1
|
Fristot E, Cambray G, Bonnet J. LactoSpanks: A Collection of IPTG Inducible Promoters for the Commensal Lactic Acid Bacteria Lactobacillus gasseri. ACS Synth Biol 2024; 13:951-957. [PMID: 38335132 DOI: 10.1021/acssynbio.3c00438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2024]
Abstract
Lactic acid bacteria (LAB) are important for many biotechnological applications such as bioproduction and engineered probiotics for therapy. Inducible promoters are key gene expression control elements, yet those available in LAB are mainly based on bacteriocin systems and have many drawbacks, including large gene clusters, costly inducer peptides, and little portability to in vivo settings. Using Lactobacillus gasseri, a model commensal bacteria from the human gut, we report the engineering of synthetic LactoSpanks promoters (Pls), a collection of variable strength inducible promoters controlled by the LacI repressor from E. coli and induced by isopropyl β-d-1-thiogalactopyranoside (IPTG). We first show that the Phyper-spank promoter from Bacillus subtilis is functional in L. gasseri, albeit with substantial leakage. We then construct and screen a semirational library of Phyper-spank variants to select a set of four IPTG-inducible promoters that span a range of expression levels and exhibit reduced leakages and operational dynamic ranges (from ca. 9 to 28 fold-change). With their low genetic footprint and simplicity of use, LactoSpanks will support many applications in L. gasseri, and potentially other lactic acid and Gram-positive bacteria.
Collapse
Affiliation(s)
- Elsa Fristot
- Centre de Biologie Structurale (CBS), University of Montpellier, INSERM U1054, CNRS UMR 5048, 34090 Montpellier, France
| | - Guillaume Cambray
- Centre de Biologie Structurale (CBS), University of Montpellier, INSERM U1054, CNRS UMR 5048, 34090 Montpellier, France
- Diversité des Génomes et Interactions Microorganismes Insectes (DGIMI), University of Montpellier, INRAE UMR1333, 34090 Montpellier, France
| | - Jerome Bonnet
- Centre de Biologie Structurale (CBS), University of Montpellier, INSERM U1054, CNRS UMR 5048, 34090 Montpellier, France
| |
Collapse
|
2
|
Xu JM, Wu ZS, Zhao KJ, Xi ZJ, Wang LY, Cheng F, Xue YP, Zheng YG. IPTG-induced high protein expression for whole-cell biosynthesis of L-phosphinothricin. Biotechnol J 2023; 18:e2300027. [PMID: 37265188 DOI: 10.1002/biot.202300027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 04/20/2023] [Accepted: 05/19/2023] [Indexed: 06/03/2023]
Abstract
BACKGROUND Biocatalytic production of L-phosphinothricin (L-PPT) is currently the most promising method. In this work, we use an Escherichia coli strain coexpressing of D-amino acid oxidase and catalase (E. coli DAAO-CAT) to oxidation biocatalytic D-PPT to PPO, then use the second E. coli strain coexpressing glutamate dehydrogenase and formate dehydrogenase (E. coli GluDH-FDH) to reduce biocatalytic PPO to L-PPT. MAIN METHODS AND MAJOR RESULTS We compared the effects of different concentrations of IPTG or lactose on protein expression and enzyme activity in 5 L fermenter. The best induction conditions for E. coli DAAO-CAT were 0.05 mM IPTG, induction for 18 h at 28°C. The specific enzyme activities of DAAO and CAT were 153.20 U g-1 and 896.23 U g-1 , respectively. The optimal induction conditions for E. coli GluDH-FDH were 0.2 mM IPTG, induction for 19 h at 28°C. The specific enzyme activities of GluDH and FDH were 41.72 U g-1 and 109.70 U g-1 , respectively. The 200 mM D-PPT was biocatalyzed by E. coli DAAO-CAT for 4 h with space-time yield of 9.0 g·L-1 ·h-1 and conversion rate of over 99.0%. Then 220 mM PPO was converted to L-PPT by E. coli GluDH-FDH for 3 h with space-time yield of 14.5 g·L-1 ·h-1 and conversion rate of over 99.0%. To our knowledge, this is the most efficient biocatalytic reaction for L-PPT production. CONCLUSIONS AND IMPLICATIONS We found that IPTG has advantages compared with lactose in the enzyme activity and biomass of E. coli DAAO-CAT and E. coli GluDH-FDH, and IPTG is more environmentally friendly. Our data implicated that IPTG can replace lactose in terms of economic feasibility and effectiveness for scaled-up industrial fermentations.
Collapse
Affiliation(s)
- Jian-Miao Xu
- Institute of Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, P. R. China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Zhou-Sheng Wu
- Institute of Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, P. R. China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Ke-Ji Zhao
- Institute of Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, P. R. China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Zhi-Jie Xi
- Institute of Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, P. R. China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Liu-Yu Wang
- Institute of Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, P. R. China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Feng Cheng
- Institute of Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, P. R. China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Ya-Ping Xue
- Institute of Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, P. R. China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Yu-Guo Zheng
- Institute of Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, P. R. China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China
| |
Collapse
|
3
|
Simas RG, Pessoa Junior A, Long PF. Mechanistic aspects of IPTG (isopropylthio-β-galactoside) transport across the cytoplasmic membrane of Escherichia coli-a rate limiting step in the induction of recombinant protein expression. J Ind Microbiol Biotechnol 2023; 50:kuad034. [PMID: 37849239 PMCID: PMC10639102 DOI: 10.1093/jimb/kuad034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 10/16/2023] [Indexed: 10/19/2023]
Abstract
Coupling transcription of a cloned gene to the lac operon with induction by isopropylthio-β-galactoside (IPTG) has been a favoured approach for recombinant protein expression using Escherichia coli as a heterologous host for more than six decades. Despite a wealth of experimental data gleaned over this period, a quantitative relationship between extracellular IPTG concentration and consequent levels of recombinant protein expression remains surprisingly elusive across a broad spectrum of experimental conditions. This is because gene expression under lac operon regulation is tightly correlated with intracellular IPTG concentration due to allosteric regulation of the lac repressor protein (lacY). An in-silico mathematical model established that uptake of IPTG across the cytoplasmic membrane of E. coli by simple diffusion was negligible. Conversely, lacY mediated active transport was a rapid process, taking only some seconds for internal and external IPTG concentrations to equalize. Optimizing kcat and KM parameters by targeted mutation of the galactoside binding site in lacY could be a future strategy to improve the performance of recombinant protein expression. For example, if kcat were reduced whilst KM was increased, active transport of IPTG across the cytoplasmic membrane would be reduced, thereby lessening the metabolic burden on the cell and expediating accumulation of recombinant protein. The computational model described herein is made freely available and is amenable to optimize recombinant protein expression in other heterologous hosts. ONE-SENTENCE SUMMARY A computational model made freely available to optimize recombinant protein expression in Escherichia coli other heterologous hosts.
Collapse
Affiliation(s)
- Rodrigo G Simas
- Faculty of Life Sciences & Medicine, King's College London, 150 Stamford Street, London SE1 9NH, UK
- Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, Av. Prof. Lineu Prestes, 580, B16, 05508-000 São Paulo, SP, Brazil
| | - Adalberto Pessoa Junior
- Faculty of Life Sciences & Medicine, King's College London, 150 Stamford Street, London SE1 9NH, UK
- Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, Av. Prof. Lineu Prestes, 580, B16, 05508-000 São Paulo, SP, Brazil
| | - Paul F Long
- Faculty of Life Sciences & Medicine, King's College London, 150 Stamford Street, London SE1 9NH, UK
- Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, Av. Prof. Lineu Prestes, 580, B16, 05508-000 São Paulo, SP, Brazil
| |
Collapse
|
4
|
Abstract
Many Escherichia coli expression vectors make use of the lac operon. In general, the lac operator (lacO) is located downstream from the promoter of the target gene, so that binding of the lac repressor blocks transcription initiation until lactose or the isopropyl-β-d-thiogalactopyranoside (IPTG) analog is added. The protocol given here is intended for use with IPTG-inducible vectors. l-Arabinose-inducible systems derived from the ara operon offer an alternative to expression systems based on the lac operon; guidance for their use is also provided.
Collapse
|
5
|
Yu TC, Liu WL, Brinck MS, Davis JE, Shek J, Bower G, Einav T, Insigne KD, Phillips R, Kosuri S, Urtecho G. Multiplexed characterization of rationally designed promoter architectures deconstructs combinatorial logic for IPTG-inducible systems. Nat Commun 2021; 12:325. [PMID: 33436562 PMCID: PMC7804116 DOI: 10.1038/s41467-020-20094-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 11/04/2020] [Indexed: 12/21/2022] Open
Abstract
A crucial step towards engineering biological systems is the ability to precisely tune the genetic response to environmental stimuli. In the case of Escherichia coli inducible promoters, our incomplete understanding of the relationship between sequence composition and gene expression hinders our ability to predictably control transcriptional responses. Here, we profile the expression dynamics of 8269 rationally designed, IPTG-inducible promoters that collectively explore the individual and combinatorial effects of RNA polymerase and LacI repressor binding site strengths. We then fit a statistical mechanics model to measured expression that accurately models gene expression and reveals properties of theoretically optimal inducible promoters. Furthermore, we characterize three alternative promoter architectures and show that repositioning binding sites within promoters influences the types of combinatorial effects observed between promoter elements. In total, this approach enables us to deconstruct relationships between inducible promoter elements and discover practical insights for engineering inducible promoters with desirable characteristics.
Collapse
Affiliation(s)
- Timothy C Yu
- Department of Bioengineering, University of California, Los Angeles, CA, 90095, USA
| | - Winnie L Liu
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA, 90095, USA
| | - Marcia S Brinck
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA, 90095, USA
| | - Jessica E Davis
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
| | - Jeremy Shek
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
| | - Grace Bower
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA, 90095, USA
| | - Tal Einav
- Department of Physics, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Kimberly D Insigne
- Bioinformatics Interdepartmental Graduate Program, University of California, Los Angeles, CA, 90095, USA
| | - Rob Phillips
- Department of Physics, California Institute of Technology, Pasadena, CA, 91125, USA
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
- Department of Applied Physics, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Sriram Kosuri
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA.
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA, 90095, USA.
- Institute for Quantitative and Computational Biosciences (QCB), University of California, Los Angeles, Los Angeles, CA, 90095, USA.
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA, 90095, USA.
- Molecular Biology Interdepartmental Doctoral Program, University of California, Los Angeles, CA, 90095, USA.
| | - Guillaume Urtecho
- Molecular Biology Interdepartmental Doctoral Program, University of California, Los Angeles, CA, 90095, USA.
| |
Collapse
|
6
|
Galluccio M, Indiveri C. Heterologous Overexpression of Human FAD Synthase Isoforms 1 and 2. Methods Mol Biol 2021; 2280:55-67. [PMID: 33751429 DOI: 10.1007/978-1-0716-1286-6_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The study of human FAD synthase enzymes requires a recombinant strategy to produce large amount of purified proteins in a soluble form. E. coli was exploited to this aim. To achieve the production of FAD synthase in a large scale, E. coli strains, plasmids (promoter, tags), growth temperature, inducer concentration, medium composition, and osmotic pressure were optimized. To date there is no universal protocol for protein expression, but for each protein a specific combination of "expression parameters" can be selected in order to maximize the results. An experimental protocol for the expression of two isoforms of the human FAD synthase was set up. The final procedures are based on the use of E. coli Rosetta(DE3) strain. Two different plasmids were used to obtain optimal amount of the two protein isoforms. In both cases, following the addition of the IPTG inducer, the growth temperature was lowered to increase the solubility of the recombinant protein. The detailed procedures for FAD synthase isoform 1 and isoform 2 overproduction are described in this protocol.
