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1.
Cell ; 179(1): 106-119.e16, 2019 Sep 19.
Article in English | MEDLINE | ID: mdl-31539491

ABSTRACT

Genes are often transcribed by multiple RNA polymerases (RNAPs) at densities that can vary widely across genes and environmental conditions. Here, we provide in vitro and in vivo evidence for a built-in mechanism by which co-transcribing RNAPs display either collaborative or antagonistic dynamics over long distances (>2 kb) through transcription-induced DNA supercoiling. In Escherichia coli, when the promoter is active, co-transcribing RNAPs translocate faster than a single RNAP, but their average speed is not altered by large variations in promoter strength and thus RNAP density. Environmentally induced promoter repression reduces the elongation efficiency of already-loaded RNAPs, causing premature termination and quick synthesis arrest of no-longer-needed proteins. This negative effect appears independent of RNAP convoy formation and is abrogated by topoisomerase I activity. Antagonistic dynamics can also occur between RNAPs from divergently transcribed gene pairs. Our findings may be broadly applicable given that transcription on topologically constrained DNA is the norm across organisms.


Subject(s)
DNA, Bacterial/genetics , DNA, Superhelical/genetics , DNA-Directed RNA Polymerases/genetics , Escherichia coli/genetics , Transcription, Genetic , DNA-Directed RNA Polymerases/chemistry , Gene Expression Regulation, Bacterial/genetics , Glucose/pharmacology , Glycosides/pharmacology , Isopropyl Thiogalactoside/pharmacology , Kinetics , Lac Operon/drug effects , Lac Operon/genetics , Plasmids/genetics , Promoter Regions, Genetic/genetics , RNA, Bacterial/genetics , Real-Time Polymerase Chain Reaction , Rifampin/pharmacology
2.
Protein Expr Purif ; 221: 106516, 2024 Sep.
Article in English | MEDLINE | ID: mdl-38801985

ABSTRACT

Galectins are a large and diverse protein family defined by the presence of a carbohydrate recognition domain (CRD) that binds ß-galactosides. They play important roles in early development, tissue regeneration, immune homeostasis, pathogen recognition, and cancer. In many cases, studies that examine galectin biology and the effect of manipulating galectins are aided by, or require the ability to express and purify, specific members of the galectin family. In many cases, E. coli is employed as a heterologous expression system, and galectin expression is induced with isopropyl ß-galactoside (IPTG). Here, we show that galectin-3 recognizes IPTG with micromolar affinity and that as IPTG induces expression, newly synthesized galectin can bind and sequester cytosolic IPTG, potentially repressing further expression. To circumvent this putative inhibitory feedback loop, we utilized an autoinduction protocol that lacks IPTG, leading to significantly increased yields of galectin-3. Much of this work was done within the context of a course-based undergraduate research experience, indicating the ease and reproducibility of the resulting expression and purification protocols.


Subject(s)
Escherichia coli , Galectin 3 , Isopropyl Thiogalactoside , Galectin 3/genetics , Galectin 3/metabolism , Galectin 3/biosynthesis , Galectin 3/chemistry , Escherichia coli/genetics , Escherichia coli/metabolism , Humans , Isopropyl Thiogalactoside/pharmacology , Gene Expression , Galectins/genetics , Galectins/metabolism , Galectins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/isolation & purification , Recombinant Proteins/metabolism , Recombinant Proteins/biosynthesis , Recombinant Proteins/chemistry , Blood Proteins/genetics , Blood Proteins/metabolism
3.
Mol Biol Rep ; 51(1): 628, 2024 May 08.
Article in English | MEDLINE | ID: mdl-38717629

