identified from L. monocytogenes through RNA-seq. • Fluorescent tracer of L. monocytogenes (P18) was performed in vitro and in vivo. • A well-characterized constitutive promoter P18 could improve the expression level of a foreign antigen UreB in L. monocytogenes.
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Affiliation(s)
- Junfei Ma
- School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Qianyu Ji
- School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Shuying Wang
- School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Jingxuan Qiu
- School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Qing Liu
- School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China. .,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China.
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Sindhu R, Madhavan A, Arun KB, Pugazhendhi A, Reshmy R, Awasthi MK, Sirohi R, Tarafdar A, Pandey A, Binod P. Metabolic circuits and gene regulators in polyhydroxyalkanoate producing organisms: Intervention strategies for enhanced production. BIORESOURCE TECHNOLOGY 2021; 327:124791. [PMID: 33579565 DOI: 10.1016/j.biortech.2021.124791] [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: 11/30/2020] [Revised: 01/19/2021] [Accepted: 01/23/2021] [Indexed: 06/12/2023]
Abstract
Worldwide worries upsurge concerning environmental pollutions triggered by the accumulation of plastic wastes. Biopolymers are promising candidates for resolving these difficulties by replacing non-biodegradable plastics. Among biopolymers, polyhydroxyalkanoates (PHAs), are natural polymers that are synthesized and accumulated in a range of microorganisms, are considered as promising biopolymers since they have biocompatibility, biodegradability, and other physico-chemical properties comparable to those of synthetic plastics. Consequently, considerable research have been attempted to advance a better understanding of mechanisms related to the metabolic synthesis and characteristics of PHAs and to develop native and recombinant microorganisms that can proficiently produce PHAs comprising desired monomers with high titer and productivity for industrial applications. Recent developments in metabolic engineering and synthetic biology applied to enhance PHA synthesis include, promoter engineering, ribosome-binding site (RBS) engineering, development of synthetic constructs etc. This review gives a brief overview of metabolic routes and regulators of PHA production and its intervention strategies.
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Affiliation(s)
- Raveendran Sindhu
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Trivandrum 695 019, Kerala, India
| | - Aravind Madhavan
- Rajiv Gandhi Centre for Biotechnology, Trivandrum 695 014, Kerala, India
| | - K B Arun
- Rajiv Gandhi Centre for Biotechnology, Trivandrum 695 014, Kerala, India
| | - Arivalagan Pugazhendhi
- Innovative Green Product Synthesis and Renewable Environment Development Research Group, Faculty of Environment and Labour Safety, Ton Duc Thang University, Ho Chi Minh City, Viet Nam
| | - R Reshmy
- Post Graduate and Research Department of Chemistry, Bishop Moore College, Mavelikara 690 110, Kerala, India
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A & F University, Yangling, Shaanxi Province 712100, PR China
| | - Ranjna Sirohi
- Department of Post Harvest Process and Food Engineering, G.B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263 145, India
| | - Ayon Tarafdar
- Divison of Livestock Production and Management, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243 122, Uttar Pradesh, India
| | - Ashok Pandey
- Centre for Innovation and Translational Research, CSIR- Indian Institute for Toxicology Research (CSIR-IITR), 31 MG Marg, Lucknow 226 001, India
| | - Parameswaran Binod
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Trivandrum 695 019, Kerala, India.
