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Duan J, Yuan B, Jia F, Li X, Chen C, Li G. Development of an Efficient and Seamless Genetic Manipulation Method for Xenorhabdus and Its Application for Enhancing the Production of Fabclavines. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:274-283. [PMID: 38109418 DOI: 10.1021/acs.jafc.3c04136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
Xenorhabdus can produce numerous natural products, but their development has been hampered by the lack of a seamless genetic manipulation method. In this study, we compared several lethal genes and determined the sacB gene as the most effective counter-selection marker and then established a dual selection/counter-selection system by integrating neo and sacB genes into one cassette. This provides an efficient and seamless genetic manipulation method for Xenorhabdus. Using this method, DNA fragments ranging from 205 to 47,788 bp in length were seamlessly knocked out or replaced with impressively high positive rates of 80 to 100% in Xenorhabdus budapestensis XBD8. In addition, the method was successfully applied with good efficiency (45-100%) in Xenorhabdus nematophila CB6. To further validate the method, different constitutive promoters were used to replace the native fclC promoter in a batch experiment. The positivity rate remained consistently high, at 46.3%. In comparison to WT XBD8, the recombinant strain MX14 demonstrated a significant increase in the production of fabclavine 7 and fabclavine 8 by 4.97-fold and 3.22-fold, respectively, while the overall production of fabclavines was enhanced by 3.52-fold.
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Affiliation(s)
- Jiaqi Duan
- State Key Laboratory for Biology of Plant Diseases and Insect Pests/Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agri-Product Quality and Safety, Ministry of Agriculture, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Baoming Yuan
- State Key Laboratory for Biology of Plant Diseases and Insect Pests/Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agri-Product Quality and Safety, Ministry of Agriculture, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Fenglian Jia
- State Key Laboratory for Biology of Plant Diseases and Insect Pests/Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agri-Product Quality and Safety, Ministry of Agriculture, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xiaohui Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests/Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agri-Product Quality and Safety, Ministry of Agriculture, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Chang Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests/Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agri-Product Quality and Safety, Ministry of Agriculture, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Beijing Green Agricultural Science and Technology Group Co., Ltd, Beijing 100193, China
| | - Guangyue Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests/Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agri-Product Quality and Safety, Ministry of Agriculture, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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Shikina E, Kovalevsky R, Shirkovskaya A, Toukach P. Prospective bacterial and fungal sources of hyaluronic acid: A review. Comput Struct Biotechnol J 2022; 20:6214-6236. [PMID: 36420162 PMCID: PMC9676211 DOI: 10.1016/j.csbj.2022.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 11/05/2022] [Accepted: 11/05/2022] [Indexed: 11/11/2022] Open
Abstract
The unique biological and rheological properties make hyaluronic acid a sought-after material for medicine and cosmetology. Due to very high purity requirements for hyaluronic acid in medical applications, the profitability of streptococcal fermentation is reduced. Production of hyaluronic acid by recombinant systems is considered a promising alternative. Variations in combinations of expressed genes and fermentation conditions alter the yield and molecular weight of produced hyaluronic acid. This review is devoted to the current state of hyaluronic acid production by recombinant bacterial and fungal organisms.
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Bajaj P, Manjunath K, Varadarajan R. Structural and functional determinants inferred from deep mutational scans. Protein Sci 2022; 31:e4357. [PMID: 35762712 DOI: 10.1002/pro.4357] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 04/04/2022] [Accepted: 05/11/2022] [Indexed: 11/08/2022]
Abstract
Mutations that affect protein binding to a cognate partner primarily occur either at buried residues or at exposed residues directly involved in partner binding. Distinguishing between these two categories based solely on mutational phenotypes is challenging. The bacterial toxin CcdB kills cells by binding to DNA Gyrase. Cell death is prevented by binding to its cognate antitoxin CcdA, at an extended interface that partially overlaps with the GyrA binding site. Using the CcdAB toxin-antitoxin (TA) system as a model, a comprehensive site-saturation mutagenesis library of CcdB was generated in its native operonic context. The mutational sensitivity of each mutant was estimated by evaluating the relative abundance of each mutant in two strains, one resistant and the other sensitive to the toxic activity of the CcdB toxin, through deep sequencing. The ability to bind CcdA was inferred through a RelE reporter gene assay, since the CcdAB complex binds to its own promoter, repressing transcription. By analyzing mutant phenotypes in the CcdB-sensitive, CcdB-resistant, and RelE reporter strains, it was possible to assign residues to buried, CcdA interacting or GyrA interacting sites. A few mutants were individually constructed, expressed, and biophysically characterized to validate molecular mechanisms responsible for the observed phenotypes. Residues inferred to be important for antitoxin binding, are also likely to be important for rejuvenating CcdB from the CcdB-Gyrase complex. Therefore, even in the absence of structural information, when coupled to appropriate genetic screens, such high-throughput strategies can be deployed for predicting structural and functional determinants of proteins.