ABSTRACT

Autoinduction systems in Escherichia coli can control the production of proteins without the addition of a particular inducer. In the present study, we optimized the heterologous expression of Moloney Murine Leukemia Virus derived Reverse Transcriptase (MMLV-RT) in E. coli. Among 4 autoinduction media, media Imperial College resulted the highest MMLV-RT overexpression in E. coli BL21 Star (DE3) with incubation time 96 h. The enzyme was produced most optimum in soluble fraction of lysate cells. The MMLV-RT was then purified using the Immobilized Metal Affinity Chromatography method and had specific activity of 629.4 U/mg. The system resulted lower specific activity and longer incubation of the enzyme than a classical Isopropyl ß-D-1-thiogalactopyranoside (IPTG)-induction system. However, the autoinduction resulted higher yield of the enzyme than the conventional induction (27.8%). Techno Economic Analysis revealed that this method could produce MMLV-RT using autoinduction at half the cost of MMLV-RT production by IPTG-induction. Bioprocessing techniques are necessary to conduct to obtain higher quality of MMLV-RT under autoinduction system.


Subject(s)
Escherichia coli , Moloney murine leukemia virus , RNA-Directed DNA Polymerase , Escherichia coli/genetics , Escherichia coli/metabolism , Moloney murine leukemia virus/genetics , Moloney murine leukemia virus/enzymology , RNA-Directed DNA Polymerase/metabolism , RNA-Directed DNA Polymerase/genetics , Isopropyl Thiogalactoside/pharmacology , Recombinant Proteins/metabolism , Recombinant Proteins/genetics , Culture Media
4.
Nat Chem Biol ; 17(1): 71-79, 2021 01.
Article in English | MEDLINE | ID: mdl-32895498

ABSTRACT

Control of the lac operon with isopropyl ß-D-1-thiogalactopyranoside (IPTG) has been used to regulate gene expression in Escherichia coli for countless applications, including metabolic engineering and recombinant protein production. However, optogenetics offers unique capabilities, such as easy tunability, reversibility, dynamic induction strength and spatial control, that are difficult to obtain with chemical inducers. We have developed a series of circuits for optogenetic regulation of the lac operon, which we call OptoLAC, to control gene expression from various IPTG-inducible promoters using only blue light. Applying them to metabolic engineering improves mevalonate and isobutanol production by 24% and 27% respectively, compared to IPTG induction, in light-controlled fermentations scalable to at least two-litre bioreactors. Furthermore, OptoLAC circuits enable control of recombinant protein production, reaching yields comparable to IPTG induction but with easier tunability of expression. OptoLAC circuits are potentially useful to confer light control over other cell functions originally designed to be IPTG-inducible.


Subject(s)
Escherichia coli/radiation effects , Gene Expression Regulation, Bacterial , Lac Operon/radiation effects , Metabolic Engineering/methods , Optogenetics/methods , Bioreactors , Butanols/metabolism , Butanols/pharmacology , Escherichia coli/genetics , Escherichia coli/metabolism , Isopropyl Thiogalactoside/pharmacology , Light , Light Signal Transduction , Mevalonic Acid/metabolism , Mevalonic Acid/pharmacology , Promoter Regions, Genetic
5.
J Ind Microbiol Biotechnol ; 50(1)2023 Feb 17.
Article in English | MEDLINE | ID: mdl-37849239

ABSTRACT

Coupling transcription of a cloned gene to the lac operon with induction by isopropylthio-ß-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.


Subject(s)
Escherichia coli , Galactosides , Escherichia coli/genetics , Escherichia coli/metabolism , Isopropyl Thiogalactoside/metabolism , Isopropyl Thiogalactoside/pharmacology , Galactosides/metabolism , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Cell Membrane/metabolism
6.
World J Microbiol Biotechnol ; 39(6): 143, 2023 Apr 01.
Article in English | MEDLINE | ID: mdl-37004690

