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Adaptive Enzyme

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Edmund Maser – One of the best experts on this subject based on the ideXlab platform.

  • regulation of the steroid inducible 3α hydroxysteroid dehydrogenase carbonyl reductase gene incomamonas testosteroni
    Journal of Biological Chemistry, 2001
    Co-Authors: Guangming Xiong, Edmund Maser
    Abstract:

    Abstract The Comamonas testosteroni3α-hydroxysteroid dehydrogenase/carbonyl reductase gene (hsdA) codes for an Adaptive Enzyme in the degradation of steroid compounds. However, no information was available on the molecular regulation of steroid-inducible genes nor on the mechanism of steroid signaling in procaryotes. We, therefore, investigated thecis- and trans-acting elements ofhsdA expression to infer the mechanism of its molecular regulation by steroids. The gene was localized on a 5.257-kilobase EcoRI fragment of C. testosteroni chromosomal DNA. The promoter was characterized, and the transcriptional start site was identified. Two palindromic operator domains were found upstream of hsdA. A new gene coding for a trans-acting negative regulator (repressor A, RepA) ofhsdA expression was characterized. The specific interaction between RepA, testosterone, and the operator domain is demonstrated. From our results we conclude that hsdA is under negative transcriptional control by an adjacent gene product (RepA). Accordingly, induction of hsdA by steroids in fact is a derepression, where steroidal inducers bind to the repressor, thereby preventing its binding to the hsdA operator.

  • regulation of the steroid inducible 3α hydroxysteroid dehydrogenase carbonyl reductase gene in comamonas testosteroni
    Journal of Biological Chemistry, 2001
    Co-Authors: Guangming Xiong, Edmund Maser
    Abstract:

    Abstract The Comamonas testosteroni3α-hydroxysteroid dehydrogenase/carbonyl reductase gene (hsdA) codes for an Adaptive Enzyme in the degradation of steroid compounds. However, no information was available on the molecular regulation of steroid-inducible genes nor on the mechanism of steroid signaling in procaryotes. We, therefore, investigated thecis- and trans-acting elements ofhsdA expression to infer the mechanism of its molecular regulation by steroids. The gene was localized on a 5.257-kilobase EcoRI fragment of C. testosteroni chromosomal DNA. The promoter was characterized, and the transcriptional start site was identified. Two palindromic operator domains were found upstream of hsdA. A new gene coding for a trans-acting negative regulator (repressor A, RepA) ofhsdA expression was characterized. The specific interaction between RepA, testosterone, and the operator domain is demonstrated. From our results we conclude that hsdA is under negative transcriptional control by an adjacent gene product (RepA). Accordingly, induction of hsdA by steroids in fact is a derepression, where steroidal inducers bind to the repressor, thereby preventing its binding to the hsdA operator.

Ming-jing Hwang – One of the best experts on this subject based on the ideXlab platform.

  • Understanding system dynamics of an Adaptive Enzyme network from globally profiled kinetic parameters
    BMC Systems Biology, 2014
    Co-Authors: Austin Wt Chiang, Wei-chung Liu, Pep Charusanti, Ming-jing Hwang
    Abstract:

    Background A major challenge in mathematical modeling of biological systems is to determine how model parameters contribute to systems dynamics. As biological processes are often complex in nature, it is desirable to address this issue using a systematic approach. Here, we propose a simple methodology that first performs an enrichment test to find patterns in the values of globally profiled kinetic parameters with which a model can produce the required system dynamics; this is then followed by a statistical test to elucidate the association between individual parameters and different parts of the system’s dynamics. Results We demonstrate our methodology on a prototype biological system of perfect adaptation dynamics, namely the chemotaxis model for Escherichia coli . Our results agreed well with those derived from experimental data and theoretical studies in the literature. Using this model system, we showed that there are motifs in kinetic parameters and that these motifs are governed by constraints of the specified system dynamics. Conclusions A systematic approach based on enrichment statistical tests has been developed to elucidate the relationships between model parameters and the roles they play in affecting system dynamics of a prototype biological network. The proposed approach is generally applicable and therefore can find wide use in systems biology modeling research.

  • Understanding system dynamics of an Adaptive Enzyme network from globally profiled kinetic parameters
    BMC systems biology, 2014
    Co-Authors: Austin Wt Chiang, Wei-chung Liu, Pep Charusanti, Ming-jing Hwang
    Abstract:

    Background A major challenge in mathematical modeling of biological systems is to determine how model parameters contribute to systems dynamics. As biological processes are often complex in nature, it is desirable to address this issue using a systematic approach. Here, we propose a simple methodology that first performs an enrichment test to find patterns in the values of globally profiled kinetic parameters with which a model can produce the required system dynamics; this is then followed by a statistical test to elucidate the association between individual parameters and different parts of the system’s dynamics.

Guangming Xiong – One of the best experts on this subject based on the ideXlab platform.

  • regulation of the steroid inducible 3α hydroxysteroid dehydrogenase carbonyl reductase gene incomamonas testosteroni
    Journal of Biological Chemistry, 2001
    Co-Authors: Guangming Xiong, Edmund Maser
    Abstract:

    Abstract The Comamonas testosteroni3α-hydroxysteroid dehydrogenase/carbonyl reductase gene (hsdA) codes for an Adaptive Enzyme in the degradation of steroid compounds. However, no information was available on the molecular regulation of steroid-inducible genes nor on the mechanism of steroid signaling in procaryotes. We, therefore, investigated thecis- and trans-acting elements ofhsdA expression to infer the mechanism of its molecular regulation by steroids. The gene was localized on a 5.257-kilobase EcoRI fragment of C. testosteroni chromosomal DNA. The promoter was characterized, and the transcriptional start site was identified. Two palindromic operator domains were found upstream of hsdA. A new gene coding for a trans-acting negative regulator (repressor A, RepA) ofhsdA expression was characterized. The specific interaction between RepA, testosterone, and the operator domain is demonstrated. From our results we conclude that hsdA is under negative transcriptional control by an adjacent gene product (RepA). Accordingly, induction of hsdA by steroids in fact is a derepression, where steroidal inducers bind to the repressor, thereby preventing its binding to the hsdA operator.

