A cAMP-independent carbohydrate-driven mechanism inhibits tnaA expression and TnaA enzyme activity in Escherichia coli

Li, Gang; Young, Kevin

doi:10.1099/mic.0.080705-0

Cited by 20 publications

(26 citation statements)

References 30 publications

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“…Furthermore, cAMP is actively transported out of a cell leading to a smaller concentration of intracellular cAMP. Following Kuhlman et al ., we will assume that the intracellular cAMP concentration is proportional to the extracellular concentration, namely, γ [ M ] (with 0 < γ < 1) [ 43 , 44 ]. Hence, the concentration of active CRP satisfies where the fraction of active CRP is given by Fig 2(A) as …”

Section: Resultsmentioning

confidence: 99%

Theoretical analysis of inducer and operator binding for cyclic-AMP receptor protein mutants

Einav¹,

Duque²,

Phillips³

2018

PLoS ONE

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Allosteric transcription factors undergo binding events at inducer binding sites as well as at distinct DNA binding domains, and it is difficult to disentangle the structural and functional consequences of these two classes of interactions. We compare the ability of two statistical mechanical models—the Monod-Wyman-Changeux (MWC) and the Koshland-Némethy-Filmer (KNF) models of protein conformational change—to characterize the multi-step activation mechanism of the broadly acting cyclic-AMP receptor protein (CRP). We first consider the allosteric transition resulting from cyclic-AMP binding to CRP, then analyze how CRP binds to its operator, and finally investigate the ability of CRP to activate gene expression. We use these models to examine a beautiful recent experiment that created a single-chain version of the CRP homodimer, creating six mutants using all possible combinations of the wild type, D53H, and S62F subunits. We demonstrate that the MWC model can explain the behavior of all six mutants using a small, self-consistent set of parameters whose complexity scales with the number of subunits, providing a significant benefit over previous models. In comparison, the KNF model not only leads to a poorer characterization of the available data but also fails to generate parameter values in line with the available structural knowledge of CRP. In addition, we discuss how the conceptual framework developed here for CRP enables us to not merely analyze data retrospectively, but has the predictive power to determine how combinations of mutations will interact, how double mutants will behave, and how each construct would regulate gene expression.

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Section: Resultsmentioning

confidence: 99%

Theoretical analysis of inducer and operator binding for cyclic-AMP receptor protein mutants

Einav¹,

Duque²,

Phillips³

2018

PLoS ONE

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“…38 ) to test indoxyl production under various carbon sources. Previous reports have shown that the expression and activity of TnaA, an E. coli enzyme required for conversion of tryptophan to indole, is repressed by glucose 8,39 , but not by glycerol 40 . Indeed, a glycerol-fed culture produced 400 mg/L indigo after 24 h growth in EZ Rich defined medium when an optimal concentration of tryptophan (over 15 mM or 3.1 g/L) was co-fed, whereas a culture grown with glucose instead of glycerol produced almost no indigo (Supplementary Fig.…”

Section: Resultsmentioning

confidence: 97%

Employing a biochemical protecting group for a sustainable indigo dyeing strategy

et al. 2018

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Indigo is an ancient dye uniquely capable of producing the signature tones in blue denim; however, the dyeing process requires chemical steps that are environmentally damaging. We describe a sustainable dyeing strategy that not only circumvents the use of toxic reagents for indigo chemical synthesis but also removes the need for a reducing agent for dye solubilization. This strategy utilizes a glucose moiety as a biochemical protecting group to stabilize the reactive indigo precursor indoxyl to form indican, preventing spontaneous oxidation to crystalline indigo during microbial fermentation. Application of a β-glucosidase removes the protecting group from indican, resulting in indigo crystal formation in the cotton fibers. We identified the gene coding for the glucosyltransferase PtUGT1 from the indigo plant Polygonum tinctorium and solved the structure of PtUGT1. Heterologous expression of PtUGT1 in Escherichia coli supported high indican conversion, and biosynthesized indican was used to dye cotton swatches and a garment.

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“…TnaC is a regulatory peptide encoded by the leader of the tnaAB operon, which codes tryptophanase (52,53). tnaC, tnaCA and tnaCAB transcripts were all down-regulated in the pcnB mutant (Supplementary Figure S11A and B, Supplementary Tables S2 and S3).…”

Section: Resultsmentioning

confidence: 99%

Landscape of RNA polyadenylation inE. coli

et al. 2016

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Polyadenylation is thought to be involved in the degradation and quality control of bacterial RNAs but relatively few examples have been investigated. We used a combination of 5΄-tagRACE and RNA-seq to analyze the total RNA content from a wild-type strain and from a poly(A)polymerase deleted mutant. A total of 178 transcripts were either up- or down-regulated in the mutant when compared to the wild-type strain. Poly(A)polymerase up-regulates the expression of all genes related to the FliA regulon and several previously unknown transcripts, including numerous transporters. Notable down-regulation of genes in the expression of antigen 43 and components of the type 1 fimbriae was detected. The major consequence of the absence of poly(A)polymerase was the accumulation of numerous sRNAs, antisense transcripts, REP sequences and RNA fragments resulting from the processing of entire transcripts. A new algorithm to analyze the position and composition of post-transcriptional modifications based on the sequence of unencoded 3΄-ends, was developed to identify polyadenylated molecules. Overall our results shed new light on the broad spectrum of action of polyadenylation on gene expression and demonstrate the importance of poly(A) dependent degradation to remove structured RNA fragments.

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A cAMP-independent carbohydrate-driven mechanism inhibits tnaA expression and TnaA enzyme activity in Escherichia coli

Cited by 20 publications

References 30 publications

Theoretical analysis of inducer and operator binding for cyclic-AMP receptor protein mutants

Theoretical analysis of inducer and operator binding for cyclic-AMP receptor protein mutants

Employing a biochemical protecting group for a sustainable indigo dyeing strategy

Landscape of RNA polyadenylation inE. coli

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