ABSTRACT

The IPTG-inducible promoter family, Pgrac, allows high protein expression levels in an inducible manner. In this study, we constructed IPTG-inducible expression vectors containing strong Pgrac promoters that allow integration of the transgene at either the amyE or lacA locus or both loci in Bacillus subtilis. Our novel integrative expression vectors based on Pgrac promoters could control the repression of protein production in the absence and the induction in the presence of an inducer, IPTG. The ß-galactosidase (BgaB) protein levels were 9.0%, 15% and 30% of the total cellular protein in the B. subtilis strains carrying single cassettes with the Pgrac01, Pgrac100 or Pgrac212 promoters, respectively. The maximal induction ratio of Pgrac01-bgaB was 35.5 while that of Pgrac100-bgaB was 7.5 and that of Pgrac212-bgaB was 9. The inducible expression of GFP and BgaB protein was stably maintained for 24 h, with the highest yield of GFP being 24% of cell total protein while the maximum amount of BgaB was found to be 38%. A dual integration of two copies of the gfp+ gene into the B. subtilis genome at the lacA and amyE loci resulted in a yield of about 40% of total cellular protein and a 1.74-fold increase in GFP compared with single-integrated strains containing the same Pgrac212 promoter. The capability of protein production from low to high levels of these inducible integrative systems is useful for fundamental and applied research in B. subtilis.


Subject(s)
Bacillus subtilis , Genetic Vectors , Bacillus subtilis/metabolism , Isopropyl Thiogalactoside/metabolism , Isopropyl Thiogalactoside/pharmacology , Recombinant Proteins/genetics , Promoter Regions, Genetic , Genetic Vectors/genetics
7.
Mol Syst Biol ; 16(6): e9361, 2020 06.
Article in English | MEDLINE | ID: mdl-32529808

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.


Subject(s)
Gene Regulatory Networks , Synthetic Biology , Escherichia coli/drug effects , Escherichia coli/genetics , Gene Expression Regulation, Bacterial/drug effects , Gene Regulatory Networks/drug effects , Isopropyl Thiogalactoside/pharmacology , Models, Theoretical , Probability , Time Factors
8.
Microb Cell Fact ; 20(1): 27, 2021 Feb 01.
Article in English | MEDLINE | ID: mdl-33522916

ABSTRACT

BACKGROUND: Precise regulation of gene expression is of utmost importance for the production of complex membrane proteins (MP), enzymes or other proteins toxic to the host cell. In this article we show that genes under control of a normally Isopropyl ß-D-1-thiogalactopyranoside (IPTG)-inducible PT7-lacO promoter can be induced solely with L-arabinose in a newly constructed Escherichia coli expression host BL21-AI, a strain based on the recently published approach of bacteriophage inspired growth-decoupled recombinant protein production. RESULTS: Here, we show that BL21-AI is able to precisely regulate protein production rates on a cellular level in an L-arabinose concentration-dependent manner and simultaneously allows for reallocation of metabolic resources due to L-arabinose induced growth decoupling by the phage derived inhibitor peptide Gp2. We have successfully characterized the system under relevant fed-batch like conditions in microscale cultivation (800 µL) and generated data proofing a relevant increase in specific yields for 6 different Escherichia coli derived MP-GFP fusion proteins by using online-GFP signals, FACS analysis, SDS-PAGE and western blotting. CONCLUSIONS: In all cases tested, BL21-AI outperformed the parental strain BL21-AI, operated in growth-associated production mode. Specific MP-GFP fusion proteins yields have been improved up to 2.7-fold. Therefore, this approach allows for fine tuning of MP production or expression of multi-enzyme pathways where e.g. particular stoichiometries have to be met to optimize product flux.


Subject(s)
Arabinose/pharmacology , Bacteriophage T7/metabolism , Escherichia coli/growth & development , Escherichia coli/genetics , Gene Expression Regulation, Bacterial , Escherichia coli/drug effects , Gene Expression Regulation, Bacterial/drug effects , Genetic Engineering , Green Fluorescent Proteins/metabolism , Isopropyl Thiogalactoside/pharmacology , Kinetics , Membrane Proteins/metabolism , Promoter Regions, Genetic , Recombinant Proteins/genetics , Recombinant Proteins/metabolism
9.
Proc Natl Acad Sci U S A ; 115(26): 6572-6577, 2018 06 26.
Article in English | MEDLINE | ID: mdl-29891706

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.