Collapse
Affiliation(s)
- Michele Galluccio
- Department DiBEST (Biologia, Ecologia, Scienze della Terra) Unit of Biochemistry and Molecular Biotechnology, University of Calabria, Arcavacata di Rende, Italy
| | - Cesare Indiveri
- Department DiBEST (Biologia, Ecologia, Scienze della Terra) Unit of Biochemistry and Molecular Biotechnology, University of Calabria, Arcavacata di Rende, Italy.
| |
Collapse
|
7
|
Barbier I, Perez‐Carrasco R, Schaerli Y. Controlling spatiotemporal pattern formation in a concentration gradient with a synthetic toggle switch. Mol Syst Biol 2020; 16:e9361. [PMID: 32529808 PMCID: PMC7290156 DOI: 10.15252/msb.20199361] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 04/29/2020] [Accepted: 05/08/2020] [Indexed: 11/20/2022] Open
Abstract
The formation of spatiotemporal patterns of gene expression is frequently guided by gradients of diffusible signaling molecules. The toggle switch subnetwork, composed of two cross-repressing transcription factors, is a common component of gene regulatory networks in charge of patterning, converting the continuous information provided by the gradient into discrete abutting stripes of gene expression. We present a synthetic biology framework to understand and characterize the spatiotemporal patterning properties of the toggle switch. To this end, we built a synthetic toggle switch controllable by diffusible molecules in Escherichia coli. We analyzed the patterning capabilities of the circuit by combining quantitative measurements with a mathematical reconstruction of the underlying dynamical system. The toggle switch can produce robust patterns with sharp boundaries, governed by bistability and hysteresis. We further demonstrate how the hysteresis, position, timing, and precision of the boundary can be controlled, highlighting the dynamical flexibility of the circuit.
Collapse
Affiliation(s)
- Içvara Barbier
- Department of Fundamental MicrobiologyUniversity of LausanneLausanneSwitzerland
| | - Rubén Perez‐Carrasco
- Department of Life SciencesImperial College LondonSouth Kensington CampusLondonUK
- Department of MathematicsUniversity College LondonLondonUK
| | - Yolanda Schaerli
- Department of Fundamental MicrobiologyUniversity of LausanneLausanneSwitzerland
| |
Collapse
|
8
|
Tran TT, Charles TC. Lactic acid containing polymers produced in engineered Sinorhizobium meliloti and Pseudomonas putida. PLoS One 2020; 15:e0218302. [PMID: 32191710 PMCID: PMC7082056 DOI: 10.1371/journal.pone.0218302] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 02/18/2020] [Indexed: 01/17/2023] Open
Abstract
This study demonstrates that novel polymer production can be achieved by introducing pTAM, a broad-host-range plasmid expressing codon-optimized genes encoding Clostridium propionicum propionate CoA transferase (PctCp, Pct532) and a modified Pseudomonas sp. MBEL 6–19 polyhydroxyalkanoate (PHA) synthase 1 (PhaC1Ps6-19, PhaC1400), into phaC mutant strains of the native polymer producers Sinorhizobium meliloti and Pseudomonas putida. Both phenotypic analysis and gas chromatography analysis indicated the synthesis and accumulation of biopolymers in S. meliloti and P. putida strains. Expression in S. meliloti resulted in the production of PLA homopolymer up to 3.2% dried cell weight (DCW). The quaterpolymer P (3HB-co-LA-co-3HHx-co-3HO) was produced by expression in P. putida. The P. putida phaC mutant strain produced this type of polymer the most efficiently with polymer content of 42% DCW when cultured in defined media with the addition of sodium octanoate. This is the first report, to our knowledge, of the production of a range of different biopolymers using the same plasmid-based system in different backgrounds. In addition, it is the first time that the novel polymer (P(3HB-co-LA-co-3HHx-co-3HO)), has been reported being produced in bacteria.
Collapse
Affiliation(s)
- Tam T. Tran
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Trevor C. Charles
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
- * E-mail:
| |
Collapse
|
9
|
Knoot CJ, Biswas S, Pakrasi HB. Tunable Repression of Key Photosynthetic Processes Using Cas12a CRISPR Interference in the Fast-Growing Cyanobacterium Synechococcus sp. UTEX 2973. ACS Synth Biol 2020; 9:132-143. [PMID: 31829621 DOI: 10.1021/acssynbio.9b00417] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Cyanobacteria are photoautotrophic prokaryotes that serve as key model organisms to study basic photosynthetic processes and are potential carbon-negative production chassis for commodity and high-value chemicals. The development of new synthetic biology tools and improvement of current ones is a requisite for furthering these organisms as models and production vehicles. CRISPR interference (CRISPRi) allows for targeted gene repression using a DNase-dead Cas nuclease ("dCas"). Here, we describe a titratable dCas12a (dCpf1) CRISPRi system and apply it to repress key photosynthetic processes in the fast-growing cyanobacterium Synechococcus sp. UTEX 2973 (S2973). The system relies on a lac repressor system that retains tight regulation in the absence of inducer (0-10% repression) while maintaining the capability for >90% repression of high-abundance gene targets. We determined that dCas12a is less toxic than dCas9. We tested the efficacy of the system toward eYFP and three native targets in S2973: the phycobilisome antenna, glycogen synthesis, and photosystem I (PSI), an essential part of the photosynthetic electron transport chain in oxygenic photoautotrophs. PSI was knocked down indirectly by repressing the protein factor BtpA involved in stabilizing core PSI proteins. We could reduce cellular PSI titer by 87% under photoautotrophic conditions, and we characterized these cells to gain insights into the response of the strain to the low PSI content. The ability to tightly regulate and time the (de)repression of essential genes in trans will allow for the study of photosynthetic processes that are not accessible using knockout mutants.
Collapse
Affiliation(s)
- Cory J Knoot
- Department of Biology , Washington University , St. Louis , Missouri United States
| | - Sandeep Biswas
- Department of Biology , Washington University , St. Louis , Missouri United States
| | - Himadri B Pakrasi
- Department of Biology , Washington University , St. Louis , Missouri United States
| |
Collapse
|
10
|
Le VD, Phan TTP, Nguyen TM, Brunsveld L, Schumann W, Nguyen HD. Using the IPTG-Inducible Pgrac212 Promoter for Overexpression of Human Rhinovirus 3C Protease Fusions in the Cytoplasm of Bacillus subtilis Cells. Curr Microbiol 2019; 76:1477-1486. [PMID: 31612259 DOI: 10.1007/s00284-019-01783-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 09/27/2019] [Indexed: 01/19/2023]
Abstract
Expression and secretion of recombinant proteins in the endotoxin-free bacterium, Bacillus subtilis, has been thoroughly studied, but overexpression in the cytoplasm has been limited to only a few proteins. Here, we used the robust IPTG-inducible promoter, Pgrac212, to overexpress human rhinovirus 3C protease (HRV3C) in the cytoplasm of B. subtilis cells. A novel solubility tag, the N-terminal domain of the lysS gene of B. subtilis coding for a lysyl-tRNA synthetase was placed at the N terminus with a cleavage site for the endoprotease HRV3C, followed by His-HRV3C or His-GST-HRV3C. The recombinant protease was purified by using a Ni-NTA column. In this study, the His-HRV3C and His-GST-HRV3C proteases were overexpressed in the cytoplasm of B. subtilis at 11% and 16% of the total cellular proteins, respectively. The specific protease activities were 8065 U/mg for His-HRV3C and 3623 U/mg for His-GST-HRV3C. The purified enzymes were used to cleave two different substrates followed by purification of the two different protein targets, the green fluorescent protein and the beta-galactosidase. In conclusion, the combination of an inducible promoter Pgrac212 and a solubility tag allowed the overexpression of the HRV3C protease in the cytoplasm of B. subtilis. The resulting fusion protein was purified using a nickel column and was active in cleaving target proteins to remove the fusion tags. This study offers an effective method for producing recombinant proteins in the cytoplasm of endotoxin-free bacteria.
Collapse
Affiliation(s)
- Vuong Duong Le
- Center for Bioscience and Biotechnology, University of Science-VNUHCM, 227 Nguyen Van Cu Dist. 5, Hochiminh, Vietnam
- Ho Chi Minh City University of Technology (HUTECH), 475A Dien Bien Phu Str., Binh Thanh Dist., Hochiminh, Vietnam
- Department of Microbiology, University of Science-VNUHCM, 227 Nguyen Van Cu Dist. 5, Hochiminh, Vietnam
| | - Trang Thi Phuong Phan
- Center for Bioscience and Biotechnology, University of Science-VNUHCM, 227 Nguyen Van Cu Dist. 5, Hochiminh, Vietnam
- Laboratory of Molecular Biotechnology, University of Science-VNUHCM, 227 Nguyen Van Cu Dist. 5, Hochiminh, Vietnam
| | - Tri Minh Nguyen
- Center for Bioscience and Biotechnology, University of Science-VNUHCM, 227 Nguyen Van Cu Dist. 5, Hochiminh, Vietnam
- Ho Chi Minh City University of Technology (HUTECH), 475A Dien Bien Phu Str., Binh Thanh Dist., Hochiminh, Vietnam
| | - Luc Brunsveld
- Laboratory of Chemical Biology & Institute of Complex Molecular Systems, Department of Biomedical Engineering, Technische Universiteit Eindhoven, Eindhoven, Netherlands
| | - Wolfgang Schumann
- Center for Bioscience and Biotechnology, University of Science-VNUHCM, 227 Nguyen Van Cu Dist. 5, Hochiminh, Vietnam
- Institute of Genetics, University of Bayreuth, 95440, Bayreuth, Germany
| | - Hoang Duc Nguyen
- Center for Bioscience and Biotechnology, University of Science-VNUHCM, 227 Nguyen Van Cu Dist. 5, Hochiminh, Vietnam.
- Department of Microbiology, University of Science-VNUHCM, 227 Nguyen Van Cu Dist. 5, Hochiminh, Vietnam.
| |
Collapse
|
11
|
Srinivas S, Hu Z, Cronan JE. Escherichia coli vectors having stringently repressible replication origins allow a streamlining of Crispr/Cas9 gene editing. Plasmid 2019; 103:53-62. [PMID: 31047915 PMCID: PMC7260698 DOI: 10.1016/j.plasmid.2019.04.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 04/15/2019] [Accepted: 04/26/2019] [Indexed: 02/05/2023]
Abstract
Readily curable plasmids facilitate the construction of plasmid-free bacterial strains after the plasmid encoded genes are no longer needed. The most popular of these plasmids features a temperature-sensitive (Ts) pSC101 origin of replication which can readily revert during usage and cannot be used to construct Ts mutations in essential genes. Plasmid pAM34 which contains an IPTG-dependent origin of replication largely overcomes this issue but is limited by carrying the most commonly utilized antibiotic selection and replication origin. This study describes the construction of an expanded series of plasmid vectors having replication origins of p15a, RSF1030 or RSF1031 that like pAM34 have IPTG-dependent replication. Surprisingly, these plasmids can be cured in fewer generations than pAM34. Derivatives of pAM34 with alternative antibiotic selection markers were also constructed. The utility of these vectors is demonstrated in the construction of a CRISPR-Cas9 system consisting of an IPTG-dependent Cas9 plasmid and a curable guide RNA plasmid having a streptomycin counterselection marker. This system was successfully demonstrated by construction of point mutations, deletions and insertions in the E. coli genome with a very high efficiency and in a shorter timescale than extant methods. The plasmids themselves were readily cured either together or singly from the resultant strains with minimal effort.
