The Experts below are selected from a list of 3537 Experts worldwide ranked by ideXlab platform
Fenfei Leng - One of the best experts on this subject based on the ideXlab platform.
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direct observation of a 91 bp Laci mediated negatively supercoiled dna loop by atomic force microscope
FEBS Letters, 2016Co-Authors: Geraldine Fulcrand, Prem P Chapagain, David Dunlap, Fenfei LengAbstract:Escherichia coli Lactose repressor (LacI), a tetrameric protein, is a paradigmatic transcriptional factor that controls the expression of LacZYA in the Lac Operon. It specifically binds to the O1, O2, and O3 operators of the Lac promoter, forms DNA loops, and regulates transcription of the Lac Operon. In this article, utilizing combined techniques of DNA-nicking assay and AFM imaging, we directly observed a 91 bp LacI-mediated, negatively supercoiled DNA loop mimicking the DNA loop between the O1 and O3 operators in the Lac promoter.
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dna supercoiling a critical signal regulating the basal expression of the Lac Operon in escherichia coli
Scientific Reports, 2016Co-Authors: Geraldine Fulcrand, Prem P Chapagain, David Dunlap, Samantha Dages, Xiaoduo Zhi, Bernard S Gerstman, Fenfei LengAbstract:Escherichia coli Lac repressor (LacI) is a paradigmatic transcriptional factor that controls the expression of LacZYA in the Lac Operon. This tetrameric protein specifically binds to the O1, O2 and O3 operators of the Lac Operon and forms a DNA loop to repress transcription from the adjacent Lac promoter. In this article, we demonstrate that upon binding to the O1 and O2 operators at their native positions LacI constrains three (-) supercoils within the 401-bp DNA loop of the Lac promoter and forms a topological barrier. The stability of LacI-mediated DNA topological barriers is directly proportional to its DNA binding affinity. However, we find that DNA supercoiling modulates the basal expression from the Lac Operon in E. coli. Our results are consistent with the hypothesis that LacI functions as a topological barrier to constrain free, unconstrained (-) supercoils within the 401-bp DNA loop of the Lac promoter. These constrained (-) supercoils enhance LacI's DNA-binding affinity and thereby the repression of the promoter. Thus, LacI binding is superhelically modulated to control the expression of LacZYA in the Lac Operon under varying growth conditions.
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Lactose repressor functions as a dna topological barrier in escherichia coli Lactose Operon
Biophysical Journal, 2013Co-Authors: Geraldine Fulcrand, Steven Eichelbaum, Fenfei LengAbstract:Escherichia coli Lac repressor (LacI) is a paradigm transcriptional factor that controls the expression of three genes in the Lac Operon. It is a tetrameric protein, specifically binds to Lac operators, such as O1, O2 and O3, and forms a DNA loop to negatively control transcription initiation. Previously, we found that LacI upon binding to multiple LacO1 operators is capable of acting as a DNA topological barrier to block DNA supercoil diffusion and dividing a supercoiled DNA molecule into two independent topological domains (Leng et al. (2011) Proc Natl Acad Sci USA 108: 19973-78). In this study, we showed that LacI is able to function as a topological barrier and block supercoil diffusion upon binding to O1, O2, and O3 operators in the Lac Operon. Specifically, we demonstrated that LacI kept two supercoils within the 401 bp DNA-loop between O1 and O2 operators. Additionally, We carried out time course studies to determine the stability of the topological barriers that are produced by the different LacI-operator complexes. Our results showed that the stability of the topological barriers correlates with the DNA-binding affinity of LacI to the different operators i.e., O1, O2, O3, and Os operators. Furthermore, we confirmed our previous observation in which LacI is able to “keep” certain superhelical energy to stabilize LacI-LacO1 complexes. Our results can be explained by a model in which LacI behaves as a topological barrier in the Lac Operon to regulate the expression of LacZYA genes in Escherichia coli cells.
Patrick J Biggs - One of the best experts on this subject based on the ideXlab platform.