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Differential Effects of Homologous Transcriptional Regulators NicR2A, NicR2B1, and NicR2B2 and Endogenous Ectopic Strong Promoters on Nicotine Metabolism in Pseudomonas sp. Strain JY-Q. Appl Environ Microbiol 2021; 87:AEM.02457-20. [PMID: 33187996 DOI: 10.1128/aem.02457-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 11/04/2020] [Indexed: 01/27/2023] Open
Abstract
Nicotine is a toxic environmental pollutant that widely exists in tobacco wastes. As a natural nicotine-degrading strain, Pseudomonas sp. strain JY-Q still has difficulties degrading high concentrations of nicotine. In this study, we investigated the effect of two homologous transcriptional regulators and endogenous ectopic strong promoters on the efficiency of nicotine degradation. Comparative genomics analysis showed that two homologous transcriptional regulators, namely, NicR2A and NicR2Bs (NicR2B1 plus NicR2B2), can repress nicotine degradation gene expression. When both nicR2A and nicR2Bs were deleted, the resulting mutant JY-Q ΔnicR2A ΔnicR2B1 ΔnicR2B2 (QΔABs) exhibits a 17% higher nicotine degradation efficiency than wild-type JY-Q. Transcriptome sequencing (RNA-seq) analysis showed that the transcription levels (fragments per kilobase per million [FPKM] value) of six genes were higher than those of the other genes in JY-Q. Based on the genetic organization of these genes, three putative promoters, PRS28250 , PRS09985 , and PRS24685 , were identified. Their promoter activities were evaluated by comparing their expression levels using reverse transcriptase quantitative PCR (RT-qPCR). We found that the transcription levels of RS28250, RS09985, and RS24685 were respectively 16.8, 2.6, and 1.6 times higher than that of hspB2, encoding 6-hydroxy-3-succinylpyridine hydroxylase, which is involved in nicotine degradation. Thus, two strong endogenous promoters, namely, PRS28250 and PRS09985 , were selected to replace the original promoters of nic2 gene clusters. The effect of the endogenous ectopic promoter was also related to the position of target gene clusters. When the promoter PRS28250 replaced the promoter of hspB2, the resultant mutant QΔABs-ΔPhspB2 ::PRS28250 exhibited nicotine-degrading efficiency 69% higher than that of JY-Q. This research suggests a feasible strategy to enhance strains' capacity for nicotine degradation by removal of repressing regulatory proteins and replacing the target promoter with strong endogenous ectopic promoters.IMPORTANCE This study evaluated the differential effects of homologous NicR2A and NicR2Bs and endogenous ectopic strong promoters on nicotine metabolism in Pseudomonas sp. strain JY-Q. Based on our differential analysis, a feasible strategy is presented to modify wild-type (WT) strain JY-Q by removing repressing regulatory proteins NicR2A and NicR2Bs and replacing the target promoter with strong endogenous ectopic promoters. The resulting mutants exhibited high tolerance and degradation of nicotine. These findings should be beneficial for improving the pollutant-degrading capacity of natural strains through genomic modification.
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Ai M, Zhu Y, Jia X. Recent advances in constructing artificial microbial consortia for the production of medium-chain-length polyhydroxyalkanoates. World J Microbiol Biotechnol 2021; 37:2. [PMID: 33392870 DOI: 10.1007/s11274-020-02986-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 12/20/2020] [Indexed: 11/29/2022]
Abstract
Polyhydroxyalkanoates (PHAs) are a class of high-molecular-weight polyesters made from hydroxy fatty acid monomers. PHAs produced by microorganisms have diverse structures, variable physical properties, and good biodegradability. They exhibit similar physical properties to petroleum-based plastics but are much more environmentally friendly. Medium-chain-length polyhydroxyalkanoates (mcl-PHAs), in particular, have attracted much interest because of their low crystallinity, low glass transition temperature, low tensile strength, high elongation at break, and customizable structure. Nevertheless, high production costs have hindered their practical application. The use of genetically modified organisms can reduce production costs by expanding the scope of substrate utilization, improving the conversion efficiency of substrate to product, and increasing the yield of mcl-PHAs. The yield of mcl-PHAs produced by a pure culture of an engineered microorganism was not high enough because of the limitations of the metabolic capacity of a single microorganism. The construction of artificial microbial consortia and the optimization of microbial co-cultivation have been studied. This type of approach avoids the addition of precursor substances and helps synthesize mcl-PHAs more efficiently. In this paper, we reviewed the design and construction principles and optimized control strategies for artificial microbial consortia that produce mcl-PHAs. We described the metabolic advantages of co-cultivating artificial microbial consortia using low-value substrates and discussed future perspectives on the production of mcl-PHAs using artificial microbial consortia.