Collapse
Affiliation(s)
- Swaminath Srinivas
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States of America
| | - Zhe Hu
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States of America
| | - John E Cronan
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States of America; Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States of America.
| |
Collapse
|
12
|
Gauttam R, Seibold GM, Mueller P, Weil T, Weiß T, Handrick R, Eikmanns BJ. A simple dual-inducible CRISPR interference system for multiple gene targeting in Corynebacterium glutamicum. Plasmid 2019; 103:25-35. [PMID: 30954454 DOI: 10.1016/j.plasmid.2019.04.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 04/03/2019] [Accepted: 04/03/2019] [Indexed: 10/27/2022]
Abstract
The development of CRISPR interference (CRISPRi) technology has dramatically increased the pace and the precision of target identification during platform strain development. In order to develop a simple, reliable, and dual-inducible CRISPRi system for the industrially relevant Corynebacterium glutamicum, we combined two different inducible repressor systems in a single plasmid to separately regulate the expression of dCas9 (anhydro-tetracycline-inducible) and a given single guide RNA (IPTG-inducible). The functionality of the resulting vector was demonstrated by targeting the l-arginine biosynthesis pathway in C. glutamicum. By co-expressing dCas9 and a specific single guide RNA targeting the 5'-region of the argininosuccinate lyase gene argH, the specific activity of the target enzyme was down-regulated and in a l-arginine production strain, l-arginine formation was shifted towards citrulline formation. The system was also employed for down-regulation of multiple genes by concatenating sgRNA sequences encoded on one plasmid. Simultaneous down-regulated expression of both argH and the phosphoglucose isomerase gene pgi proved the potential of the system for multiplex targeting. The system can be a promising tool for further pathway engineering in C. glutamicum. Cumulative effects on targeted genes can be rapidly evaluated avoiding tedious and time-consuming traditional gene knockout approaches.
Collapse
Affiliation(s)
- Rahul Gauttam
- Institute of Microbiology and Biotechnology, University of Ulm, Ulm, Germany
| | - Gerd M Seibold
- Institute of Microbiology and Biotechnology, University of Ulm, Ulm, Germany
| | - Phillipp Mueller
- Institute of Applied Biotechnology, Biberach University of Applied Sciences, Biberach, Germany
| | - Tatjana Weil
- Institute of Microbiology and Biotechnology, University of Ulm, Ulm, Germany
| | - Tamara Weiß
- Institute of Microbiology and Biotechnology, University of Ulm, Ulm, Germany
| | - René Handrick
- Institute of Applied Biotechnology, Biberach University of Applied Sciences, Biberach, Germany
| | - Bernhard J Eikmanns
- Institute of Microbiology and Biotechnology, University of Ulm, Ulm, Germany.
| |
Collapse
|
13
|
Abstract
Hypoxia, a condition of reduced oxygen, occurs in a wide variety of biological contexts, including solid tumors and bacterial biofilms, which are relevant to human health. Consequently, the development of chemical tools to study hypoxia is vital. Here we report a hypoxia-activated, small-molecule-mediated gene expression system using a bioreductive prodrug of the inducer isopropyl 1-thio-β-d-galactopyranoside. As a proof-of-concept we have placed the production of a green fluorescent protein under the control of hypoxia. Our system has the potential to be extended to regulate the production of any given protein of choice.
Collapse
Affiliation(s)
- Sarah L Collins
- Department of Chemistry, Chemistry Research Laboratory , University of Oxford , Mansfield Road , Oxford OX1 3TA , U.K
- Cancer Research U.K./MRC Oxford Institute for Radiation Oncology, Department of Oncology , University of Oxford , Old Road Campus Research Building , Oxford OX3 7DQ , U.K
| | - Jaideep Saha
- Department of Chemistry, Chemistry Research Laboratory , University of Oxford , Mansfield Road , Oxford OX1 3TA , U.K
| | - Laure C Bouchez
- Chemical Biology and Therapeutics , Novartis Institutes for BioMedical Research , Fabrikstrasse 22 , 4054 Basel , Switzerland
| | - Ester M Hammond
- Cancer Research U.K./MRC Oxford Institute for Radiation Oncology, Department of Oncology , University of Oxford , Old Road Campus Research Building , Oxford OX3 7DQ , U.K
| | - Stuart J Conway
- Department of Chemistry, Chemistry Research Laboratory , University of Oxford , Mansfield Road , Oxford OX1 3TA , U.K
| |
Collapse
|
14
|
Zeng Y, Jones AM, Thomas EE, Nassif B, Silberg JJ, Segatori L. A Split Transcriptional Repressor That Links Protein Solubility to an Orthogonal Genetic Circuit. ACS Synth Biol 2018; 7:2126-2138. [PMID: 30089365 PMCID: PMC6858789 DOI: 10.1021/acssynbio.8b00129] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Monitoring the aggregation of proteins within the cellular environment is key to investigating the molecular mechanisms underlying the formation of off-pathway protein assemblies associated with the development of disease and testing therapeutic strategies to prevent the accumulation of non-native conformations. It remains challenging, however, to couple protein aggregation events underlying the cellular pathogenesis of a disease to genetic circuits and monitor their progression in a quantitative fashion using synthetic biology tools. To link the aggregation propensity of a target protein to the expression of an easily detectable reporter, we investigated the use of a transcriptional AND gate system based on complementation of a split transcription factor. We first identified two-fragment tetracycline repressor (TetR) variants that can be regulated via ligand-dependent induction and demonstrated that split TetR variants can function as transcriptional AND gates in both bacteria and mammalian cells. We then adapted split TetR for use as an aggregation sensor. Protein aggregation was detected by monitoring complementation between a larger TetR fragment that serves as a "detector" and a smaller TetR fragment expressed as a fusion to an aggregation-prone protein that serves as a "sensor" of the target protein aggregation status. This split TetR represents a novel genetic component that can be used for a wide range of applications in bacterial as well as mammalian synthetic biology and a much needed cell-based sensor for monitoring a protein's conformational status in complex cellular environments.
Collapse
Affiliation(s)
- Yimeng Zeng
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, USA
| | - Alicia M. Jones
- Department of Biosciences, Rice University, Houston, Texas 77005, USA
| | - Emily E. Thomas
- Department of Biosciences, Rice University, Houston, Texas 77005, USA
| | - Barbara Nassif
- Department of Biosciences, Rice University, Houston, Texas 77005, USA
| | - Jonathan J. Silberg
- Department of Biosciences, Rice University, Houston, Texas 77005, USA
- Department of Bioengineering, Rice University, Houston, Texas 77005, USA
| | - Laura Segatori
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, USA
- Department of Biosciences, Rice University, Houston, Texas 77005, USA
- Department of Bioengineering, Rice University, Houston, Texas 77005, USA
| |
Collapse
|
15
|
Johnston C, Mortier-Barriere I, Khemici V, Polard P. Fine-tuning cellular levels of DprA ensures transformant fitness in the human pathogen Streptococcus pneumoniae. Mol Microbiol 2018; 109:663-675. [PMID: 29995987 DOI: 10.1111/mmi.14068] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/26/2018] [Indexed: 01/12/2023]
Abstract
Natural genetic transformation is a widespread mechanism of horizontal gene transfer. It involves the internalization of exogenous DNA as single strands and chromosomal integration via homologous recombination, promoting acquisition of new genetic traits. Transformation occurs during a distinct physiological state called competence. In Streptococcus pneumoniae, competence is controlled by ComDE, a two-component system induced by an exported peptide pheromone. DprA is universal among transformable species, strongly induced during pneumococcal competence, and crucial for pneumococcal transformation. Pneumococcal DprA plays three crucial roles in transformation and competence. Firstly, DprA protects internalized DNA from degradation. Secondly, DprA loads the homologous recombinase RecA onto transforming DNA to promote transformation. Finally, DprA interacts with the response regulator ComE to shut-off competence. Here, we explored the effect of altering the cellular levels of DprA on these three roles. High cellular levels of DprA were not required for the primary role of DprA as a transformation-dedicated recombinase loader or for protection of transforming DNA. In contrast, full expression of dprA was required for optimal competence shut-off and transformant fitness. High cellular levels of DprA thus ensure the fitness of pneumococcal transformants by mediating competence shut-off. This promotes survival and propagation of transformants, maximizing pneumococcal adaptive potential.
Collapse
Affiliation(s)
- Calum Johnston
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), UMR5100, Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique (CNRS), Toulouse, France
- Université de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Isabelle Mortier-Barriere
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), UMR5100, Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique (CNRS), Toulouse, France
- Université de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Vanessa Khemici
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), UMR5100, Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique (CNRS), Toulouse, France
- Université de Toulouse, Université Paul Sabatier, Toulouse, France
- Department of Microbiology and Molecular Medicine, CMU, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Patrice Polard
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), UMR5100, Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique (CNRS), Toulouse, France
- Université de Toulouse, Université Paul Sabatier, Toulouse, France
| |
Collapse
|
16
|
Abstract
The origin of biological morphology and form is one of the deepest problems in science, underlying our understanding of development and the functioning of living systems. In 1952, Alan Turing showed that chemical morphogenesis could arise from a linear instability of a spatially uniform state, giving rise to periodic pattern formation in reaction-diffusion systems but only those with a rapidly diffusing inhibitor and a slowly diffusing activator. These conditions are disappointingly hard to achieve in nature, and the role of Turing instabilities in biological pattern formation has been called into question. Recently, the theory was extended to include noisy activator-inhibitor birth and death processes. Surprisingly, this stochastic Turing theory predicts the existence of patterns over a wide range of parameters, in particular with no severe requirement on the ratio of activator-inhibitor diffusion coefficients. To explore whether this mechanism is viable in practice, we have genetically engineered a synthetic bacterial population in which the signaling molecules form a stochastic activator-inhibitor system. The synthetic pattern-forming gene circuit destabilizes an initially homogenous lawn of genetically engineered bacteria, producing disordered patterns with tunable features on a spatial scale much larger than that of a single cell. Spatial correlations of the experimental patterns agree quantitatively with the signature predicted by theory. These results show that Turing-type pattern-forming mechanisms, if driven by stochasticity, can potentially underlie a broad range of biological patterns. These findings provide the groundwork for a unified picture of biological morphogenesis, arising from a combination of stochastic gene expression and dynamical instabilities.
Collapse
Affiliation(s)
- David Karig
- Research and Exploratory Development Department, Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218
| | - K Michael Martini
- Department of Physics, Center for the Physics of Living Cells and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Ting Lu
- Department of Bioengineering and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Nicholas A DeLateur
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Nigel Goldenfeld
- Department of Physics, Center for the Physics of Living Cells and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801;
| | - Ron Weiss
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| |
Collapse
|
17
|
Lahiri S, Nghe P, Tans SJ, Rosinberg ML, Lacoste D. Information-theoretic analysis of the directional influence between cellular processes. PLoS One 2017; 12:e0187431. [PMID: 29121044 PMCID: PMC5679622 DOI: 10.1371/journal.pone.0187431] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Accepted: 10/19/2017] [Indexed: 11/25/2022] Open
Abstract
Inferring the directionality of interactions between cellular processes is a major challenge in systems biology. Time-lagged correlations allow to discriminate between alternative models, but they still rely on assumed underlying interactions. Here, we use the transfer entropy (TE), an information-theoretic quantity that quantifies the directional influence between fluctuating variables in a model-free way. We present a theoretical approach to compute the transfer entropy, even when the noise has an extrinsic component or in the presence of feedback. We re-analyze the experimental data from Kiviet et al. (2014) where fluctuations in gene expression of metabolic enzymes and growth rate have been measured in single cells of E. coli. We confirm the formerly detected modes between growth and gene expression, while prescribing more stringent conditions on the structure of noise sources. We furthermore point out practical requirements in terms of length of time series and sampling time which must be satisfied in order to infer optimally transfer entropy from times series of fluctuations.