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Insights into the Geobacillus stearothermophilus species based on phylogenomic principles
BMC Microbiology, 2017Co-Authors: Sara A Burgess, D Lindsay, Steve Flint, Patrick J BiggsAbstract:The genus Geobacillus comprises bacteria that are Gram positive, thermophilic spore-formers, which are found in a variety of environments from hot-springs, cool soils, to food manufacturing plants, including dairy manufacturing plants. Despite considerable interest in the use of Geobacillus spp. for biotechnological applications, the taxonomy of this genus is unclear, in part because of differences in DNA-DNA hybridization (DDH) similarity values between studies. In addition, it is also difficult to use phenotypic characteristics to define a bacterial species. For example, G. stearothermophilus was traditionally defined as a species that does not utilise Lactose, but the ability of dairy strains of G. stearothermophilus to use Lactose has now been well established. This study compared the genome sequences of 63 Geobacillus isolates and showed that based on two different genomic approaches (core genome comparisons and average nucleotide identity) the Geobacillus genus could be divided into sixteen taxa for those Geobacillus strains that have genome sequences available thus far. In addition, using Geobacillus stearothermophilus as an example, we show that inclusion of the accessory genome, as well as phenotypic characteristics, is not suitable for defining this species. For example, this is the first study to provide evidence of dairy adaptation in G. stearothermophilus - a phenotypic feature not typically considered standard in this species - by identifying the presence of a putative Lac Operon in four dairy strains. The traditional polyphasic approach of combining both genotypic and phenotypic characteristics to define a bacterial species could not be used for G. stearothermophilus where many phenotypic characteristics vary within this taxon. Further evidence of this discordant use of phenotypic traits was provided by analysis of the accessory genome, where the dairy strains contained a putative Lac Operon. Based on the findings from this study, we recommend that novel bacterial species should be defined using a core genome approach.
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Insights into the Geobacillus stearothermophilus species based on phylogenomic principles
'Springer Science and Business Media LLC', 2017Co-Authors: Sara A Burgess, D Lindsay, S. H. Flint, M. P. Cox, Patrick J BiggsAbstract:Abstract Background The genus Geobacillus comprises bacteria that are Gram positive, thermophilic spore-formers, which are found in a variety of environments from hot-springs, cool soils, to food manufacturing plants, including dairy manufacturing plants. Despite considerable interest in the use of Geobacillus spp. for biotechnological applications, the taxonomy of this genus is unclear, in part because of differences in DNA-DNA hybridization (DDH) similarity values between studies. In addition, it is also difficult to use phenotypic characteristics to define a bacterial species. For example, G. stearothermophilus was traditionally defined as a species that does not utilise Lactose, but the ability of dairy strains of G. stearothermophilus to use Lactose has now been well established. Results This study compared the genome sequences of 63 Geobacillus isolates and showed that based on two different genomic approaches (core genome comparisons and average nucleotide identity) the Geobacillus genus could be divided into sixteen taxa for those Geobacillus strains that have genome sequences available thus far. In addition, using Geobacillus stearothermophilus as an example, we show that inclusion of the accessory genome, as well as phenotypic characteristics, is not suitable for defining this species. For example, this is the first study to provide evidence of dairy adaptation in G. stearothermophilus - a phenotypic feature not typically considered standard in this species - by identifying the presence of a putative Lac Operon in four dairy strains. Conclusions The traditional polyphasic approach of combining both genotypic and phenotypic characteristics to define a bacterial species could not be used for G. stearothermophilus where many phenotypic characteristics vary within this taxon. Further evidence of this discordant use of phenotypic traits was provided by analysis of the accessory genome, where the dairy strains contained a putative Lac Operon. Based on the findings from this study, we recommend that novel bacterial species should be defined using a core genome approach
Geraldine Fulcrand - One of the best experts on this subject based on the ideXlab platform.
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direct observation of a 91 bp Laci mediated negatively supercoiled dna loop by atomic force microscope
FEBS Letters, 2016Co-Authors: Geraldine Fulcrand, Prem P Chapagain, David Dunlap, Fenfei LengAbstract:Escherichia coli Lactose repressor (LacI), a tetrameric protein, is a paradigmatic transcriptional factor that controls the expression of LacZYA in the Lac Operon. It specifically binds to the O1, O2, and O3 operators of the Lac promoter, forms DNA loops, and regulates transcription of the Lac Operon. In this article, utilizing combined techniques of DNA-nicking assay and AFM imaging, we directly observed a 91 bp LacI-mediated, negatively supercoiled DNA loop mimicking the DNA loop between the O1 and O3 operators in the Lac promoter.
