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

Tomohiro Shimada, Eri Momiyama, Yuki Yamanaka, Hiroki Watanabe, Kaneyoshi Yamamoto, Akira Ishihama

Research output: Contribution to journalLetterpeer-review

12 Citations (Scopus)

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 the regulation network of XynR is still fixed within the CR4-6 prophage without significant influence over the host E. coli K-12.

Original languageEnglish
Article numberfnx220
JournalFEMS microbiology letters
Volume364
Issue number22
DOIs
Publication statusPublished - 1 Nov 2017

Keywords

  • Cryptic prophage
  • Escherichia coli K-12
  • Genomic SELEX
  • Transcription factor
  • Xylan utilization
  • Xylose catabolism

Fingerprint

Dive into the research topics of 'Regulatory role of XynR (YagI) in catabolism of xylonate in Escherichia coli K-12'. Together they form a unique fingerprint.

Cite this