Collapse
Affiliation(s)
- Sourabh Lahiri
- Gulliver laboratory, PSL Research University, ESPCI, 10 rue de Vauquelin, 75231 Paris Cedex 05, France
| | - Philippe Nghe
- Laboratory of Biochemistry, PSL Research University, ESPCI, 10 rue de Vauquelin, 75231 Paris Cedex 05, France
| | - Sander J. Tans
- FOM Institute AMOLF, Science Park, 104, 1098 XG Amsterdam, the Netherlands
| | - Martin Luc Rosinberg
- Laboratoire de Physique Théorique de la Matière Condensée, Université Pierre et Marie Curie, CNRS UMR 7600, 4 place Jussieu, 75252 Paris Cedex 05, France
| | - David Lacoste
- Gulliver laboratory, PSL Research University, ESPCI, 10 rue de Vauquelin, 75231 Paris Cedex 05, France
- * E-mail:
| |
Collapse
|
18
|
Lodato PB, Thuraisamy T, Richards J, Belasco JG. Effect of RNase E deficiency on translocon protein synthesis in an RNase E-inducible strain of enterohemorrhagic Escherichia coli O157:H7. FEMS Microbiol Lett 2017; 364:3871349. [PMID: 28854682 PMCID: PMC5827626 DOI: 10.1093/femsle/fnx131] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 06/19/2017] [Indexed: 11/12/2022] Open
Abstract
Enterohemorrhagic Escherichia coli (EHEC) is a food-borne pathogen that assembles a type III secretion system (T3SS) on its surface. The last portion of the T3SS, called the 'translocon', is composed of a filament and a pore complex that is inserted into the membrane of intestinal epithelial cells. The genes encoding the translocon (espADB) are part of the LEE4 operon. Their expression is regulated by a complex post-transcriptional mechanism that involves the processing of LEE4 mRNA by the essential endoribonuclease RNase E. Here, we report the construction of an EHEC strain (TEA028-rne) in which RNase E can be induced by adding IPTG to the culture medium. EHEC cells deficient in RNase E displayed an abnormal morphology and slower growth, in agreement with published observations in E. coli K-12. Under those conditions, EspA and EspB were produced at higher concentrations, and protein secretion still occurred. These results indicate that RNase E negatively regulates translocon protein synthesis and demonstrate the utility of E. coli strain TEA028-rne as a tool for investigating the influence of this ribonuclease on EHEC gene expression in vitro.
Collapse
Affiliation(s)
- Patricia B. Lodato
- Department of Biology, New Mexico State University, Las Cruces, NM 88003-8006, USA
| | - Thujitha Thuraisamy
- Department of Biology, New Mexico State University, Las Cruces, NM 88003-8006, USA
| | - Jamie Richards
- Kimmel Center for Biology and Medicine at the Skirball Institute and the Department of Microbiology, New York University School of Medicine, New York, NY 10016-6402, USA
| | - Joel G. Belasco
- Kimmel Center for Biology and Medicine at the Skirball Institute and the Department of Microbiology, New York University School of Medicine, New York, NY 10016-6402, USA
| |
Collapse
|
19
|
Zhao C, Zhao J, Wang W, Fan Y, Ma C, Zhang D, Lv Y. Expression of MLAA34-HSP70 fusion gene constructed by SOE-PCR. Pak J Pharm Sci 2017; 30:1125-1127. [PMID: 28671094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
To construct the pIRES2-MLAA34-HSP70 recombinant vector and express the MLAA34-HSP70 recombinant proteins in Escherichia coli (E. coli). The MLAA34 and the HSP70 genes were extracted from U937 cells by RT-PCR, and then we amplified the fusion gene MLAA34-HSP70 by SOE-PCR and inserted it into the pIRES2-EGFP vector to construct the pIRES2-MLAA34-HSP70 recombinant vector. We amplified the fusion gene MLAA34-HSP70 successfully and identified the correctness of pIRES2-MLAA34-HSP70 recombinant vector by PCR and restriction endonuclease. Moreover, the MLAA34-HSP70 recombinant proteins expressed in E. coli were consistent with the expected molecular weight. We constructed the pIRES2-MLAA34-HSP70 recombinant vector successfully and the MLAA34-HSP70 recombinant proteins were successfully expressed by the induction of IPTG.
Collapse
Affiliation(s)
- Chen Zhao
- Department of Blood Test of Jilin Medical University, Jilin, Jilin, China
| | - Jiaqi Zhao
- Department of Blood Test of Jilin Medical University, Jilin, Jilin, China
| | - Wanying Wang
- Department of Blood Test of Jilin Medical University, Jilin, Jilin, China
| | - Yening Fan
- Department of Blood Test of Jilin Medical University, Jilin, Jilin, China
| | - Chunping Ma
- Department of Blood Test of Jilin Medical University, Jilin, Jilin, China
| | - Donghong Zhang
- Department of Blood Test of Jilin Medical University, Jilin, Jilin, China
| | - Yang Lv
- Department of Blood Test of Jilin Medical University, Jilin, Jilin, China
| |
Collapse
|
20
|
Jadaun JS, Sangwan NS, Narnoliya LK, Tripathi S, Sangwan RS. Withania coagulans tryptophan decarboxylase gene cloning, heterologous expression, and catalytic characteristics of the recombinant enzyme. Protoplasma 2017; 254:181-192. [PMID: 26795344 DOI: 10.1007/s00709-015-0929-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 12/10/2015] [Indexed: 05/14/2023]
Abstract
Tryptophan decarboxylase (EC 4.1.1.28) catalyzes pyridoxal 5'-phosphate (PLP)-dependent decarboxylation of tryptophan to produce tryptamine for recruitment in a myriad of biosynthetic pathways of metabolites possessing indolyl moiety. A recent report of certain indolyl metabolites in Withania species calls for a possible predominant functional role of tryptophan decarboxylase (TDC) in the genome of Withania species to facilitate production of the indolyl progenitor molecule, tryptamine. Therefore, with this metabolic prospection, we have identified and cloned a full-length cDNA sequence of TDC from aerial tissues of Withania coagulans. The functional WcTDC gene comprises of 1506 bp open reading frame (ORF) encoding a 502 amino acid protein with calculated molecular mass and pI value of 56.38 kDa and 8.35, respectively. The gene was expressed in Escherichia coli, and the recombinant enzyme was affinity-purified to homogeneity to discern its kinetics of catalysis. The enzyme (WcTDC) exhibited much higher Km value for tryptophan than for pyridoxal 5'-phosphate and was dedicated to catalyze decarboxylation of only tryptophan or, to a limited extent, of its analogue (like 5-hydroxy tryptophan). The observed optimal catalytic functionality of the enzyme on the slightly basic side of the pH scale and at slightly higher temperatures reflected adaptability of the plant to hot and arid regions, the predominant natural habitat of the herb. This pertains to be the first report on cloning and characterization of heterologously expressed recombinant enzyme from W. coagulans and forms a starting point to further understanding of withanamide biosynthesis.
Collapse
Affiliation(s)
- Jyoti Singh Jadaun
- CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow, 226015, India
| | - Neelam Singh Sangwan
- CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow, 226015, India
| | - Lokesh Kumar Narnoliya
- CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow, 226015, India
| | - Sandhya Tripathi
- CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow, 226015, India
| | - Rajender Singh Sangwan
- CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow, 226015, India.
- Center of Innovative and Applied Bioprocessing (CIAB), C-127, Phase-8, Industrial Area, S.A.S. Nagar, Mohali, 160071, Punjab, India.
| |
Collapse
|
21
|
Li C, Yue Z, Feng F, Xi C, Zang H, An X, Liu K. A novel strategy for acetonitrile wastewater treatment by using a recombinant bacterium with biofilm-forming and nitrile-degrading capability. Chemosphere 2016; 161:224-232. [PMID: 27434252 DOI: 10.1016/j.chemosphere.2016.07.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 06/01/2016] [Accepted: 07/06/2016] [Indexed: 06/06/2023]
Abstract
There is a great need for efficient acetonitrile removal technology in wastewater treatment to reduce the discharge of this pollutant in untreated wastewater. In this study, a nitrilase gene (nit) isolated from a nitrile-degrading bacterium (Rhodococcus rhodochrous BX2) was cloned and transformed into a biofilm-forming bacterium (Bacillus subtilis N4) that expressed the recombinant protein upon isopropylthio-β-galactoside (IPTG) induction. The recombinant bacterium (B. subtilis N4-pHT01-nit) formed strong biofilms and had nitrile-degrading capability. Further testing demonstrated that biofilms formed by B. subtilis N4-pHT01-nit were highly resistant to loading shock from acetonitrile and almost completely degraded the initial concentration of acetonitrile (800 mg L(-1)) within 24 h in a moving bed biofilm reactor (MBBR) after operation for 35 d. The bacterial composition of the biofilm, identified by high-throughput sequencing, in a reactor in which the B. subtilis N4-pHT01-nit bacterium was introduced indicated that the engineered bacterium was successfully immobilized in the reactor and became dominant genus. This work demonstrates that an engineered bacterium with nitrile-degrading and biofilm-forming capacity can improve the degradation of contaminants in wastewater. This approach offers a novel strategy for enhancing the biological oxidation of toxic pollutants in wastewater.
Collapse
Affiliation(s)
- Chunyan Li
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, Heilongjiang, PR China.
| | - Zhenlei Yue
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, Heilongjiang, PR China
| | - Fengzhao Feng
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, Heilongjiang, PR China
| | - Chuanwu Xi
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Hailian Zang
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, Heilongjiang, PR China
| | - Xuejiao An
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, Heilongjiang, PR China
| | - Keran Liu
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, Heilongjiang, PR China
| |
Collapse
|
22
|
Cheng Z, Jiang J, Wu H, Li Z, Ye Q. Enhanced production of 3-hydroxypropionic acid from glucose via malonyl-CoA pathway by engineered Escherichia coli. Bioresour Technol 2016; 200:897-904. [PMID: 26606325 DOI: 10.1016/j.biortech.2015.10.107] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 10/27/2015] [Accepted: 10/28/2015] [Indexed: 06/05/2023]
Abstract
In this study, production of 3-HP via malonyl-CoA was investigated by using metabolically engineered Escherichia coli carrying heterogeneous acetyl-CoA carboxylase (Acc) from Corynebacterium glutamicum and codon-optimized malonyl-CoA reductase (MCR) from Chloroflexus aurantiacus. Three engineered E. coli strains with different host-vector systems were constructed and investigated. The results indicated that the combination of E. coli BL21(DE3) and pET28a was the most efficient host-vector system for 3-HP production, and the highest concentration of 3-HP attained in shake flask cultivation reached 1.80g/L by the strain BE-MDA with induction at 0.25mM IPTG and 25°C, and supplementation of NaHCO3 and biotin. In fed-batch fermentation performed in a 5-L reactor, the concentration of 3-HP achieved 10.08g/L in 36h.
Collapse
Affiliation(s)
- Zhuan Cheng
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Jiaqi Jiang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Hui Wu
- 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.
| | - Qin Ye
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| |
Collapse
|
23
|
Denkovskienė E, Paškevičius Š, Werner S, Gleba Y, Ražanskienė A. Inducible Expression of Agrobacterium Virulence Gene VirE2 for Stringent Regulation of T-DNA Transfer in Plant Transient Expression Systems. Mol Plant Microbe Interact 2015; 28:1247-55. [PMID: 26292850 DOI: 10.1094/mpmi-05-15-0102-r] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Agrotransfection with viral vectors is an effective solution for the transient production of valuable proteins in plants grown in contained facilities. Transfection methods suitable for field applications are desirable for the production of high-volume products and for the transient molecular reprogramming of plants. The use of genetically modified (GM) Agrobacterium strains for plant transfections faces substantial biosafety issues. The environmental biosafety of GM Agrobacterium strains could be improved by regulating their T-DNA transfer via chemically inducible expression of virE2, one of the essential Agrobacterium virulence genes. In order to identify strong and stringently regulated promoters in Agrobacterium strains, we evaluated isopropyl-β-d-thiogalactoside-inducible promoters Plac, Ptac, PT7/lacO, and PT5/lacOlacO and cumic acid-inducible promoters PlacUV5/CuO, Ptac/CuO, PT5/CuO, and PvirE/CuO. Nicotiana benthamiana plants were transfected with a virE2-deficient A. tumefaciens strain containing transient expression vectors harboring inducible virE2 expression cassettes and containing a marker green fluorescent protein (GFP) gene in their T-DNA region. Evaluation of T-DNA transfer was achieved by counting GFP expression foci on plant leaves. The virE2 expression from cumic acid-induced promoters resulted in 47 to 72% of wild-type T-DNA transfer. Here, we present efficient and tightly regulated promoters for gene expression in A. tumefaciens and a novel approach to address environmental biosafety concerns in agrobiotechnology.