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dna supercoiling a critical signal regulating the basal expression of the Lac Operon in escherichia coli
Scientific Reports, 2016Co-Authors: Geraldine Fulcrand, Prem P Chapagain, David Dunlap, Samantha Dages, Xiaoduo Zhi, Bernard S Gerstman, Fenfei LengAbstract:Escherichia coli Lac repressor (LacI) is a paradigmatic transcriptional factor that controls the expression of LacZYA in the Lac Operon. This tetrameric protein specifically binds to the O1, O2 and O3 operators of the Lac Operon and forms a DNA loop to repress transcription from the adjacent Lac promoter. In this article, we demonstrate that upon binding to the O1 and O2 operators at their native positions LacI constrains three (-) supercoils within the 401-bp DNA loop of the Lac promoter and forms a topological barrier. The stability of LacI-mediated DNA topological barriers is directly proportional to its DNA binding affinity. However, we find that DNA supercoiling modulates the basal expression from the Lac Operon in E. coli. Our results are consistent with the hypothesis that LacI functions as a topological barrier to constrain free, unconstrained (-) supercoils within the 401-bp DNA loop of the Lac promoter. These constrained (-) supercoils enhance LacI's DNA-binding affinity and thereby the repression of the promoter. Thus, LacI binding is superhelically modulated to control the expression of LacZYA in the Lac Operon under varying growth conditions.
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Lactose repressor functions as a dna topological barrier in escherichia coli Lactose Operon
Biophysical Journal, 2013Co-Authors: Geraldine Fulcrand, Steven Eichelbaum, Fenfei LengAbstract:Escherichia coli Lac repressor (LacI) is a paradigm transcriptional factor that controls the expression of three genes in the Lac Operon. It is a tetrameric protein, specifically binds to Lac operators, such as O1, O2 and O3, and forms a DNA loop to negatively control transcription initiation. Previously, we found that LacI upon binding to multiple LacO1 operators is capable of acting as a DNA topological barrier to block DNA supercoil diffusion and dividing a supercoiled DNA molecule into two independent topological domains (Leng et al. (2011) Proc Natl Acad Sci USA 108: 19973-78). In this study, we showed that LacI is able to function as a topological barrier and block supercoil diffusion upon binding to O1, O2, and O3 operators in the Lac Operon. Specifically, we demonstrated that LacI kept two supercoils within the 401 bp DNA-loop between O1 and O2 operators. Additionally, We carried out time course studies to determine the stability of the topological barriers that are produced by the different LacI-operator complexes. Our results showed that the stability of the topological barriers correlates with the DNA-binding affinity of LacI to the different operators i.e., O1, O2, O3, and Os operators. Furthermore, we confirmed our previous observation in which LacI is able to “keep” certain superhelical energy to stabilize LacI-LacO1 complexes. Our results can be explained by a model in which LacI behaves as a topological barrier in the Lac Operon to regulate the expression of LacZYA genes in Escherichia coli cells.
Sara A Burgess - One of the best experts on this subject based on the ideXlab platform.
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Insights into the Geobacillus stearothermophilus species based on phylogenomic principles
BMC Microbiology, 2017Co-Authors: Sara A Burgess, D Lindsay, Steve Flint, Patrick J BiggsAbstract:The genus Geobacillus comprises bacteria that are Gram positive, thermophilic spore-formers, which are found in a variety of environments from hot-springs, cool soils, to food manufacturing plants, including dairy manufacturing plants. Despite considerable interest in the use of Geobacillus spp. for biotechnological applications, the taxonomy of this genus is unclear, in part because of differences in DNA-DNA hybridization (DDH) similarity values between studies. In addition, it is also difficult to use phenotypic characteristics to define a bacterial species. For example, G. stearothermophilus was traditionally defined as a species that does not utilise Lactose, but the ability of dairy strains of G. stearothermophilus to use Lactose has now been well established. This study compared the genome sequences of 63 Geobacillus isolates and showed that based on two different genomic approaches (core genome comparisons and average nucleotide identity) the Geobacillus genus could be divided into sixteen taxa for those Geobacillus strains that have genome sequences available thus far. In addition, using Geobacillus stearothermophilus as an example, we show that inclusion of the accessory genome, as well as phenotypic characteristics, is not suitable for defining this species. For example, this is the first study to provide evidence of dairy adaptation in G. stearothermophilus - a phenotypic feature not typically considered standard in this species - by identifying the presence of a putative Lac Operon in four dairy strains. The traditional polyphasic approach of combining both genotypic and phenotypic characteristics to define a bacterial species could not be used for G. stearothermophilus where many phenotypic characteristics vary within this taxon. Further evidence of this discordant use of phenotypic traits was provided by analysis of the accessory genome, where the dairy strains contained a putative Lac Operon. Based on the findings from this study, we recommend that novel bacterial species should be defined using a core genome approach.