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Affiliation(s)
- Mingmei Ai
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Yinzhuang Zhu
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Xiaoqiang Jia
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, China.
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, 300072, China.
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15
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Liu H, Wang Y, Hou Y, Li Z. Fitness of Chassis Cells and Metabolic Pathways for l-Cysteine Overproduction in Escherichia coli. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:14928-14937. [PMID: 33264003 DOI: 10.1021/acs.jafc.0c06134] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
l-Cysteine is a ubiquitous and unique sulfur-containing amino acid with numerous applications in agricultural and food industries. The efficient production of l-cysteine via microbial fermentation has received a great deal of attention. In this study, the fitness of different Escherichia coli K-12 strains harboring plasmid pLH03 was investigated. The enhancement of the precursor synthetic pathway and thiosulfate assimilation pathway resulted in the good performance of the E. coli BW25113 strain. The expression levels of synthetic pathway genes were optimized by two constitutive promoters to assess their effects on cysteine production. In conjunction, the main degradation pathway genes were also deleted for more efficient production of cysteine. l-Cysteine production was further increased through the manipulation of the sulfur transcription regulator cysB and sulfur supplementation. After process optimization in a 1.5 L bioreactor, LH2A1M0BΔYTS-pLH03 [BW25113 Ptrc2-serA Ptrc1-cysMPtrc-cysBΔyhaMΔtnaAΔsdaA-(pLH03)] accumulated 8.34 g/L cysteine, laying a foundation for application in the cysteine fermentation industry.
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Affiliation(s)
- Han Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Yu Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Yehua Hou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Zhimin Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
- Shanghai Collaborative Innovation Center for Biomanufacturing Technology, 130 Meilong Road, Shanghai 200237, China
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16
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Zhang F, Huo K, Song X, Quan Y, Wang S, Zhang Z, Gao W, Yang C. Engineering of a genome-reduced strain Bacillus amyloliquefaciens for enhancing surfactin production. Microb Cell Fact 2020; 19:223. [PMID: 33287813 PMCID: PMC7720510 DOI: 10.1186/s12934-020-01485-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 11/28/2020] [Indexed: 01/17/2023] Open
Abstract
Background Genome reduction and metabolic engineering have emerged as intensive research hotspots for constructing the promising functional chassis and various microbial cell factories. Surfactin, a lipopeptide-type biosurfactant with broad spectrum antibiotic activity, has wide application prospects in anticancer therapy, biocontrol and bioremediation. Bacillus amyloliquefaciens LL3, previously isolated by our lab, contains an intact srfA operon in the genome for surfactin biosynthesis. Results In this study, a genome-reduced strain GR167 lacking ~ 4.18% of the B. amyloliquefaciens LL3 genome was constructed by deleting some unnecessary genomic regions. Compared with the strain NK-1 (LL3 derivative, ΔuppΔpMC1), GR167 exhibited faster growth rate, higher transformation efficiency, increased intracellular reducing power level and higher heterologous protein expression capacity. Furthermore, the chassis strain GR167 was engineered for enhanced surfactin production. Firstly, the iturin and fengycin biosynthetic gene clusters were deleted from GR167 to generate GR167ID. Subsequently, two promoters PRsuc and PRtpxi from LL3 were obtained by RNA-seq and promoter strength characterization, and then they were individually substituted for the native srfA promoter in GR167ID to generate GR167IDS and GR167IDT. The best mutant GR167IDS showed a 678-fold improvement in the transcriptional level of the srfA operon relative to GR167ID, and it produced 311.35 mg/L surfactin, with a 10.4-fold increase relative to GR167. Conclusions The genome-reduced strain GR167 was advantageous over the parental strain in several industrially relevant physiological traits assessed and it was highlighted as a chassis strain for further genetic modification. In future studies, further reduction of the LL3 genome can be expected to create high-performance chassis for synthetic biology applications.