Collapse
Affiliation(s)
- Erna Denkovskienė
- 1 Nomads UAB, Graičiūno 8, LT-02241, Vilnius, Lithuania
- 3 Institute of Biotechnology of Vilnius University, Graičiūno 8, LT-02241, Vilnius, Lithuania
| | | | - Stefan Werner
- 2 Nomad Bioscience GmbH, Biozentrum Halle, Weinbergweg 22, D-06120 Halle (Saale), Germany
| | - Yuri Gleba
- 2 Nomad Bioscience GmbH, Biozentrum Halle, Weinbergweg 22, D-06120 Halle (Saale), Germany
| | | |
Collapse
|
24
|
Ravishankar S, Ambady A, Ramu H, Mudugal NV, Tunduguru R, Anbarasu A, Sharma UK, Sambandamurthy VK, Ramaiah S. An IPTG Inducible Conditional Expression System for Mycobacteria. PLoS One 2015; 10:e0134562. [PMID: 26247874 PMCID: PMC4527713 DOI: 10.1371/journal.pone.0134562] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 07/12/2015] [Indexed: 12/21/2022] Open
Abstract
Conditional expression strains serve as a valuable tool to study the essentiality and to establish the vulnerability of a target under investigation in a drug discovery program. While essentiality implies an absolute requirement of a target function, vulnerability provides valuable information on the extent to which a target function needs to be depleted to achieve bacterial growth inhibition followed by cell death. The critical feature of an ideal conditional expression system is its ability to tightly regulate gene expression to achieve the full spectrum spanning from a high level of expression in order to support growth and near zero level of expression to mimic conditions of gene knockout. A number of bacterial conditional expression systems have been reported for use in mycobacteria. The utility of an isopropylthiogalactoside (IPTG) inducible system in mycobacteria has been reported for protein overexpression and anti-sense gene expression from a replicating multi-copy plasmid. Herein, we report the development of a versatile set of non-replicating IPTG inducible vectors for mycobacteria which can be used for generation of conditional expression strains through homologous recombination. The role of a single lac operator versus a double lac operator to regulate gene expression was evaluated by monitoring the expression levels of β-galactosidase in Mycobacterium smegmatis. These studies indicated a significant level of leaky expression from the vector with a single lac operator but none from the vector with double lac operator. The significance of the double lac operator vector for target validation was established by monitoring the growth kinetics of an inhA, a rpoB and a ftsZ conditional expression strain grown in the presence of different concentrations of IPTG. The utility of this inducible system in identifying target specific inhibitors was established by screening a focussed library of small molecules using an inhA and a rpoB conditional expression strain.
Collapse
Affiliation(s)
- Sudha Ravishankar
- AstraZeneca India Pvt Ltd, Bellary Road, Hebbal, Bengaluru, Karnataka, India
- * E-mail:
| | - Anisha Ambady
- AstraZeneca India Pvt Ltd, Bellary Road, Hebbal, Bengaluru, Karnataka, India
| | - Haripriya Ramu
- AstraZeneca India Pvt Ltd, Bellary Road, Hebbal, Bengaluru, Karnataka, India
| | - Naina Vinay Mudugal
- AstraZeneca India Pvt Ltd, Bellary Road, Hebbal, Bengaluru, Karnataka, India
| | | | - Anand Anbarasu
- School of Biosciences & Technology, VIT University, Vellore, Tamil Nadu, India
| | - Umender K. Sharma
- AstraZeneca India Pvt Ltd, Bellary Road, Hebbal, Bengaluru, Karnataka, India
| | | | - Sudha Ramaiah
- School of Biosciences & Technology, VIT University, Vellore, Tamil Nadu, India
| |
Collapse
|
25
|
Panahi R, Vasheghani-Farahani E, Shojaosadati SA, Bambai B. [Auto-inducible expression system based on the SigB-dependent ohrB promoter in Bacillus subtilis]. Mol Biol (Mosk) 2015; 48:970-6. [PMID: 25845237 DOI: 10.7868/s0026898414060135] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The reliable production of heterologous proteins is important in the field of industrial biotechnology. This can be achieved by applying auto-inducible gene expression systems. The development of a Bacillus subtilis expression plasmid harboring SigB-dependent ohrB promoter was reported. The expression system was subjected to high cell density cultivation to produce xylanase as a stable model protein. The recombinant strain was cultured in a synthetic medium containing glucose as the carbon source. The exponential fed-batch feeding strategy was applied to prevent substrate inhibition. A sharp increase of xylanase activity (about 6-fold) at the end of the fermentation was observed as a result of sigma factor B (SigB) protein activation, supporting auto-inducibility of the expression system. For the control strain a specific induction of the xylanase activity was not observed. The recombinant strain was capable to offer a 5-fold increase in xylanase activity in comparison with the control strain. In addition, the constructed system displayed catabolite repression resistance ability. This SigB-dependent expression system can be considered as a biotechnology tool and an alternative to eliminate the cost of conventional inducers, e.g. isopropyl-β-galactopyranoside.
Collapse
|
26
|
Abstract
Shotgun sequencing and assembly of a large, complex genome can be both expensive and challenging to accurately reconstruct the true genome sequence. Repetitive DNA arrays, paralogous sequences, polyploidy, and heterozygosity are main factors that plague de novo genome sequencing projects that typically result in highly fragmented assemblies and are difficult to extract biological meaning. Targeted, sub-genomic sequencing offers complexity reduction by removing distal segments of the genome and a systematic mechanism for exploring prioritized genomic content through BAC sequencing. If one isolates and sequences the genome fraction that encodes the relevant biological information, then it is possible to reduce overall sequencing costs and efforts that target a genomic segment. This chapter describes the sub-genome assembly protocol for an organism based upon a BAC tiling path derived from a genome-scale physical map or from fine mapping using BACs to target sub-genomic regions. Methods that are described include BAC isolation and mapping, DNA sequencing, and sequence assembly.
Collapse
|
27
|
Shis D, Hussain F, Meinhardt S, Swint-Kruse L, Bennett MR. Modular, multi-input transcriptional logic gating with orthogonal LacI/GalR family chimeras. ACS Synth Biol 2014; 3:645-51. [PMID: 25035932 PMCID: PMC4210161 DOI: 10.1021/sb500262f] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Indexed: 12/22/2022]
Abstract
In prokaryotes, the construction of synthetic, multi-input promoters is constrained by the number of transcription factors that can simultaneously regulate a single promoter. This fundamental engineering constraint is an obstacle to synthetic biologists because it limits the computational capacity of engineered gene circuits. Here, we demonstrate that complex multi-input transcriptional logic gating can be achieved through the use of ligand-inducible chimeric transcription factors assembled from the LacI/GalR family. These modular chimeras each contain a ligand-binding domain and a DNA-binding domain, both of which are chosen from a library of possibilities. When two or more chimeras have the same DNA-binding domain, they independently and simultaneously regulate any promoter containing the appropriate operator site. In this manner, simple transcriptional AND gating is possible through the combination of two chimeras, and multiple-input AND gating is possible with the simultaneous use of three or even four chimeras. Furthermore, we demonstrate that orthogonal DNA-binding domains and their cognate operators allow the coexpression of multiple, orthogonal AND gates. Altogether, this work provides synthetic biologists with novel, ligand-inducible logic gates and greatly expands the possibilities for engineering complex synthetic gene circuits.
Collapse
Affiliation(s)
- David
L. Shis
- Department
of Biochemistry & Cell Biology, Rice
University, Houston, Texas 77005, United
States
| | - Faiza Hussain
- Department
of Biochemistry & Cell Biology, Rice
University, Houston, Texas 77005, United
States
| | - Sarah Meinhardt
- Department
of Biochemistry & Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas 66160, United States
| | - Liskin Swint-Kruse
- Department
of Biochemistry & Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas 66160, United States
| | - Matthew R. Bennett
- Department
of Biochemistry & Cell Biology, Rice
University, Houston, Texas 77005, United
States
| |
Collapse
|
28
|
Chen T, Zhu N, Xia H. Aerobic production of succinate from arabinose by metabolically engineered Corynebacterium glutamicum. Bioresour Technol 2014; 151:411-4. [PMID: 24169202 DOI: 10.1016/j.biortech.2013.10.017] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Revised: 10/02/2013] [Accepted: 10/07/2013] [Indexed: 05/25/2023]
Abstract
Arabinose is considered as an ideal feedstock for the microbial production of value-added chemicals due to its abundance in hemicellulosic wastes. In this study, the araBAD operon from Escherichia coli was introduced into succinate-producing Corynebacterium glutamicum, which enabled aerobic production of succinate using arabinose as sole carbon source. The engineered strain ZX1 (pXaraBAD, pEacsAgltA) produced 74.4 mM succinate with a yield of 0.58 mol (mol arabinose)(-1), which represented 69.9% of the theoretically maximal yield. Moreover, this strain produced 110.2 mM succinate using combined substrates of glucose and arabinose. To date, this is the highest succinate production under aerobic conditions in minimal medium.
Collapse
Affiliation(s)
- Tao Chen
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, People's Republic of China; Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, People's Republic of China.
| | | | | |
Collapse
|
29
|
Gatti-Lafranconi P, Dijkman WP, Devenish SRA, Hollfelder F. A single mutation in the core domain of the lac repressor reduces leakiness. Microb Cell Fact 2013; 12:67. [PMID: 23834731 PMCID: PMC3722110 DOI: 10.1186/1475-2859-12-67] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 06/29/2013] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND The lac operon provides cells with the ability to switch from glucose to lactose metabolism precisely when necessary. This metabolic switch is mediated by the lac repressor (LacI), which in the absence of lactose binds to the operator DNA sequence to inhibit transcription. Allosteric rearrangements triggered by binding of the lactose isomer allolactose to the core domain of the repressor impede DNA binding and lift repression. In Nature, the ability to detect and respond to environmental conditions comes at the cost of the encoded enzymes being constitutively expressed at low levels. The readily-switched regulation provided by LacI has resulted in its widespread use for protein overexpression, and its applications in molecular biology represent early examples of synthetic biology. However, the leakiness of LacI that is essential for the natural function of the lac operon leads to an increased energetic burden, and potentially toxicity, in heterologous protein production. RESULTS Analysis of the features that confer promiscuity to the inducer-binding site of LacI identified tryptophan 220 as a target for saturation mutagenesis. We found that phenylalanine (similarly to tryptophan) affords a functional repressor that is still responsive to IPTG. Characterisation of the W220F mutant, LacIWF, by measuring the time dependence of GFP production at different IPTG concentrations and at various incubation temperatures showed a 10-fold reduction in leakiness and no decrease in GFP production. Cells harbouring a cytotoxic protein under regulatory control of LacIWF showed no decrease in viability in the early phases of cell growth. Changes in responsiveness to IPTG observed in vivo are supported by the thermal shift assay behaviour of purified LacIWF with IPTG and operator DNA. CONCLUSIONS In LacI, long-range communications are responsible for the transmission of the signal from the inducer binding site to the DNA binding domain and our results are consistent with the involvement of position 220 in modulating these. The mutation of this single tryptophan residue to phenylalanine generated an enhanced repressor with a 10-fold decrease in leakiness. By minimising the energetic burden and cytotoxicity caused by leakiness, LacIWF constitutes a useful switch for protein overproduction and synthetic biology.