Subject(s)
Models, Biological , Morphogenesis/physiology , Pseudomonas aeruginosa/growth & development , 4-Butyrolactone/analogs & derivatives , 4-Butyrolactone/physiology , Bacterial Proteins/physiology , Binding, Competitive , Computer Simulation , Diffusion , Gene Expression Regulation, Bacterial , Genes, Reporter , Homoserine/analogs & derivatives , Homoserine/physiology , Isopropyl Thiogalactoside/pharmacology , Ligases/physiology , Morphogenesis/drug effects , Promoter Regions, Genetic/genetics , Pseudomonas aeruginosa/drug effects , Pseudomonas aeruginosa/metabolism , Quorum Sensing , Recombinant Proteins/metabolism , Stochastic Processes , Trans-Activators/physiology , Transcription Factors/physiology
10.
J Cell Biochem ; 121(1): 125-134, 2020 01.
Article in English | MEDLINE | ID: mdl-31232490

ABSTRACT

Escherichia coli is frequently exploited for genetic manipulations and heterologous gene expression studies. We have evaluated the metabolic profile of E. coli strain BL21 (DE3) RIL CodonPlus after genetic modifications and subjecting to the production of recombinant protein. Three genetically variable E. coli cell types were studied, normal cells (susceptible to antibiotics) cultured in simple LB medium, cells harboring ampicillin-resistant plasmid pET21a (+), grown under antibiotic stress, and cells having recombinant plasmid pET21a (+) ligated with bacterial lactate dehydrogenase gene grown under ampicillin and standard isopropyl thiogalactoside (IPTG)-induced gene expression conditions. A total of 592 metabolites were identified through liquid chromatography-mass spectrometry/mass spectrometry analysis, feature and peak detection using XCMS and CAMERA followed by precursor identification by METLIN-based procedures. Overall, 107 metabolites were found differentially regulated among genetically modified cells. Quantitative analysis has shown a significant modulation in DHNA-CoA, p-aminobenzoic acid, and citrulline levels, indicating an alteration in vitamin K, folic acid biosynthesis, and urea cycle of E. coli cells during heterologous gene expression. Modulations in energy metabolites including NADH, AMP, ADP, ATP, carbohydrate, terpenoids, fatty acid metabolites, diadenosine tetraphosphate (Ap4A), and l-carnitine advocate major metabolic rearrangements. Our study provides a broader insight into the metabolic adaptations of bacterial cells during gene manipulation experiments that can be prolonged to improve the yield of heterologous gene products and concomitant production of valuable biomolecules.


Subject(s)
Escherichia coli/metabolism , Gene Expression Profiling , Gene Expression Regulation, Bacterial , Metabolome , 4-Aminobenzoic Acid/pharmacology , Ampicillin/pharmacology , Anti-Bacterial Agents/pharmacology , Carbohydrates/chemistry , Chromatography, Ion Exchange , Chromatography, Liquid , Citrulline/metabolism , Citrulline/pharmacology , Codon , Coenzyme A/metabolism , Drug Resistance, Bacterial , Escherichia coli/genetics , Escherichia coli Proteins/metabolism , Folic Acid/metabolism , Isopropyl Thiogalactoside/pharmacology , Metabolomics , Oxo-Acid-Lyases/metabolism , Recombinant Proteins/metabolism , Tandem Mass Spectrometry , Terpenes/metabolism , Urea/metabolism , Vitamin K/metabolism
11.
Protein Expr Purif ; 170: 105593, 2020 06.
Article in English | MEDLINE | ID: mdl-32032772

ABSTRACT

Cost-effectiveness is an important issue in biotechnological manufacturing industry and using alternative cheap materials with the same benefits has been noticed in most literatures. Isopropyl ß-d-1-thiogalactopyranoside (IPTG), a well-known chemical element for induction of protein expression, has several disadvantages such as high expense and toxicity. In this study, we aimed to introduce skimmed milk as an alternative material for protein expression by induction of lac operon. In this way, Escherichia coli BL21 (DE3) bacteria were induced using 1 mM IPTG or 1.0% (w/v) skimmed milk. Protein purification was performed using Ni-NTA (nickel-nitrilotriacetic acid) for His-tagged recombinant proteins and protein purity was evaluated by SDS-PAGE. Results showed high level of recombinant protein expression using skimmed milk, and interestingly, the growth rate of bacteria improved. Our findings suggested that skimmed milk can be a suitable alternative for induction of recombinant protein expression, which has advantages such as more availability and affordability, in comparison to IPTG supplementation.