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Affiliation(s)
- Fang Zhang
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, Key Laboratory of Bioactive Materials for Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Kaiyue Huo
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, Key Laboratory of Bioactive Materials for Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Xingyi Song
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, Key Laboratory of Bioactive Materials for Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Yufen Quan
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, Key Laboratory of Bioactive Materials for Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Shufang Wang
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, Key Laboratory of Bioactive Materials for Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Zhiling Zhang
- Department of Oral and Maxillofacial Radiology, Tianjin Stomatological Hospital, School of Medicine, Nankai University, Tianjin, 300041, China. .,Tianjin Key Laboratory of Oral and Maxillofacial Function Reconstruction, Tianjin, 300041, China.
| | - Weixia Gao
- MOE Key Laboratory of Industrial Fermentation Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China.
| | - Chao Yang
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, Key Laboratory of Bioactive Materials for Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China.
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Fan X, Zhang Y, Zhao F, Liu Y, Zhao Y, Wang S, Liu R, Yang C. Genome reduction enhances production of polyhydroxyalkanoate and alginate oligosaccharide in Pseudomonas mendocina. Int J Biol Macromol 2020; 163:2023-2031. [DOI: 10.1016/j.ijbiomac.2020.09.067] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 08/11/2020] [Accepted: 09/10/2020] [Indexed: 12/15/2022]
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18
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Zhang X, Lin Y, Wu Q, Wang Y, Chen GQ. Synthetic Biology and Genome-Editing Tools for Improving PHA Metabolic Engineering. Trends Biotechnol 2020; 38:689-700. [DOI: 10.1016/j.tibtech.2019.10.006] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 10/13/2019] [Accepted: 10/14/2019] [Indexed: 12/17/2022]
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Liang P, Zhang Y, Xu B, Zhao Y, Liu X, Gao W, Ma T, Yang C, Wang S, Liu R. Deletion of genomic islands in the Pseudomonas putida KT2440 genome can create an optimal chassis for synthetic biology applications. Microb Cell Fact 2020; 19:70. [PMID: 32188438 PMCID: PMC7081699 DOI: 10.1186/s12934-020-01329-w] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 03/12/2020] [Indexed: 01/05/2023] Open
Abstract
Background Genome streamlining is a feasible strategy for constructing an optimum microbial chassis for synthetic biology applications. Genomic islands (GIs) are usually regarded as foreign DNA sequences, which can be obtained by horizontal gene transfer among microorganisms. A model strain Pseudomonas putida KT2440 has broad applications in biocatalysis, biotransformation and biodegradation. Results In this study, the identified GIs in P. putida KT2440 accounting for 4.12% of the total genome size were deleted to generate a series of genome-reduced strains. The mutant KTU-U13 with the largest deletion was advantageous over the original strain KTU in several physiological characteristics evaluated. The mutant KTU-U13 showed high plasmid transformation efficiency and heterologous protein expression capacity compared with the original strain KTU. The metabolic phenotype analysis showed that the types of carbon sources utilized by the mutant KTU-U13 and the utilization capabilities for certain carbon sources were increased greatly. The polyhydroxyalkanoate (PHA) yield and cell dry weight of the mutant KTU-U13 were improved significantly compared with the original strain KTU. The chromosomal integration efficiencies for the γ-hexachlorocyclohexane (γ-HCH) and 1,2,3-trichloropropane (TCP) biodegradation pathways were improved greatly when using the mutant KTU-U13 as the recipient cell and enhanced degradation of γ-HCH and TCP by the mutant KTU-U13 was also observed. The mutant KTU-U13 was able to stably express a plasmid-borne zeaxanthin biosynthetic pathway, suggesting the excellent genetic stability of the mutant. Conclusions These desirable traits make the GIs-deleted mutant KTU-U13 an optimum chassis for synthetic biology applications. The present study suggests that the systematic deletion of GIs in bacteria may be a useful approach for generating an optimal chassis for the construction of microbial cell factories.