Collapse
Affiliation(s)
| | - Willem P Dijkman
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Sean RA Devenish
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| |
Collapse
|
30
|
Kwak S, Park YC, Seo JH. Biosynthesis of 3-hydroxypropionic acid from glycerol in recombinant Escherichia coli expressing Lactobacillus brevis dhaB and dhaR gene clusters and E. coli K-12 aldH. Bioresour Technol 2013; 135:432-439. [PMID: 23246300 DOI: 10.1016/j.biortech.2012.11.063] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Revised: 11/08/2012] [Accepted: 11/09/2012] [Indexed: 06/01/2023]
Abstract
3-Hydroxypropionic acid (3-HP) is a value-added chemical for polymer synthesis. For biosynthesis of 3-HP from glycerol, two dhaB and dhaR clusters encoding glycerol dehydratase and its reactivating factor, respectively, were cloned from Lactobacillus brevis KCTC33069 and expressed in Escherichia coli. Coexpression of dhaB and dhaR allowed the recombinant E. coli to convert glycerol to 3-hydroxypropionaldehyde, an intermediate of 3-HP biosynthesis. To produce 3-HP from glycerol, fed-batch fermentation with a two-step feeding strategy was designed to separate the cell growth from the 3-HP production stages. Finally, E. coli JHS00947 expressing L .brevis dhaB and dhaR, and E. coli aldH produced 14.3g/L 3-HP with 0.26 g/L-h productivity, which were 14.6 and 8.53 times higher than those of the batch culture. In conclusion, overexpression of L. brevis dhaB and dhaR clusters and E. coli aldH, and implementation of the two-step feeding strategy enabled recombinant E. coli to convert glycerol to 3-HP efficiently.
Collapse
Affiliation(s)
- Suryang Kwak
- Interdisciplinary Program for Bioengineering, Seoul National University, Seoul 151-921, Republic of Korea
| | | | | |
Collapse
|
31
|
Nausch H, Huckauf J, Koslowski R, Meyer U, Broer I, Mikschofsky H. Recombinant production of human interleukin 6 in Escherichia coli. PLoS One 2013; 8:e54933. [PMID: 23372793 PMCID: PMC3553018 DOI: 10.1371/journal.pone.0054933] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2012] [Accepted: 12/18/2012] [Indexed: 02/02/2023] Open
Abstract
In this study, we compared basic expression approaches for the efficient expression of bioactive recombinant human interleukin-6 (IL6), as an example for a difficult-to-express protein. We tested these approaches in a laboratory scale in order to pioneer the commercial production of this protein in Escherichia coli (E. coli). Among the various strategies, which were tested under Research and Development (R&D) conditions, aggregation-prone IL6 was solubilized most effectively by co-expressing cytoplasmic chaperones. Expression of a Glutathion-S-Transferase (GST) fusion protein was not efficient to increase IL6 solubility. Alteration of the cultivation temperature significantly increased the solubility in both cases, whereas reduced concentrations of IPTG to induce expression of the T7lac-promotor only had a positive effect on chaperone-assisted expression. The biological activity was comparable to that of commercial IL6. Targeting the expressed protein to an oxidizing environment was not effective in the generation of soluble IL6. Taken together, the presence of chaperones and a lowered cultivation temperature seem effective to isolate large quantities of soluble IL6. This approach led to in vivo soluble, functional protein fractions and reduces purification and refolding requirements caused by downstream purification procedures. The final yield of soluble recombinant protein averaged approximately 2.6 mg IL6/liter of cell culture. These findings might be beneficial for the development of the large-scale production of IL6 under the conditions of current good manufacturing practice (cGMP).
Collapse
Affiliation(s)
- Henrik Nausch
- Department of Agrobiotechnology, Agricultural and Environmental Faculty, University of Rostock, Rostock, Germany
| | - Jana Huckauf
- Department of Agrobiotechnology, Agricultural and Environmental Faculty, University of Rostock, Rostock, Germany
| | | | | | - Inge Broer
- Department of Agrobiotechnology, Agricultural and Environmental Faculty, University of Rostock, Rostock, Germany
- * E-mail:
| | - Heike Mikschofsky
- Department of Agrobiotechnology, Agricultural and Environmental Faculty, University of Rostock, Rostock, Germany
| |
Collapse
|
32
|
Benedetti IM, de Lorenzo V, Silva-Rocha R. Quantitative, non-disruptive monitoring of transcription in single cells with a broad-host range GFP-luxCDABE dual reporter system. PLoS One 2012; 7:e52000. [PMID: 23284849 PMCID: PMC3532404 DOI: 10.1371/journal.pone.0052000] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Accepted: 11/09/2012] [Indexed: 11/19/2022] Open
Abstract
A dual promoter probe system based on a tandem bi-cistronic GFP-luxCDABE reporter cassette is described and implemented. This system is assembled in two synthetic, modular, broad-host range plasmids based on pBBR1 and RK2 origins of replication, allowing its utilization in an extensive number of gram-negative bacteria. We analyze the performance of this dual cassette in two hosts, Escherichia coli and Pseudomonas putida, by examining the induction properties of the lacI(q)-Ptrc expression system in the first host and the Pb promoter of the benzoate degradation pathway in the second host. By quantifying the bioluminescence signal produced through the expression of the lux genes, we explore the dynamic range of induction for the two systems (Ptrc-based and Pb-based) in response to the two inducers. In addition, by quantifying the fluorescence signals produced by GFP expression, we were able to monitor the single-cell expression profile and to explore stochasticity of the same two promoters by flow cytometry. The results provided here demonstrate the power of the dual GFP-luxCDABE cassette as a new, single-step tool to assess promoter properties at both the population and single-cell levels in gram-negative bacteria.
Collapse
Affiliation(s)
- Ilaria Maria Benedetti
- Systems Biology Program, Centro Nacional de Biotecnología CSIC, Cantoblanco-Madrid, Spain
| | - Victor de Lorenzo
- Systems Biology Program, Centro Nacional de Biotecnología CSIC, Cantoblanco-Madrid, Spain
- * E-mail:
| | - Rafael Silva-Rocha
- Systems Biology Program, Centro Nacional de Biotecnología CSIC, Cantoblanco-Madrid, Spain
| |
Collapse
|
33
|
Jhamb K, Sahoo DK. Production of soluble recombinant proteins in Escherichia coli: effects of process conditions and chaperone co-expression on cell growth and production of xylanase. Bioresour Technol 2012; 123:135-143. [PMID: 22940310 DOI: 10.1016/j.biortech.2012.07.011] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Revised: 07/06/2012] [Accepted: 07/07/2012] [Indexed: 06/01/2023]
Abstract
In this study, effects of temperature, inducer concentration, time of induction and co-expression of molecular chaperones (GroEL-GroES and DnaKJE), on cell growth and solubilization of model protein, xylanases, were investigated. The yield of soluble xylanases increased with decreasing cultivation temperature and inducer level. In addition, co-expression of DnaKJE chaperone resulted in increased soluble xylanases though the time of induction of chaperone and target protein had a bearing on this yield. A combination of chaperone co-expression and partial induction resulted in ∼40% (in DnaKJE) and 33% (in GroEL-GroES) of total xylanase yield in soluble fraction. However, the conditions for maximum yield of soluble r-XynB and maximum % soluble expression of r-XynB were different. Higher expression of soluble xylanases in a scalable semi-synthetic medium showed potential of the process for soluble enzyme production.
Collapse
Affiliation(s)
- Kamna Jhamb
- CSIR - Institute of Microbial Technology, Sector 39-A, Chandigarh 160036, India
| | | |
Collapse
|
34
|
Tang L, Song CJ, Sun YJ, Li N, Wei YY, Sun Y, Yang K. [Prokaryotic expression, purification and identification of NY-ESO-1/GST fusion protein in E.coli]. Xi Bao Yu Fen Zi Mian Yi Xue Za Zhi 2012; 28:1094-1097. [PMID: 23046942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
AIM To construct an expression plasmid for NY-ESO-1 gene and identify the expression of recombinant protein NY-ESO-1/GST in E.coli. METHODS NY-ESO-1 segment was amplified from the testis cDNA library by RT-PCR and cloned into the prokaryotic expression vector pGEX4T-1 downstream tagged by GST to construct the expression plasmid pGEX-4T1-NY-ESO-1. The recombinant vector was transformed to BL21 (DE3) and NY-ESO-1/GST fusion protein was induced expression by IPTG. The protein was purified by urea elution and identified by SDS-PAGE and Western blotting. RESULTS The NY-ESO-1 segment was successfully amplified and its sequence was identical with that published in GenBank. The BL21 (DE3) pLysS containing the pGEX-4T1-NY-ESO-1 expressed a M(r); 44 000 fusion protein under the induction of IPTG. The purity of the protein was 90%. Western blotting proved that NY-ESO-1/GST had a specific reaction with anti-GST mAb. CONCLUSION The prokaryotic expression vector of NY-ESO-1 has been constructed and the fusion protein NY-ESO-1/GST of high purity is successfully expressed.
Collapse
Affiliation(s)
- Lei Tang
- Department of Immunology, Fourth Military Medical University, Xi'an, China
| | | | | | | | | | | | | |
Collapse
|
35
|
Kandhavelu M, Lloyd-Price J, Gupta A, Muthukrishnan AB, Yli-Harja O, Ribeiro AS. Regulation of mean and noise of the in vivo kinetics of transcription under the control of the lac/ara-1 promoter. FEBS Lett 2012; 586:3870-5. [PMID: 23017207 DOI: 10.1016/j.febslet.2012.09.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Revised: 09/03/2012] [Accepted: 09/06/2012] [Indexed: 11/19/2022]
Abstract
The kinetics of transcription initiation in Escherichia coli depend on the duration of two rate-limiting steps, the closed and the open complex formation. In a lac promoter variant, P(lac/ara-1), the kinetics of these steps is controlled by IPTG and arabinose. From in vivo single-RNA measurements, we find that induction affects the mean and normalized variance of the intervals between consecutive RNA productions. Transcript production is sub-Poissonian in all conditions tested. The kinetics of each step is independently controlled by a different inducer. We conclude that the regulatory mechanism of P(lac/ara-1) allows the stochasticity of gene expression to be environment-dependent.
Collapse
Affiliation(s)
- Meenakshisundaram Kandhavelu
- Laboratory of Biosystem Dynamics, Department of Signal Processing, Tampere University of Technology, 33101 Tampere, Finland
| | | | | | | | | | | |
Collapse
|
36
|
Bhomkar P, Materi W, Wishart DS. The bacterial nanorecorder: engineering E. coli to function as a chemical recording device. PLoS One 2011; 6:e27559. [PMID: 22132112 PMCID: PMC3223186 DOI: 10.1371/journal.pone.0027559] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Accepted: 10/19/2011] [Indexed: 02/02/2023] Open
Abstract
Synthetic biology is an emerging branch of molecular biology that uses synthetic genetic constructs to create man-made cells or organisms that are capable of performing novel and/or useful applications. Using a synthetic chemically sensitive genetic toggle switch to activate appropriate fluorescent protein indicators (GFP, RFP) and a cell division inhibitor (minC), we have created a novel E. coli strain that can be used as a highly specific, yet simple and inexpensive chemical recording device. This biological "nanorecorder" can be used to determine both the type and the time at which a brief chemical exposure event has occurred. In particular, we show that the short-term exposure (15-30 min) of cells harboring this synthetic genetic circuit to small molecule signals (anhydrotetracycline or IPTG) triggered long-term and uniform cell elongation, with cell length being directly proportional to the time elapsed following a brief chemical exposure. This work demonstrates that facile modification of an existing genetic toggle switch can be exploited to generate a robust, biologically-based "nanorecorder" that could potentially be adapted to detect, respond and record a wide range of chemical stimuli that may vary over time and space.