Subject(s)
Bacterial Proteins/genetics , Escherichia coli/drug effects , Flagellin/genetics , Lactose/pharmacology , Milk/chemistry , Recombinant Fusion Proteins/genetics , Animals , Bacterial Proteins/metabolism , Cloning, Molecular , Escherichia coli/genetics , Escherichia coli/metabolism , Flagellin/metabolism , Gene Expression , Genetic Vectors/chemistry , Genetic Vectors/metabolism , Histidine/genetics , Histidine/metabolism , Isopropyl Thiogalactoside/pharmacology , Lac Operon/drug effects , Oligopeptides/genetics , Oligopeptides/metabolism , Recombinant Fusion Proteins/metabolism , Salmonella typhimurium/chemistry
12.
Mol Biol Rep ; 47(8): 5943-5951, 2020 Aug.
Article in English | MEDLINE | ID: mdl-32696344

ABSTRACT

Escherichia coli is a widely-used cell factory for recombinant protein production, nevertheless, high amount of produced protein is seen in aggregated form. The purpose of this study was to improve the solubility of recombinant bovine sex-determining region Y protein (rbSRY) by exploring the effect of temperature, inducer, and water-arginine mixed solvent. Codon-optimized rbSRY expressed in Rosetta-gami B (DE3) pLysS and purified by NI-NTA His-select affinity chromatography in the native and denaturing conditions. A three-dimensional model of SRY was built and studied through molecular dynamics simulations in water and in the presence of L-arginine as co-solvent. Results indicated the significant effects of temperature and IPTG concentration (P < 0.001) on the solubility of rbSRY. The binding activity of native, inclusion bodies and refolded fractions to anti-rbSRY monoclonal antibody were concentration-dependent (P < 0.001). Based on molecular modeling results, the propensity of fragments in the N-terminal domain to form ß-sheet and the relative instability of α-helices in terminal domains are the probable reasons for the high aggregation potential of SRY, which are mitigated in the presence of L-arginine. Altogether, our rbSRY protein was properly produced and applying appropriate culture conditions could help enhance its solubility, refold inclusion bodies, and improve its activity upon refolding.


Subject(s)
Arginine/pharmacology , Sex-Determining Region Y Protein/chemistry , Animals , Antibodies, Monoclonal/immunology , Antibody Affinity , Antigen-Antibody Reactions , Cattle , Chromatography, Affinity , Cloning, Molecular , Escherichia coli , Genes, Synthetic , Isopropyl Thiogalactoside/pharmacology , Models, Molecular , Molecular Dynamics Simulation , Protein Conformation/drug effects , Protein Folding/drug effects , Recombinant Proteins/chemistry , Recombinant Proteins/isolation & purification , Sex-Determining Region Y Protein/genetics , Sex-Determining Region Y Protein/immunology , Sex-Determining Region Y Protein/isolation & purification , Solubility , Solvents , Temperature , Water
13.
Proc Natl Acad Sci U S A ; 114(9): 2200-2205, 2017 02 28.
Article in English | MEDLINE | ID: mdl-28202725

ABSTRACT

Living systems, such as bacteria, yeasts, and mammalian cells, can be genetically programmed with synthetic circuits that execute sensing, computing, memory, and response functions. Integrating these functional living components into materials and devices will provide powerful tools for scientific research and enable new technological applications. However, it has been a grand challenge to maintain the viability, functionality, and safety of living components in freestanding materials and devices, which frequently undergo deformations during applications. Here, we report the design of a set of living materials and devices based on stretchable, robust, and biocompatible hydrogel-elastomer hybrids that host various types of genetically engineered bacterial cells. The hydrogel provides sustainable supplies of water and nutrients, and the elastomer is air-permeable, maintaining long-term viability and functionality of the encapsulated cells. Communication between different bacterial strains and with the environment is achieved via diffusion of molecules in the hydrogel. The high stretchability and robustness of the hydrogel-elastomer hybrids prevent leakage of cells from the living materials and devices, even under large deformations. We show functions and applications of stretchable living sensors that are responsive to multiple chemicals in a variety of form factors, including skin patches and gloves-based sensors. We further develop a quantitative model that couples transportation of signaling molecules and cellular response to aid the design of future living materials and devices.


