Regulatory role of XynR (YagI) in catabolism of xylonate in Escherichia coli K-12

FEMS Microbiology Letters
Tomohiro ShimadaAkira Ishihama

Abstract

The genome of Escherichia coli K-12 contains ten cryptic phages, altogether constituting about 3.6% of the genome in sequence. Among more than 200 predicted genes in these cryptic phages, 14 putative transcription factor (TF) genes exist, but their regulatory functions remain unidentified. As an initial attempt to make a breakthrough for understanding the regulatory roles of cryptic phage-encoded TFs, we tried to identify the regulatory function of CP4-6 cryptic prophage-encoded YagI with unknown function. After SELEX screening, YagI was found to bind mainly at a single site within the spacer of bidirectional transcription units, yagA (encoding another uncharacterized TF) and yagEF (encoding 2-keto-3-deoxy gluconate aldolase, and dehydratase, respectively) within this prophage region. YagEF enzymes are involved in the catabolism of xylose downstream from xylonate. We then designated YagI as XynR (regulator of xylonate catabolism), one of the rare single-target TFs. In agreement with this predicted regulatory function, the activity of XynR was suggested to be controlled by xylonate. Even though low-affinity binding sites of XynR were identified in the E. coli K-12 genome, they all were inside open reading frames, implying that t...Continue Reading

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Citations

Mar 13, 2018·Nucleic Acids Research·Tomohiro ShimadaAkira Ishihama
Apr 16, 2020·Microbial Cell Factories·Zhongxi ZhangJian Hao
Jul 14, 2018·Applied Microbiology and Biotechnology·Kris Niño G ValdehuesaWook-Jin Chung
Aug 24, 2018·Nucleic Acids Research·Ye GaoBernhard O Palsson
Jan 2, 2020·Scientific Reports·Tomohiro ShimadaAkira Ishihama
Jul 4, 2021·Applied Microbiology and Biotechnology·Angelo B BañaresWook-Jin Chung

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