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Affiliation(s)
- Priyanka Bajaj
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Kavyashree Manjunath
- Centre for Chemical Biology and Therapeutics, Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India
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Baas-Thomas MS, Oehm SB, Ostrov N, Church GM. Characterization of ColE1 Production for Robust tolC Plate Dual-Selection in E. coli. ACS Synth Biol 2022; 11:2009-2014. [PMID: 35666547 PMCID: PMC9208019 DOI: 10.1021/acssynbio.2c00061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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Bacterial selection
is an indispensable tool for E. coli genetic
engineering. Marker genes allow for mutant isolation even
at low editing efficiencies. TolC is an especially
useful E. coli marker: its presence can be selected
for with sodium dodecyl sulfate, while its absence can be selected
for with the bactericidal protein ColE1. However, utilization of this
selection system is greatly limited by the lack of commercially available
ColE1 protein. Here, we provide a simple, plate-based, ColE1 negative-selection
protocol that does not require purification of ColE1. Using agar plates
containing a nonpurified lysate from a ColE1-production strain, we
achieved a stringent negative selection with an escape rate of 10–7. Using this powerful negative-selection assay, we
then performed the scarless deletion of multiple, large genomic loci
(>10 kb), screening only 12 colonies each. We hope this accessible
protocol for ColE1 production will lower the barrier of entry for
any lab that wishes to harness tolC’s dual
selection for genetic engineering.
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Affiliation(s)
| | - Sebastian B Oehm
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Nili Ostrov
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - George M Church
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States.,Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts 02115, United States
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Chen W, Chen R, He L, Wu X. Development and optimization of Lysis gene E as a counter-selection marker with high stringency. Biotechnol J 2022; 17:e2100423. [PMID: 35373931 DOI: 10.1002/biot.202100423] [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: 08/10/2021] [Revised: 03/19/2022] [Accepted: 04/01/2022] [Indexed: 11/09/2022]
Abstract
BACKGROUND Seamless modification of bacterial chromosomes is widely performed in both theoretical and practical research. For this purpose, excellent counter-selection marker genes with high stringency are needed. MAIN METHODS AND MAJOR RESULTS The lysis gene E was first constructed under the control of the PL promoter and the cI857 repressor. At 42°C, it could effectively kill Escherichia coli and seamless modification in this bacterium using E as a counter-selection marker was successfully conducted. It also works in another gram-negative strain, Serratia marcescens, under the control of the Arac/PBAD regulatory system. By combining lysis gene E and kil, the counter-selection frequencies of the PL -kil-sd-E cassette in E. coli reached 4.9 × 10-8 and 3.2 × 10-8 at two test loci, which are very close to frequencies observed with the best counter-selection systems reported, the inducible toxin systems. Under the control of the Arac/PBAD , the counter-selection frequency of PBAD -kil-sd-E in S. marcescens reached the level of 10-7 at four test loci. By expressing the araC gene from plasmid pKDsg-ack, 5- to 17-fold improvements in counter-selection stringency were observed at these loci. A surprisingly low counter-selection frequency of 4.9 × 10-9 was obtained at the marR-1 locus, which reflects the highest stringency for a counter-selection cassette reported thus far. Similarly, at the araB locus of E. coli, the counter-selection frequency of PBAD -kil-sd-E was 3 × 10-9 after introducing plasmid pKDsg-ack. CONCLUSIONS AND IMPLICATIONS We have developed and optimized a new universal counter-selection marker based on lysis gene E. The best counter-selection stringency of this new marker exceeds the inducible toxin system several fold. Our work can also provide inspiration for improving counter-selection stringency based on existing markers. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Wei Chen
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, 510006, China.,Guangdong Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Ruyi Chen
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Ling He
- Guangdong Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Xiaotong Wu
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, 510006, China
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Rapid Genome Modification in Serratia marcescens Through Red Homologous Recombination. Appl Biochem Biotechnol 2021; 193:2916-2931. [PMID: 33970425 DOI: 10.1007/s12010-021-03576-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 05/04/2021] [Indexed: 10/21/2022]
Abstract
Despite the great potential of Serratia marcescens in industrial applications, lack of powerful genetic modification tools limits understanding of the regulatory networks of the useful metabolites and therefore restricts their mass production. To meet the urgent demand, we established a genome-editing strategy for S. marcescens based on Red recombineering in this study. Without host modification in advance, nucA and pigA were substituted by PCR-amplified resistance genes. No long homologous arms were required at the two sides of resistance genes. Using this procedure, the fragment at the S. marcescens as large as 20 kb was easily deleted. Then we constructed a counter-selection gene kil constructed under the control of inducible PBAD operon, which demonstrates obvious lethality to S. marcescens. Subsequently, GmR-kil double selection cassette was inserted into the CDS of pigA gene. Using single-stranded DNA-mediated recombination, this insertion mutation was efficiently repaired through kil counter-selection. A powerful genetic modification platform based on Red recombineering system was successfully established for S. marcescens. Multiple types of modification and multiple recombination strategies can all be performed easily in this species. We hope this study will be useful for the theoretical research and the research of metabolic engineering in S. marcescens.