Subject(s)
Biocompatible Materials/chemical synthesis , Biosensing Techniques , Elastomers/chemical synthesis , Escherichia coli/chemistry , Green Fluorescent Proteins/genetics , Hydrogels/chemical synthesis , Acyl-Butyrolactones/analysis , Acyl-Butyrolactones/pharmacology , Biological Transport , Cells, Immobilized/metabolism , Chemical Engineering/methods , Escherichia coli/genetics , Escherichia coli/metabolism , Genes, Reporter , Green Fluorescent Proteins/metabolism , Isopropyl Thiogalactoside/analysis , Isopropyl Thiogalactoside/pharmacology , Quorum Sensing
14.
Mol Microbiol ; 108(5): 578-594, 2018 06.
Article in English | MEDLINE | ID: mdl-29537126

ABSTRACT

The Corynebacterium glutamicum R grtA (cgR_2936), grtB (cgR_2934) and grtC (cgR_2933) genes were identified as paralogs encoding glutamine-rich toxic proteins. We also identified a new antisense small RNA AsgR (antisense sRNA for grtA) that overlaps the 3' end of the grtA gene. Single over-expressions of grtA, grtB and grtC resulted in complete inhibition of Escherichia coli cell growth. This growth was rescued by co-expression of AsgR. Similar effects were observed in C. glutamicum, although the toxicities of these proteins were moderate. Inhibition of AsgR transcription resulted in increased levels and prolonged half-lives of grtA, grtB and grtC mRNAs. We also found that the expression levels of grtA, grtB and grtC were increased in an RNase III deletion mutant. Primer extension analysis revealed the RNase III cleavage site to be in the 3' untranslated region (3'-UTR) of the grtA mRNA. The expression levels of grtA, grtB and grtC were increased after exposure to several stresses, including heat shock, treatment with penicillin G, lysozyme or H2 O2 . The deletions of grtABC and asgR genes resulted in decreased survival rate under several stresses. These results indicate that GrtABC and AsgR constitute a type I toxin-antitoxin-like system in C. glutamicum.


Subject(s)
Bacterial Toxins/metabolism , Corynebacterium glutamicum/genetics , RNA, Antisense/metabolism , Sequence Deletion , Toxin-Antitoxin Systems/genetics , Amino Acid Sequence , Bacterial Toxins/genetics , Corynebacterium glutamicum/drug effects , Escherichia coli/drug effects , Escherichia coli/genetics , Escherichia coli/physiology , Glutamine/metabolism , Hydrogen Peroxide/pharmacology , Isopropyl Thiogalactoside/pharmacology , Penicillin G/pharmacology , RNA, Antisense/genetics , Stress, Physiological/drug effects , Toxin-Antitoxin Systems/drug effects
15.
Mol Microbiol ; 109(5): 663-675, 2018 09.
Article in English | MEDLINE | ID: mdl-29995987

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.


Subject(s)
Bacterial Proteins/metabolism , DNA Transformation Competence/physiology , Membrane Proteins/metabolism , Streptococcus pneumoniae/physiology , Streptococcus pneumoniae/pathogenicity , Transformation, Bacterial/physiology , Adaptation, Physiological , Bacterial Proteins/genetics , DNA Primers/genetics , DNA Primers/metabolism , DNA Transformation Competence/drug effects , DNA, Single-Stranded/genetics , DNA, Single-Stranded/metabolism , Homologous Recombination , Humans , Isopropyl Thiogalactoside/pharmacology , Membrane Proteins/genetics , Rec A Recombinases/genetics , Rec A Recombinases/metabolism , Streptococcus pneumoniae/drug effects , Streptococcus pneumoniae/genetics , Transformation, Bacterial/drug effects
16.
Plasmid ; 103: 53-62, 2019 05.
Article in English | MEDLINE | ID: mdl-31047915

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.