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Insights into the Geobacillus stearothermophilus species based on phylogenomic principles
'Springer Science and Business Media LLC', 2017Co-Authors: Sara A Burgess, D Lindsay, S. H. Flint, M. P. Cox, Patrick J BiggsAbstract:Abstract Background The genus Geobacillus comprises bacteria that are Gram positive, thermophilic spore-formers, which are found in a variety of environments from hot-springs, cool soils, to food manufacturing plants, including dairy manufacturing plants. Despite considerable interest in the use of Geobacillus spp. for biotechnological applications, the taxonomy of this genus is unclear, in part because of differences in DNA-DNA hybridization (DDH) similarity values between studies. In addition, it is also difficult to use phenotypic characteristics to define a bacterial species. For example, G. stearothermophilus was traditionally defined as a species that does not utilise Lactose, but the ability of dairy strains of G. stearothermophilus to use Lactose has now been well established. Results This study compared the genome sequences of 63 Geobacillus isolates and showed that based on two different genomic approaches (core genome comparisons and average nucleotide identity) the Geobacillus genus could be divided into sixteen taxa for those Geobacillus strains that have genome sequences available thus far. In addition, using Geobacillus stearothermophilus as an example, we show that inclusion of the accessory genome, as well as phenotypic characteristics, is not suitable for defining this species. For example, this is the first study to provide evidence of dairy adaptation in G. stearothermophilus - a phenotypic feature not typically considered standard in this species - by identifying the presence of a putative Lac Operon in four dairy strains. Conclusions The traditional polyphasic approach of combining both genotypic and phenotypic characteristics to define a bacterial species could not be used for G. stearothermophilus where many phenotypic characteristics vary within this taxon. Further evidence of this discordant use of phenotypic traits was provided by analysis of the accessory genome, where the dairy strains contained a putative Lac Operon. Based on the findings from this study, we recommend that novel bacterial species should be defined using a core genome approach
Moises Santillan - One of the best experts on this subject based on the ideXlab platform.
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bistable behavior of the Lac Operon in e coli when induced with a mixture of Lactose and tmg
Frontiers in Physiology, 2010Co-Authors: Orlando Diazhernandez, Moises SantillanAbstract:In this work we investigate multistability in the Lac Operon of Escherichia coli when it is induced by a mixture of Lactose and the non-metabolizable thiomethyl gaLactoside (TMG). In accordance with previously published experimental results and computer simulations, our simulations predict that: (1) when the system is induced by TMG, the system shows a discernible bistable behavior while, (2) when the system is induced by Lactose, bistability does not disappear but excessively high concentrations of Lactose would be required to observe it. Finally, our simulation results predict that when a mixture of Lactose and TMG is used, the bistability region in the extracellular glucose concentration vs. extracellular Lactose concentration parameter space changes in such a way that the model predictions regarding bistability could be tested experimentally. These experiments could help to solve a recent controversy regarding the existence of bistability in the Lac Operon under natural conditions.
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origin of bistability in the Lac Operon
Biophysical Journal, 2007Co-Authors: Moises Santillan, Michael C Mackey, Eduardo S ZeronAbstract:Multistability is an emergent dynamic property that has been invoked to explain multiple coexisting biological states. In this work, we investigate the origin of bistability in the Lac Operon. To do this, we develop a mathematical model for the regulatory pathway in this system and compare the model predictions with other experimental results in which a nonmetabolizable inducer was employed. We investigate the effect of Lactose metabolism using this model, and show that it greatly modifies the bistable region in the external Lactose (Le) versus external glucose (Ge) parameter space. The model also predicts that Lactose metabolism can cause bistability to disappear for very low Ge. We have also carried out stochastic numerical simulations of the model for several values of Ge and Le. Our results indicate that bistability can help guarantee that Escherichia coli consumes glucose and Lactose in the most efficient possible way. Namely, the Lac Operon is induced only when there is almost no glucose in the growing medium, but if Le is high, the Operon induction level increases abruptly when the levels of glucose in the environment decrease to very low values. We demonstrate that this behavior could not be obtained without bistability if the stability of the induced and uninduced states is to be preserved. Finally, we point out that the present methods and results may be useful to study the emergence of multistability in biological systems other than the Lac Operon.