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Affiliation(s)
- Peixin Liang
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, Nankai University, Tianjin, 300071, China
| | - Yiting Zhang
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, Nankai University, Tianjin, 300071, China
| | - Bo Xu
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, Nankai University, Tianjin, 300071, China
| | - Yuxin Zhao
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, Nankai University, Tianjin, 300071, China
| | - Xiangsheng Liu
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, Nankai University, Tianjin, 300071, China
| | - Weixia Gao
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, Nankai University, Tianjin, 300071, China
| | - Ting Ma
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, Nankai University, Tianjin, 300071, China
| | - Chao Yang
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, Nankai University, Tianjin, 300071, China.
| | - Shufang Wang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China.
| | - Ruihua Liu
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China.
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20
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Liu H, Hou Y, Wang Y, Li Z. Enhancement of Sulfur Conversion Rate in the Production of l-Cysteine by Engineered Escherichia coli. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:250-257. [PMID: 31823602 DOI: 10.1021/acs.jafc.9b06330] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Cysteine is a commercially important sulfur-containing amino acid widely used as a supplement in the agricultural and food industries. It is extremely desirable to achieve a high sulfur conversion rate in the fermentation-based cysteine production. Here, the metabolic engineering of Escherichia coli was performed to enhance the sulfur conversion rate in cysteine biosynthesis. Accordingly, the reduction of sulfur loss by the regulator decR and its yhaOM operons were deleted. serACB was integrated into chromosome with constitutive promoter to coordinately increase sulfur utilization. The sulfur assimilation pathways and sulfur transcriptional regulator cysB were overexpressed to regulate sulfur metabolism and enhance sulfur conversion significantly. After the process optimization in fed-batch fermentation, LH16 [SLH02 ΔyhaM Ptrc1-serACB-cysM-nrdH-(pLH03, pTrc99a-cysB)] produced 7.5 g/L of cysteine with a sulfur conversion rate of 90.11%. These results indicate that cysteine production by LH16 is a valuable process in the agricultural and food industries.
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Affiliation(s)
- Han Liu
- State Key Laboratory of Bioreactor Engineering , East China University of Science and Technology , 130 Meilong Road , Shanghai 200237 , China
| | - Yehua Hou
- State Key Laboratory of Bioreactor Engineering , East China University of Science and Technology , 130 Meilong Road , Shanghai 200237 , China
| | - Yu Wang
- State Key Laboratory of Bioreactor Engineering , East China University of Science and Technology , 130 Meilong Road , Shanghai 200237 , China
| | - Zhimin Li
- State Key Laboratory of Bioreactor Engineering , East China University of Science and Technology , 130 Meilong Road , Shanghai 200237 , China
- Shanghai Collaborative Innovation Center for Biomanufacturing Technology , 130 Meilong Road , Shanghai 200237 , China
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21
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Zhao F, He F, Liu X, Shi J, Liang J, Wang S, Yang C, Liu R. Metabolic engineering of Pseudomonas mendocina NK-01 for enhanced production of medium-chain-length polyhydroxyalkanoates with enriched content of the dominant monomer. Int J Biol Macromol 2019; 154:1596-1605. [PMID: 31706817 DOI: 10.1016/j.ijbiomac.2019.11.044] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 11/02/2019] [Accepted: 11/06/2019] [Indexed: 10/25/2022]
Abstract
In this study, six genes involved in β-oxidation pathway of P. mendocina NK-01 were deleted to construct mutant strains NKU-∆β1 and NKU-∆β5. Compared with the wild strain NKU, the mcl-PHA titers of NKU-∆β5 were respectively increased by 5.58- and 4.85-fold for culturing with sodium octanoate and sodium decanoate. And the mcl-PHA titers of NKU-∆β1 was increased by 10.02-fold for culturing with dodecanoic acid. The contents of dominant monomers 3-hydroxydecanoate (3HD) and 3-hydroxydodecanoate (3HDD) of the mcl-PHA synthesized by NKU-∆β5 were obviously increased to 90.01 and 58.60 mol%, respectively. Further deletion of genes phaG and phaZ, the 3HD and 3HDD contents were further improved to 94.71 and 68.67 mol%, respectively. The highest molecular weight of mcl-PHA obtained in this study was 80.79 × 104 Da, which was higher than the previously reported mcl-PHA. With the increase of dominant monomer contents, the synthesized mcl-PHA showed better thermal properties, mechanical properties and crystallization properties. Interestingly, the cell size of NKU-∆β5 was larger than that of NKU due to the accumulation of more PHA granules. This study indicated that a systematically metabolic engineering approach for P. mendocina NK-01 could significantly improve the mcl-PHA titer, dominant monomer contents and physical properties of mcl-PHA.