Subject(s)
CRISPR-Cas Systems , Escherichia coli/genetics , Gene Editing/methods , Gene Expression Regulation, Bacterial/drug effects , Genome, Bacterial , Plasmids/chemistry , Base Sequence , CRISPR-Associated Protein 9/genetics , CRISPR-Associated Protein 9/metabolism , Escherichia coli/drug effects , Escherichia coli/metabolism , Isopropyl Thiogalactoside/pharmacology , Mutation , Plasmids/metabolism , RNA, Guide, Kinetoplastida/genetics , RNA, Guide, Kinetoplastida/metabolism , Replication Origin , Streptomycin/pharmacology , Temperature
17.
Plasmid ; 103: 25-35, 2019 05.
Article in English | MEDLINE | ID: mdl-30954454

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.


Subject(s)
Bacterial Proteins/genetics , CRISPR-Cas Systems , Corynebacterium glutamicum/genetics , Gene Expression Regulation, Bacterial/drug effects , Gene Targeting/methods , Plasmids/chemistry , Arginine/biosynthesis , Argininosuccinate Lyase/genetics , Argininosuccinate Lyase/metabolism , Bacterial Proteins/metabolism , Base Pairing , Base Sequence , CRISPR-Associated Protein 9/genetics , CRISPR-Associated Protein 9/metabolism , Citrulline/biosynthesis , Corynebacterium glutamicum/drug effects , Corynebacterium glutamicum/metabolism , Glucose-6-Phosphate Isomerase/genetics , Glucose-6-Phosphate Isomerase/metabolism , Isopropyl Thiogalactoside/pharmacology , Plasmids/metabolism , RNA, Guide, Kinetoplastida/genetics , RNA, Guide, Kinetoplastida/metabolism , Tetracyclines/pharmacology
18.
Curr Microbiol ; 76(12): 1477-1486, 2019 Dec.
Article in English | MEDLINE | ID: mdl-31612259

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.


Subject(s)
Bacillus subtilis/genetics , Cysteine Endopeptidases/genetics , Cytoplasm/metabolism , Industrial Microbiology/methods , Promoter Regions, Genetic/genetics , Recombinant Fusion Proteins/genetics , Rhinovirus/enzymology , Viral Proteins/genetics , 3C Viral Proteases , Bacillus subtilis/metabolism , Cloning, Molecular , Cysteine Endopeptidases/isolation & purification , Gene Expression/drug effects , Green Fluorescent Proteins/genetics , Isopropyl Thiogalactoside/pharmacology , Lysine-tRNA Ligase/genetics , Recombinant Fusion Proteins/isolation & purification , Recombinant Fusion Proteins/metabolism , Rhinovirus/genetics , Solubility , Viral Proteins/isolation & purification , beta-Galactosidase/genetics
19.
J Basic Microbiol ; 59(4): 359-367, 2019 Apr.
Article in English | MEDLINE | ID: mdl-30672599

ABSTRACT

An agarase gene (agaM1) was cloned, expressed and characterized by using Escherichia coli as host strain, revealing the outstanding properties of recombinant AgaM1 (rAgaM1) in agarose degradation and neoagaro-oligosaccharides (NAs) production in our previous work. In current study, agaM1 was extracellularly expressed in Bacillus subtilis, and we aim to assess the ability of the supernatant of recombinant B. subtilis fermentation broth containing rAgaM1 to degrade agarose without protein purification, which would save the cost of purification and avoid the activity loss during purification. The pH and temperature optima for the supernatant were 7.0 and 50 °C, respectively. The supernatant containing rAgaM1 has outstanding stability against 40 °C and 50 °C. Besides, we detailedly studied the possible influence factors of rAgaM1 expression in the supernatant, including pH, temperature, isopropyl ß-D-thiogalactoside (IPTG) concentration, initial optical density at a wavelength of 600 nm (OD600 ), and induction time, and the optimum conditions for rAgaM1 expression by B. subtilis were confirmed. Moreover, the supernatant was able to produce NAs by using the Gracilaria lemaneiformis, whose cells were broken by autoclaving, as substrate, and a total of 1.41 µmol ml-1 of NA, including neoagarotetraose and neoagarohexaose, was produced after degradation for 48 h. This ability could save the cost of substrates in NA production, although the method requires a further study. Our results reveal that the NAs with great potential in food and pharmaceutical industries could be inexpensive to make by the supernatant containing rAgaM1 of B. subtilis fermentation broth in the foreseeable future.