Collapse
Affiliation(s)
- Prasanna Bhomkar
- National Institute for Nanotechnology, Edmonton, Alberta, Canada.
| | | | | |
Collapse
|
37
|
Fang S, Li J, Liu L, Du G, Chen J. Overproduction of alkaline polygalacturonate lyase in recombinant Escherichia coli by a two-stage glycerol feeding approach. Bioresour Technol 2011; 102:10671-10678. [PMID: 21945205 DOI: 10.1016/j.biortech.2011.09.020] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Revised: 09/04/2011] [Accepted: 09/05/2011] [Indexed: 05/31/2023]
Abstract
This work aims to achieve the overproduction of alkaline polygalacturonate lyase (PGL) with recombinant Escherichia coli by a two-stage glycerol feeding approach. First, the PGL coding gene from Bacillus subtilis WSHB04-02 was expressed in E. coli BL21 (DE3) under the strong inducible T7 promoter of the pET20b (+) vector. And then the influence of media composition, induction temperature, and inducer isopropyl β-D-1-thiogalactopyranoside (IPTG) concentration on cell growth and PGL production was investigated. Finally, a two-stage glycerol feeding strategy was proposed and applied in a 3-L fermenter, where cultivation was conducted at a controlled specific growth rate (μset=0.2) during pre-induction phase, followed by a constant glycerol feeding rate of 12 ml h(-1) at post-induction phase. The total PGL yield reached 371.86 U mL(-1), which is the highest PGL production by recombinant E. coli expression system.
Collapse
Affiliation(s)
- Shuying Fang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | | | | | | | | |
Collapse
|
38
|
Korshun LN, Moĭsa LN, Ganova LA, Vudmaska MI, Kovtoniuk GV, Kiseleva EK, Spivak NI. [Influence of physiological state of Escherichia coli cells on the expression of soluble protein--recombinant analog of glycoprotein G of Herpes simplex virus of type 2]. Mikrobiol Z 2011; 73:36-46. [PMID: 22164698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
It is shown that the recombinant protein GST-HSV2gG, containing the immunodominant regions of glycoprotein G of HSV-2 is accumulated in the form of inclusion bodies or in soluble form in the Escherichia coli BL21 (DE3) cells. The ratio between protein fractions varied depending on the physiological state of cells before biosynthesis. The kinetic parameters of bacterial populations were determined by mathematical modeling of growth curves based on the Verhulst logistic function. It was established that the induction of biosynthesis in the growth acceleration phase (at OD600 = 0.3) with 0.1 mM IPTG gives the maximum yield of soluble protein (26.75 mg/l or 17.6 mg/g biomass). The target protein was purified using the immobilized metal ion affinity and affinity chromatography technologies. Antigenic activity of the soluble form of recombinant protein GST-HSV2gG, was significantly (three times) higher than that of the protein purified from inclusion bodies (p < 0.05) and was comparable with the activity of the commercial analog (p > 0.05), that allows using this product in the immunosorbent test kits for diagnosis of IgG to HSV-2.
Collapse
|
39
|
Xiang B, Wang L, Wang W, Li W, Yi M, Li X, Zeng Z, Li G. [Optimization of prokaryotic expression condition and purification of anti-cancer protein NOR1 in E.coli]. Zhong Nan Da Xue Xue Bao Yi Xue Ban 2011; 36:610-615. [PMID: 21873784 DOI: 10.3969/j.issn.1672-7347.2011.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
OBJECTIVE To optimize the induction condition of human NOR1 gene expression in E.coli. and purify NOR1 recombinant proteins. METHODS A full-length cDNA of human NOR1 was inserted into the corresponding region of pET28b expression vector to yield recombinant prokaryotic expression vector pET28b-NOR1. The prokaryotic expression vector pET28b-NOR1 was introduced into the bacterial host E.coli Rosettablue(DE3). Recombinant NOR1 protein was induced at different conditions. Induction condition was optimized to obtain high yield of recombinant protein. At last, the recombinant NOR1 protein was purified by Ni-IDE chromatography resin. RESULTS Recombinant NOR1 protein was induced by IPTG in a dose-dependent manner. Increase of kanamycin concentration and induction temperature resulted in high yield of recombinant protein. The most recombinant protein was found in inclusion bodies. The recombinant His-NOR1 protein was purified with Ni-IDE chromatography resin under denature condition. CONCLUSION IPTG, kanamycin concentration and temperature can affect the expression of recombinant NOR1 protein in pET28b system. High yield of recombinant NOR1 protein is achieved by inducing 1 mmol/L IPTG and 200 μg/mL kanamycin at 37 degree. Recombinant His-NOR1 protein with high purity is purified.
Collapse
Affiliation(s)
- Bo Xiang
- Cancer Research Institute, Central South University, Changsha 410078, China
| | | | | | | | | | | | | | | |
Collapse
|
40
|
Gholizadeh A. Over-expression, purification and functional characterization of Celosia ClpS as a fused protein in Escherichia coli. Prikl Biokhim Mikrobiol 2011; 47:408-414. [PMID: 21950114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
A ClpS homologue from Celosia cristata was expressed as maltose-binding fusion protein under the control of strong inducible tac promoter of pMALc2X vector in TB 1 strain of Escherichia coli. SDS-PAGE analysis showed that fused ClpS is produced as about 63 kDa protein in recombinant bacteria. Expressed product was purified to homogeneity with a yield of about 31 mg/l of bacterial culture. The results indicated that heterologous expression of Celosia ClpS does not affect bacterial growth under different induced conditions. Total cellular antioxidant assessment results revealed that the induction of ClpS activates the bacterial antioxidative system. Since, the purified ClpS did not exhibit antioxidant activity in vitro, we speculated a functional corelation between bacterial protelolytic apparatus and its anti-oxidative system. This prediction may contribute to our better understanding of functional relationship between proteolytic and antioxidative systems in biological worlds in the future investigations.
Collapse
Affiliation(s)
- A Gholizadeh
- Department of Molecular Biology, Research Institute for Fundamental Sciences (RIFS), University of Tabriz, Tabriz, Iran
| |
Collapse
|
41
|
McGowan EM, Alling N, Jackson EA, Yagoub D, Haass NK, Allen JD, Martinello-Wilks R. Evaluation of cell cycle arrest in estrogen responsive MCF-7 breast cancer cells: pitfalls of the MTS assay. PLoS One 2011; 6:e20623. [PMID: 21673993 PMCID: PMC3108819 DOI: 10.1371/journal.pone.0020623] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2011] [Accepted: 05/05/2011] [Indexed: 01/06/2023] Open
Abstract
Endocrine resistance is a major problem with anti-estrogen treatments and how to overcome resistance is a major concern in the clinic. Reliable measurement of cell viability, proliferation, growth inhibition and death is important in screening for drug treatment efficacy in vitro. This report describes and compares commonly used proliferation assays for induced estrogen-responsive MCF-7 breast cancer cell cycle arrest including: determination of cell number by direct counting of viable cells; or fluorescence SYBR®Green (SYBR) DNA labeling; determination of mitochondrial metabolic activity by 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium (MTS) assay; assessment of newly synthesized DNA using 5-ethynyl-2′-deoxyuridine (EdU) nucleoside analog binding and Alexa Fluor® azide visualization by fluorescence microscopy; cell-cycle phase measurement by flow cytometry. Treatment of MCF-7 cells with ICI 182780 (Faslodex), FTY720, serum deprivation or induction of the tumor suppressor p14ARF showed inhibition of cell proliferation determined by the Trypan Blue exclusion assay and SYBR DNA labeling assay. In contrast, the effects of treatment with ICI 182780 or p14ARF-induction were not confirmed using the MTS assay. Cell cycle inhibition by ICI 182780 and p14ARF-induction was further confirmed by flow cytometric analysis and EdU-DNA incorporation. To explore this discrepancy further, we showed that ICI 182780 and p14ARF-induction increased MCF-7 cell mitochondrial activity by MTS assay in individual cells compared to control cells thereby providing a misleading proliferation readout. Interrogation of p14ARF-induction on MCF-7 metabolic activity using TMRE assays and high content image analysis showed that increased mitochondrial activity was concomitant with increased mitochondrial biomass with no loss of mitochondrial membrane potential, or cell death. We conclude that, whilst p14ARF and ICI 182780 stop cell cycle progression, the cells are still viable and potential treatments utilizing these pathways may contribute to drug resistant cells. These experiments demonstrate how the combined measurement of metabolic activity and DNA labeling provides a more reliable interpretation of cancer cell response to treatment regimens.
Collapse
Affiliation(s)
- Eileen M McGowan
- Translational Cancer Research Group, School of Medical and Molecular Biosciences, Faculty of Science, University of Technology Sydney, Sydney, New South Wales, Australia.
| | | | | | | | | | | | | |
Collapse
|
42
|
Zakaria II, Rahman RNZRA, Salleh AB, Basri M. Bacteriocin release protein-mediated secretory expression of recombinant chalcone synthase in Escherichia coli. Appl Biochem Biotechnol 2011; 165:737-47. [PMID: 21633820 DOI: 10.1007/s12010-011-9292-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2011] [Accepted: 05/17/2011] [Indexed: 11/26/2022]
Abstract
Flavonoids are secondary metabolites synthesized by plants shown to exhibit health benefits such as anti-inflammatory, antioxidant, and anti-tumor effects. Thus, due to the importance of this compound, several enzymes involved in the flavonoid pathway have been cloned and characterized in Escherichia coli. However, the formation of inclusion bodies has become a major disadvantage of this approach. As an alternative, chalcone synthase from Physcomitrella patens was secreted into the medium using a bacteriocin release protein expression vector. Secretion of P. patens chalcone synthase into the culture media was achieved by co-expression with a psW1 plasmid encoding bacteriocin release protein in E. coli Tuner (DE3) plysS. The optimized conditions, which include the incubation of cells for 20 h with 40 ng/ml mitomycin C at OD(600) induction time of 0.5 was found to be the best condition for chalcone synthase secretion.
Collapse
Affiliation(s)
- Iffah Izzati Zakaria
- Faculty of Biotechnology and Biomolecular Sciences, Enzyme and Microbial Technology Research Group, Universiti Putra Malaysia, Serdang, Malaysia.
| | | | | | | |
Collapse
|
43
|
Box J, Noel KD. Controlling the expression of rhizobial genes during nodule development with elements and an inducer of the lac operon. Mol Plant Microbe Interact 2011; 24:478-486. [PMID: 21375387 DOI: 10.1094/mpmi-07-10-0155] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
A simple strategy was tested for imposing artificial regulation of rhizobial genes during nodule development. Isopropyl-β-d-1-thiogalactoside (IPTG) was added to liquid root media to sustain expression of rhizobial genes controlled by Escherichia coli lac promoter/operators and repressor gene lacI. Conversely, a rinsing protocol was devised to remove IPTG sufficiently that genes could be repressed after having been induced. gusA under this control exhibited clearly delineated expression and repression in both the determinate Rhizobium etli-Phaseolus vulgaris and the indeterminate Sinorhizobium meliloti-Medicago sativa symbioses. Apparently, IPTG was taken up in sufficiently undegraded concentrations that gene expression was derepressed even in interior portions of the nodule. Moreover, the rinsing protocol led to obvious repression of gusA. Importantly, no deleterious effects of IPTG on nodule development, infection, or nitrogen fixation were observed. An R. etli CE3 gene required for lipopolysaccharide O antigen and infection on bean was put under this control by means of a two-plasmid construct. When this construct was added to a strain with a null mutation in this gene, infection, nodule development, and nitrogenase activity all depended on the length of time before IPTG was rinsed from the roots after inoculation.
Collapse
Affiliation(s)
- Jodie Box
- Department of Biological Sciences, Marquette University, PO Box 1881, Milwaukee, WI 53201, USA
| | | |
Collapse
|
44
|
Abstract
Predator-prey system, as an essential element of ecological dynamics, has been recently studied experimentally with synthetic biology. We developed a global probabilistic landscape and flux framework to explore a synthetic predator-prey network constructed with two Escherichia coli populations. We developed a self consistent mean field method to solve multidimensional problem and uncovered the potential landscape with Mexican hat ring valley shape for predator-prey oscillations. The landscape attracts the system down to the closed oscillation ring. The probability flux drives the coherent oscillations on the ring. Both the landscape and flux are essential for the stable and coherent oscillations. The landscape topography characterized by the barrier height from the top of Mexican hat to the closed ring valley provides a quantitative measure of global stability of system. The entropy production rate for the energy dissipation is less for smaller environmental fluctuations or perturbations. The global sensitivity analysis based on the landscape topography gives specific predictions for the effects of parameters on the stability and function of the system. This may provide some clues for the global stability, robustness, function and synthetic network design.