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Li Q, Sun B, Chen J, Zhang Y, Jiang Y, Yang S. A modified pCas/pTargetF system for CRISPR-Cas9-assisted genome editing in Escherichia coli. Acta Biochim Biophys Sin (Shanghai) 2021; 53:620-627. [PMID: 33764372 DOI: 10.1093/abbs/gmab036] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Indexed: 12/14/2022] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)-associated nuclease 9 (Cas9)-based genome editing tool pCas/pTargetF system that we established previously has been widely used in Escherichia coli MG1655. However, this system failed to manipulate the genome of E. coli BL21(DE3), owing to the potential higher leaky transcription of the gRNA-pMB1 specific to pTargetF in this strain. In this study, we modified the pCas/pTargetF system by replacing the promoter of gRNA-pMB1 with a tightly regulated promoter PrhaB, changing the replicon of pCas to a nontemperature-sensitive replicon, adding the sacB gene into pCas, and replacing the original N20-specific sequence of pTargetF with ccdB gene. We call this updated system as pEcCas/pEcgRNA. We found that gRNA-pMB1 indeed showed a slightly higher leaky expression in the pCas/pTargetF system compared with pEcCas/pEcgRNA. We also confirmed that genome editing can successfully be performed in BL21(DE3) by pEcCas/pEcgRNA with high efficiency. The application of pEcCas/pEcgRNA was then expanded to the E. coli B strain BL21 StarTM (DE3), K-12 strains MG1655, DH5α, CGMCC3705, Nissle1917, W strain ATCC9637, and also another species of Enterobacteriaceae, Tatumella citrea DSM13699, without any specific modifications. Finally, the plasmid curing process was optimized to shorten the time from $\sim$60 h to $\sim$32 h. The entire protocol (including plasmid construction, editing, electroporation and mutant verification, and plasmid elimination) took only $\sim$5.5 days per round in the pEcCas/pEcgRNA system, whereas it took $\sim$7.5 days in the pCas/pTargetF system. This study established a faster-acting genome editing tool that can be used in a wider range of E. coli strains and will also be useful for other Enterobacteriaceae species.
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Affiliation(s)
- Qi Li
- College of Life Sciences, Sichuan Normal University, Chengdu 610101, China
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Bingbing Sun
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jun Chen
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yiwen Zhang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yu Jiang
- Huzhou Center of Industrial Biotechnology, Shanghai Institutes for Biological Sciences, Huzhou 313000, China
| | - Sheng Yang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- Huzhou Center of Industrial Biotechnology, Shanghai Institutes for Biological Sciences, Huzhou 313000, China
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Chen W, Chen R, Wang H, Li Y, Zhang Y, Li S. Tuning chromosomal gene expression in Escherichia coli by combining single-stranded oligonucleotides mediated recombination and kil counter selection system. J Biotechnol 2019; 307:63-68. [PMID: 31678458 DOI: 10.1016/j.jbiotec.2019.10.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 10/03/2019] [Accepted: 10/21/2019] [Indexed: 10/25/2022]
Abstract
Extensively modulating gene expression to achieve optimal flux is a critical step in metabolic engineering. Gene expression is usually modulated at the transcriptional level by controlling the strength of a promoter. However, this type of modulation is often hampered by its inability to fully sample the complete continuum of transcriptional control. In Escherichia coli, this limitation can be solved by constructing promoters with a wide range of strengths. In this study, a highly efficient method was developed to modulate a particular chromosomal gene of E. coli at a wide range of expression levels. This was achieved by combining highly efficient single-stranded oligonucleotide-mediated recombination and a stringent counter selection system kil. Using this strategy, a chromosomal library, with a range from 0.3% to 388% relative to the wild lac promoter, was easily obtained. The strength of our chromosomal promoter library was approximately 5-60 times wider in range than those of libraries reported before.
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Affiliation(s)
- Wei Chen
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou 510006, China.
| | - Ruyi Chen
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Hui Wang
- School of Biological Medicine, Beijing City University, Beijing, 10084, China
| | - Yujuan Li
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Yunyi Zhang
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Shanhu Li
- Beijing Institute of Biotechnology, Beijing 100850, China.
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