Subject(s)
Bacillus subtilis/enzymology , Bacillus subtilis/metabolism , Glycoside Hydrolases/metabolism , Oligosaccharides/biosynthesis , Bacillus subtilis/genetics , Culture Media , Enzyme Stability , Galactosides/metabolism , Gene Expression/drug effects , Glycoside Hydrolases/genetics , Hydrogen-Ion Concentration , Isopropyl Thiogalactoside/chemistry , Isopropyl Thiogalactoside/pharmacology , Oligosaccharides/metabolism , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Sepharose/metabolism , Temperature
20.
J Cell Mol Med ; 22(5): 2631-2643, 2018 05.
Article in English | MEDLINE | ID: mdl-29502342

ABSTRACT

Caveolin-1 (Cav1) is down-regulated during MK4 (MDCK cells harbouring inducible Ha-RasV12 gene) transformation by Ha-RasV12 . Cav1 overexpression abrogates the Ha-RasV12 -driven transformation of MK4 cells; however, the targeted down-regulation of Cav1 is not sufficient to mimic this transformation. Cav1-silenced cells, including MK4/shCav1 cells and MDCK/shCav1 cells, showed an increased cell area and discontinuous junction-related proteins staining. Cellular and mechanical transformations were completed when MDCK/shCav1 cells were treated with medium conditioned by MK4 cells treated with IPTG (MK4+I-CM) but not with medium conditioned by MK4 cells. Nanoparticle tracking analysis showed that Ha-RasV12 -inducing MK4 cells increased exosome-like microvesicles release compared with their normal counterparts. The cellular and mechanical transformation activities of MK4+I-CM were abolished after heat treatment and exosome depletion and were copied by exosomes derived from MK4+I-CM (MK4+I-EXs). Wnt5a, a downstream product of Ha-RasV12 , was markedly secreted by MK4+I-CM and MK4+I-EXs. Suppression of Wnt5a expression and secretion using the porcupine inhibitor C59 or Wnt5a siRNA inhibited the Ha-RasV12 - and MK4+I-CM-induced transformation of MK4 cells and MDCK/shCav1 cells, respectively. Cav1 down-regulation, either by Ha-RasV12 or targeted shRNA, increased frizzled-2 (Fzd2) protein levels without affecting its mRNA levels, suggesting a novel role of Cav1 in negatively regulating Fzd2 expression. Additionally, silencing Cav1 facilitated the internalization of MK4+I-EXs in MDCK cells. These data suggest that Cav1-dependent repression of Fzd2 and exosome uptake is potentially relevant to its antitransformation activity, which hinders the activation of Ha-RasV12 -Wnt5a-Stat3 pathway. Altogether, these results suggest that both decreasing Cav1 and increasing exosomal Wnt5a must be implemented during Ha-RasV12 -driven cell transformation.


Subject(s)
Caveolin 1/genetics , Cell Transformation, Neoplastic/genetics , Down-Regulation/genetics , Frizzled Receptors/metabolism , Signal Transduction , Wnt-5a Protein/metabolism , ras Proteins/metabolism , Animals , Cell Transformation, Neoplastic/drug effects , Cell Transformation, Neoplastic/pathology , Culture Media, Conditioned/pharmacology , Dogs , Down-Regulation/drug effects , Exosomes/drug effects , Exosomes/metabolism , Humans , Isopropyl Thiogalactoside/pharmacology , Madin Darby Canine Kidney Cells , STAT3 Transcription Factor/metabolism , Up-Regulation/drug effects
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