Guide to Genome-Wide Bacterial Transcription Factor Binding Site Prediction Using OmpR as Model

Vuong, Phu; Misra, Rajeev

doi:10.5772/24321

Cited by 4 publications

(2 citation statements)

References 52 publications

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“…Moreover, these authors identified the "RstA motif" (TACA-N 6 -TACA) upstream of the S. Typhimurium feoA gene of the feo operon (35). Although OmpR recognition sequences are quite degenerate (36,37), one of the motifs-GTTACANNNN-resembles that of RstA (Fig. 5A).…”

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confidence: 99%

Roles of the EnvZ/OmpR Two-Component System and Porins in Iron Acquisition in Escherichia coli

Gerken

Vuong

Soparkar

et al. 2020

mBio

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Escherichia coli secretes high-affinity Fe3+ chelators to solubilize and transport chelated Fe3+ via specific outer membrane receptors. In microaerobic and anaerobic growth environments, where the reduced Fe2+ form is predominant, ferrous transport systems fulfill the bacterial need for iron. Expression of genes coding for iron metabolism is controlled by Fur, which when bound to Fe2+ acts as a repressor. Work carried out here shows that the constitutively activated EnvZ/OmpR two-component system, which normally controls expression of the ompC and ompF porin genes, dramatically increases the intracellular pool of accessible iron, as determined by whole-cell electron paramagnetic resonance spectroscopy, by inducing the OmpC/FeoB-mediated ferrous transport pathway. Elevated levels of intracellular iron in turn activated Fur, which inhibited the ferric transport pathway but not the ferrous transport pathway. The data show that the positive effect of constitutively activated EnvZ/OmpR on feoB expression is sufficient to overcome the negative effect of activated Fur on feoB. In a tonB mutant, which lacks functional ferric transport systems, deletion of ompR severely impairs growth on rich medium not supplemented with iron, while the simultaneous deletion of ompC and ompF is not viable. These data, together with the observation of derepression of the Fur regulon in an OmpC mutant, show that the porins play an important role in iron homeostasis. The work presented here also resolves a long-standing paradoxical observation of the effect of certain mutant envZ alleles on iron regulon. IMPORTANCE The work presented here solved a long-standing paradox of the negative effects of certain missense alleles of envZ, which codes for kinase of the EnvZ/OmpR two-component system, on the expression of ferric uptake genes. The data revealed that the constitutive envZ alleles activate the Feo- and OmpC-mediated ferrous uptake pathway to flood the cytoplasm with accessible ferrous iron. This activates the ferric uptake regulator, Fur, which inhibits ferric uptake system but cannot inhibit the feo operon due to the positive effect of activated EnvZ/OmpR. The data also revealed the importance of porins in iron homeostasis.

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confidence: 99%

Roles of the EnvZ/OmpR Two-Component System and Porins in Iron Acquisition in Escherichia coli

Gerken

Vuong

Soparkar

et al. 2020

mBio

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“…Since the 1980s, intense research efforts have been made in this field. For prokaryotes, efficient and performant methods have been obtained (Vuong and Misr, 2011) while for most of the multicellular eukaryotes there is still a need for further development. The main difficulty for the latter organisms relies on the length of the cis-regulatory regions, which are longer than in prokaryotes (Hardison and Taylor, 2012).…”

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Exploiting Genomic Features to Improve the Prediction of Transcription Factor-Binding Sites in Plants

Rivière

Corso

Ciortan

et al. 2022

Plant and Cell Physiology

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The identification of transcription factor (TF) target genes is central in biology. A popular approach is based on the location by pattern-matching of potential cis-regulatory elements (CREs). During the last few years, tools integrating next-generation sequencing data have been developed to improve the performances of pattern-matching. However, such tools have not yet been comprehensively evaluated in plants. Hence, we developed a new streamlined method aiming at predicting CREs and target genes of plant TFs in specific organs or conditions. Our approach implements a supervised machine learning strategy, which allows to learn decision rule models using TF ChIP-chip/seq experimental data. Different layers of genomic features were integrated in predictive models: the position on the gene, the DNA-sequence conservation, the chromatin state, and various cis-regulatory element footprints. Among the tested features, the chromatin features were crucial for improving the accuracy of the method. Furthermore, we evaluated the transferability of predictive models across TFs, organs and species. Finally, we validated our method by correctly inferring the target genes of key TF controlling metabolite biosynthesis at the organ-level in Arabidopsis. We developed a tool -Wimtrap- to reproduce our approach in plant species and conditions/organs for which ChIP-chip/seq data are available. Wimtrap is a user-friendly R package that supports a R-shiny web interface and is provided with pre-built models that can be used to quickly get predictions of CREs and TF gene targets in different organs or conditions in Arabidopsis thaliana, Solanum lycopersicum, Oryza sativa, and Zea mays.

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Roles of the EnvZ/OmpR Two-Component System and Porins in Iron Acquisition inEscherichia coli

Gerken

Vuong

Soparkar

et al. 2020

Preprint

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Escherichia coli secretes high-affinity Fe3+ chelators to solubilize and transport chelated Fe3+ via specific outer membrane receptors. In microaerobic and anaerobic growth environments, where the reduced Fe2+ form is predominant, ferrous transport systems fulfill the bacterial need for iron. Expression of genes coding for iron metabolism is controlled by Fur, which when bound to Fe2+ acts as a repressor. Work carried out in this paper shows that the constitutively activated EnvZ/OmpR two-component system, which normally controls expression of the ompC and ompF porin genes, dramatically increases the intracellular pool of accessible iron, as determined by whole-cell electron paramagnetic resonance (EPR) spectroscopy, by inducing the OmpC/FeoB-mediated ferrous transport pathway. Elevated levels of intracellular iron in turn activated Fur, which inhibited the ferric but not the ferrous transport pathway. The data show that the positive effect of constitutively activated EnvZ/OmpR on feoB expression is sufficient to overcome the negative effect of activated Fur on feoB. In a tonB mutant, which lacks functional ferric transport systems, deletion of ompR severely impairs growth on rich medium not supplemented with iron, while the simultaneous deletion of ompC and ompF is not viable. These data, together with the observation of de-repression of the Fur regulon in an OmpC mutant, show that the porins play an important role in iron homeostasis. The work presented here also resolves a long-standing paradoxical observation of the effect of certain mutant envZ alleles on iron regulon.IMPORTANCEThe work presented here solved a long-standing paradox of the negative effects of certain missense alleles of envZ, which codes for kinase of the EnvZ/OmpR two component system, on the expression of ferric uptake genes. The data revealed that the constitutive envZ alleles activate the Feo- and OmpC-mediated ferrous uptake pathway to flood the cytoplasm with accessible ferrous iron. This activates the ferric uptake regulator, Fur, which inhibits ferric uptake system but cannot inhibit the feo operon due to the positive effect of activated EnvZ/OmpR. The data also revealed importance of porins in iron homeostasis.

show abstract

Guide to Genome-Wide Bacterial Transcription Factor Binding Site Prediction Using OmpR as Model

Cited by 4 publications

References 52 publications

Roles of the EnvZ/OmpR Two-Component System and Porins in Iron Acquisition in Escherichia coli

Roles of the EnvZ/OmpR Two-Component System and Porins in Iron Acquisition in Escherichia coli

Exploiting Genomic Features to Improve the Prediction of Transcription Factor-Binding Sites in Plants

Roles of the EnvZ/OmpR Two-Component System and Porins in Iron Acquisition inEscherichia coli

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