  • regulation of the steroid inducible 3α hydroxysteroid dehydrogenase carbonyl reductase gene in comamonas testosteroni
    Journal of Biological Chemistry, 2001
    Co-Authors: Guangming Xiong, Edmund Maser
    Abstract:

    Abstract The Comamonas testosteroni3α-hydroxysteroid dehydrogenase/carbonyl reductase gene (hsdA) codes for an Adaptive Enzyme in the degradation of steroid compounds. However, no information was available on the molecular regulation of steroid-inducible genes nor on the mechanism of steroid signaling in procaryotes. We, therefore, investigated thecis- and trans-acting elements ofhsdA expression to infer the mechanism of its molecular regulation by steroids. The gene was localized on a 5.257-kilobase EcoRI fragment of C. testosteroni chromosomal DNA. The promoter was characterized, and the transcriptional start site was identified. Two palindromic operator domains were found upstream of hsdA. A new gene coding for a trans-acting negative regulator (repressor A, RepA) ofhsdA expression was characterized. The specific interaction between RepA, testosterone, and the operator domain is demonstrated. From our results we conclude that hsdA is under negative transcriptional control by an adjacent gene product (RepA). Accordingly, induction of hsdA by steroids in fact is a derepression, where steroidal inducers bind to the repressor, thereby preventing its binding to the hsdA operator.

Austin Wt Chiang – One of the best experts on this subject based on the ideXlab platform.

  • Understanding system dynamics of an Adaptive Enzyme network from globally profiled kinetic parameters
    BMC Systems Biology, 2014
    Co-Authors: Austin Wt Chiang, Wei-chung Liu, Pep Charusanti, Ming-jing Hwang
    Abstract:

    Background A major challenge in mathematical modeling of biological systems is to determine how model parameters contribute to systems dynamics. As biological processes are often complex in nature, it is desirable to address this issue using a systematic approach. Here, we propose a simple methodology that first performs an enrichment test to find patterns in the values of globally profiled kinetic parameters with which a model can produce the required system dynamics; this is then followed by a statistical test to elucidate the association between individual parameters and different parts of the system’s dynamics. Results We demonstrate our methodology on a prototype biological system of perfect adaptation dynamics, namely the chemotaxis model for Escherichia coli . Our results agreed well with those derived from experimental data and theoretical studies in the literature. Using this model system, we showed that there are motifs in kinetic parameters and that these motifs are governed by constraints of the specified system dynamics. Conclusions A systematic approach based on enrichment statistical tests has been developed to elucidate the relationships between model parameters and the roles they play in affecting system dynamics of a prototype biological network. The proposed approach is generally applicable and therefore can find wide use in systems biology modeling research.

  • Understanding system dynamics of an Adaptive Enzyme network from globally profiled kinetic parameters
    BMC systems biology, 2014
    Co-Authors: Austin Wt Chiang, Wei-chung Liu, Pep Charusanti, Ming-jing Hwang
    Abstract:

    Background A major challenge in mathematical modeling of biological systems is to determine how model parameters contribute to systems dynamics. As biological processes are often complex in nature, it is desirable to address this issue using a systematic approach. Here, we propose a simple methodology that first performs an enrichment test to find patterns in the values of globally profiled kinetic parameters with which a model can produce the required system dynamics; this is then followed by a statistical test to elucidate the association between individual parameters and different parts of the system’s dynamics.

Pep Charusanti – One of the best experts on this subject based on the ideXlab platform.

  • Understanding system dynamics of an Adaptive Enzyme network from globally profiled kinetic parameters
    BMC Systems Biology, 2014
    Co-Authors: Austin Wt Chiang, Wei-chung Liu, Pep Charusanti, Ming-jing Hwang
    Abstract:

    Background A major challenge in mathematical modeling of biological systems is to determine how model parameters contribute to systems dynamics. As biological processes are often complex in nature, it is desirable to address this issue using a systematic approach. Here, we propose a simple methodology that first performs an enrichment test to find patterns in the values of globally profiled kinetic parameters with which a model can produce the required system dynamics; this is then followed by a statistical test to elucidate the association between individual parameters and different parts of the system’s dynamics. Results We demonstrate our methodology on a prototype biological system of perfect adaptation dynamics, namely the chemotaxis model for Escherichia coli . Our results agreed well with those derived from experimental data and theoretical studies in the literature. Using this model system, we showed that there are motifs in kinetic parameters and that these motifs are governed by constraints of the specified system dynamics. Conclusions A systematic approach based on enrichment statistical tests has been developed to elucidate the relationships between model parameters and the roles they play in affecting system dynamics of a prototype biological network. The proposed approach is generally applicable and therefore can find wide use in systems biology modeling research.

  • Understanding system dynamics of an Adaptive Enzyme network from globally profiled kinetic parameters
    BMC systems biology, 2014
    Co-Authors: Austin Wt Chiang, Wei-chung Liu, Pep Charusanti, Ming-jing Hwang
    Abstract:

    Background A major challenge in mathematical modeling of biological systems is to determine how model parameters contribute to systems dynamics. As biological processes are often complex in nature, it is desirable to address this issue using a systematic approach. Here, we propose a simple methodology that first performs an enrichment test to find patterns in the values of globally profiled kinetic parameters with which a model can produce the required system dynamics; this is then followed by a statistical test to elucidate the association between individual parameters and different parts of the system’s dynamics.