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Affiliation(s)
- Fengjie Zhao
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, Nankai University, Tianjin 300071, China
| | - Fanyang He
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, Nankai University, Tianjin 300071, China
| | - Xiangsheng Liu
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, Nankai University, Tianjin 300071, China
| | - Jie Shi
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China
| | - Jingnan Liang
- Core Facility of Equipment, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shufang Wang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China.
| | - Chao Yang
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, Nankai University, Tianjin 300071, China.
| | - Ruihua Liu
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China.
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22
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Kandasamy R, Rajasekaran M, Venkatesan SK, Uddin M. New Trends in the Biomanufacturing of Green Surfactants: Biobased Surfactants and Biosurfactants. ACS SYMPOSIUM SERIES 2019. [DOI: 10.1021/bk-2019-1329.ch011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Ramani Kandasamy
- Biomolecules and Biocatalysis Laboratory, Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur 603 203, Tamil Nadu, India
| | - Muneeswari Rajasekaran
- Biomolecules and Biocatalysis Laboratory, Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur 603 203, Tamil Nadu, India
| | - Swathi Krishnan Venkatesan
- Biomolecules and Biocatalysis Laboratory, Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur 603 203, Tamil Nadu, India
| | - Maseed Uddin
- Biomolecules and Biocatalysis Laboratory, Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur 603 203, Tamil Nadu, India
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Samantaray PK, Madras G, Bose S. Microbial Biofilm Membranes for Water Remediation and Photobiocatalysis. ACS SYMPOSIUM SERIES 2019. [DOI: 10.1021/bk-2019-1329.ch014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Paresh Kumar Samantaray
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, Karnataka 560012, India
- Department of Materials Engineering, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Giridhar Madras
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Suryasarathi Bose
- Department of Materials Engineering, Indian Institute of Science, Bangalore, Karnataka 560012, India
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Yadav TC, Srivastava AK, Mishra P, Singh D, Raghuwanshi N, Singh NK, Singh AK, Tiwari SK, Prasad R, Pruthi V. Electrospinning: An Efficient Biopolymer-Based Micro- and Nanofibers Fabrication Technique. ACS SYMPOSIUM SERIES 2019. [DOI: 10.1021/bk-2019-1329.ch010] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Tara Chand Yadav
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee - 247667, Uttarakhand, India
| | - Amit Kumar Srivastava
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee - 247667, Uttarakhand, India
| | - Purusottam Mishra
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee - 247667, Uttarakhand, India
| | - Divya Singh
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee - 247667, Uttarakhand, India
| | - Navdeep Raghuwanshi
- Vaccine Formulation & Research Center, Gennova (Emcure) Biopharmaceuticals Limited, Pune - 411057, Maharashtra, India
| | - Nitin Kumar Singh
- Department of Environment Science and Engineering, Marwadi Education Foundations Group of Institutions, Rajkot - 360003, Gujarat, India
| | - Amit Kumar Singh
- Department of Biochemistry, University of Allahabad, Allahabad, 211002 India
| | | | - Ramasare Prasad
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee - 247667, Uttarakhand, India
| | - Vikas Pruthi
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee - 247667, Uttarakhand, India
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