Collapse
Affiliation(s)
- Chunhe Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, China
- Graduate School of the Chinese Academy of Sciences, Beijing, China
| | - Erkang Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, China
- * E-mail: (JW); (EW)
| | - Jin Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, China
- Department of Chemistry and Physics, State University of New York at Stony Brook, Stony Brook, New York, United States of America
- * E-mail: (JW); (EW)
| |
Collapse
|
45
|
Xu XL, Zhang GL, Lv B, Yuan YJ, Li C. Recombinant glycerol dehydratase from Klebsiella pneumoniae XJPD-Li: induction optimization, purification and characterization. Prikl Biokhim Mikrobiol 2011; 47:162-167. [PMID: 22808739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Glycerol dehydratase (GDHt) is the rate limiting enzyme in the biosynthesis of 1,3-propanediol from glycerol. The optimization of inducting process for recombinant GDHt from Klebsiella pneumoniae XJPD-Li carried out to increase specific activity and ratio of soluble form. The optimum condition was inducing under the isopropyl-beta-D-thiogalactoside concentration of 0.8 mM and the temperature of 20 degrees C for 3 h. Homogeneity of GDHt then was obtained by affinity chromatography, resulted in 2.11-fold purification and an overall yield of 47.5%. The optimum pH and reaction temperature of GDHt were pH 8.0 and 45 degrees C, respectively. The K(m) for glycerol, 1,2-propanediol, 1,2-ethanediol and coenzyme B12 were 0.48, 1.43, 3.07 mM, and 10.03 nM, respectively. The GDHt showed relatively stable even under temperature of 40 degrees C and a bit blunt to oxygen. The thermo-inactivation kinetic models were fit linear under different temperatures.
Collapse
Affiliation(s)
- X L Xu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China.
| | | | | | | | | |
Collapse
|
46
|
Jiang PF, Cao JS, Liu C, Zhao HP, Zhang DL. [Cloning and expression of novel swine gene BCL-G(L) in E.coli and preparation of its polyclonal antibody in guinea pigs]. Xi Bao Yu Fen Zi Mian Yi Xue Za Zhi 2010; 26:1238-1245. [PMID: 21138691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
AIM In order to express a novel gene named as BCL-G(L); of swine in E.coli and prepare its polyclonal antibody. METHODS The contig sequence of the gene was predicted and in silicon cloned by blasting the human BCL-G(L); in swine ESTs database in NCBI. The cloning sequence was obtained by RT-PCR from swine spleen. The cloning sequence was identified by sequencing and compared with the contig sequence. Then the gene was cloned into a prokaryotic expression vector pET-32a to construct a recombinant plasmid named as pET32a-BCL-G(L);. The fusion protein pET32a-BCL-G(L); was expressed in E.coli BL21 and purified using a His-tag fusion protein purification kit. Then guinea pigs were immunized with the purified protein to get the specific polyclonal antibody. RESULTS The titer of the antibody was 1:800 detected by ELISA. The protein BCL-G(L); can be specifically detected by western blot assay using the polyclonal antibody. CONCLUSION The novel swine gene BCL-G(L); was cloned and expressed in E.coli and its polyclonal antibody was prepared successfully.
Collapse
Affiliation(s)
- Peng-Fei Jiang
- Research Laboratory of Virology, College of Veterinary Medicine, Northwest Agriculture & Forestry University, Yangling 712100, China.
| | | | | | | | | |
Collapse
|
47
|
Gan D, Zhang J, Jiang H, Jiang T, Zhu S, Cheng B. Bacterially expressed dsRNA protects maize against SCMV infection. Plant Cell Rep 2010; 29:1261-8. [PMID: 20734050 DOI: 10.1007/s00299-010-0911-z] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2010] [Revised: 08/03/2010] [Accepted: 08/05/2010] [Indexed: 05/08/2023]
Abstract
RNA interference (RNAi) is a sequence-specific, posttranscriptional gene silencing (PTGS) process in plants that is mediated by dsRNA homologous to the silenced gene(s). In this study, we report an efficient method to produce dsRNA using a bacterial expression system. Two fragments of the Sugarcane Mosaic Virus (SCMV) CP (coat protein) gene were amplified by RT-PCR, and cloned into the inverted-repeat cloning vector pUCCRNAi. The two recombinant plasmids were transformed individually into E. coli HT115, an RNase-III deficient strain, and dsRNA was induced by isopropyl-β-D: -thiogalactopyranoside (IPTG). The crude extracts of E. coli HT115 containing large amounts of dsRNA were applied to plants as a spray and the experiment confirmed a preventative efficacy. Our findings demonstrated that spraying crude dsRNA-containing extracts inhibited SCMV infection, and the dsRNA derived from an upstream region (CP1) was more effective than was dsRNA derived from a downstream region (CP2) of the SCMV CP gene. The results provide a valuable tool for plant viral control using dsRNA and the PTGS approach.
Collapse
Affiliation(s)
- Defang Gan
- Anhui Province Key Laboratory of Crop Biology, School of Life Science, Anhui Agricultural University, Hefei, 230036, China
| | | | | | | | | | | |
Collapse
|
48
|
Li Y, Hopper A, Overton T, Squire DJP, Cole J, Tovell N. Organization of the electron transfer chain to oxygen in the obligate human pathogen Neisseria gonorrhoeae: roles for cytochromes c4 and c5, but not cytochrome c2, in oxygen reduction. J Bacteriol 2010; 192:2395-406. [PMID: 20154126 PMCID: PMC2863483 DOI: 10.1128/jb.00002-10] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2010] [Accepted: 02/09/2010] [Indexed: 02/07/2023] Open
Abstract
Although Neisseria gonorrhoeae is a prolific source of eight c-type cytochromes, little is known about how its electron transfer pathways to oxygen are organized. In this study, the roles in the respiratory chain to oxygen of cytochromes c(2), c(4), and c(5), encoded by the genes cccA, cycA, and cycB, respectively, have been investigated. Single mutations in genes for either cytochrome c(4) or c(5) resulted in an increased sensitivity to growth inhibition by excess oxygen and small decreases in the respiratory capacity of the parent, which were complemented by the chromosomal integration of an ectopic, isopropyl-beta-d-thiogalactopyranoside (IPTG)-inducible copy of the cycA or cycB gene. In contrast, a cccA mutant reduced oxygen slightly more rapidly than the parent, suggesting that cccA is expressed but cytochrome c(2) is not involved in electron transfer to cytochrome oxidase. The deletion of cccA increased the sensitivity of the cycB mutant to excess oxygen but decreased the sensitivity of the cycA mutant. Despite many attempts, a double mutant defective in both cytochromes c(4) and c(5) could not be isolated. However, a strain with the ectopically encoded, IPTG-inducible cycB gene with deletions in both cycA and cycB was constructed: the growth and survival of this strain were dependent upon the addition of IPTG, so gonococcal survival is dependent upon the synthesis of either cytochrome c(4) or c(5). These results define the gonococcal electron transfer chain to oxygen in which cytochromes c(4) and c(5), but not cytochrome c(2), provide alternative pathways for electron transfer from the cytochrome bc(1) complex to the terminal oxidase cytochrome cbb(3).
Collapse
Affiliation(s)
- Ying Li
- School of Biosciences, School of Chemical Engineering, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Amanda Hopper
- School of Biosciences, School of Chemical Engineering, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Tim Overton
- School of Biosciences, School of Chemical Engineering, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Derrick J. P. Squire
- School of Biosciences, School of Chemical Engineering, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Jeffrey Cole
- School of Biosciences, School of Chemical Engineering, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Nicholas Tovell
- School of Biosciences, School of Chemical Engineering, University of Birmingham, Birmingham B15 2TT, United Kingdom
| |
Collapse
|
49
|
Demidenko ZN, Blagosklonny MV. Quantifying pharmacologic suppression of cellular senescence: prevention of cellular hypertrophy versus preservation of proliferative potential. Aging (Albany NY) 2009; 1:1008-16. [PMID: 20157583 PMCID: PMC2815749 DOI: 10.18632/aging.100115] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2009] [Accepted: 12/30/2009] [Indexed: 05/01/2023]
Abstract
Development of agents that suppress aging (aging suppressants) requires quantification of cellular senescence. Cellular senescence in vitro is characterized by a large cell morphology and permanent loss of proliferative potential. When HT-1080 cells were arrested by p21, they continued to grow exponentially in size and became hypertrophic with a 15-fold increase in the protein content per cell. These changes were mirrored by accumulation of GFP (driven by CMV promoter) per cell, which also served as a marker of cellular hypertrophy. Preservation of proliferative potential (competence) was measured by an increase in live cell number, when p21 was switched off. While modestly decreasing hypertrophy in p21-arresrted cells, rapamycin considerably preserved competence, converting senescence into quiescence. Preservation of proliferative potential (competence) correlated with inhibition of S6 phosphorylation by rapamycin. When p21 was switched off, competent cells, by resuming proliferation, became progressively less hypertrophic. Preservation of proliferative potential is a sensitive and quantitative measure of suppression of mTOR-driven senescence.
Collapse
|
50
|
Portle S, Iadevaia S, San KY, Bennett GN, Mantzaris N. Environmentally-modulated changes in fluorescence distribution in cells with oscillatory genetic network dynamics. J Biotechnol 2009; 140:203-17. [PMID: 19428715 PMCID: PMC2680770 DOI: 10.1016/j.jbiotec.2009.01.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2008] [Revised: 01/06/2009] [Accepted: 01/15/2009] [Indexed: 11/26/2022]
Abstract
We investigated the distribution of green fluorescent protein (GFP) expression levels in a population of E. coli cells expressing an artificial genetic regulatory network, known as the "repressilator". This network originally constructed by Elowitz and Leibler in 2000 consists of three cyclically-inhibiting promoter-repressor pairs. It is because of this architecture that the network has been known to oscillate at the single-cell level under certain conditions. A series of shake flask experiments were performed and analyzed using flow cytometry to test how cell populations carrying this system could be controlled extracellularly using the inducers anhydrotetracycline (aTc) and isopropyl-beta-d-thiogalactopyranoside (IPTG). With variation of [aTc], it exhibits a novel bi-threshold behavior, such that the entire culture reaches one of three steady states at a quasi-time-invariant "reference state." Also, there is significant hysteresis. Transiently, the middle state shows damping oscillations, while the low and high states show a stable steady state. The addition of IPTG serves to fine-tune the characteristics of the aTc-only expression, lowering the average and coefficient of variation (CV) of the distributions, and possibly perturbing the network to a different state. However, in modeling this system, the multiplicity and bi-threshold behavior are not theoretically possible according to the designed interactions. In order to explain this discrepancy, we hypothesize that one or more of the repressors have a significant nonspecific interaction with a promoter that does not contain its operator site. The new modeling results incorporating these extra interactions qualitatively match our experimental findings. After constructing plasmids to test these hypotheses, we discover that at least four of these interactions exist, which can create the low and high states and multiplicity seen experimentally. This genetic architecture has flexibility in its behavior that has not been demonstrated before, and the combination of experiment and modeling enlightened our understanding of the molecular interactions driving the network's behavior, leading us to discover the significance of nonspecific interactions.
Collapse
Affiliation(s)
- Stephanie Portle
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas
- Department of Bioengineering, Rice University, Houston, Texas
| | - Sergio Iadevaia
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas
| | - Ka-Yiu San
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas
- Department of Bioengineering, Rice University, Houston, Texas
| | - George N. Bennett
- Department of Biochemistry and Cell Biology, Rice University, Houston, Texas
| | - Nikos Mantzaris
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas
- Department of Bioengineering, Rice University, Houston, Texas
| |
Collapse
|