Universität zu Köln

Roy, Ria Basu (2025). Elucidating the regulatory function of LysR-type transcription regulators in Escherichia coli. PhD thesis, Universität zu Köln.

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Abstract

LysR-type transcriptional regulators (LTTRs) constitute the most abundant group of transcription regulators in bacteria. In E. coli K-12, out of the 46 LTTRs, 29 are still partially characterised or completely uncharacterised with respect to their regulatory and functional role. For the majority of these poorly and uncharacterised LTTRs, information regarding the control of the LTTR’s expression and activity, and their target genes remains limited. In this work, I characterized a subset of these partially characterized or uncharacterized LTTRs with a focus on systematic characterization of the LTTR YdcI. Out of the 17 LTTRs selected for this study, 8 LTTRs were shown to be autoregulators and for 4 of them binding to their own promoter regions was shown. A comparative RNA-seq analysis revealed the presumptive target genes of 4 LTTRs (LrhA, YafC, YdcI and YhaJ). Additionally, validation of published ChIP-exo data of YdcI by EMSA identified 10 loci including iraP (responsible for stabilization of stress sigma factor), genes related to transport across the membrane and the TCA cycle as specific targets of this LTTR. A consensus DNA-binding motif for YdcI has also been identified in this work. Another finding of this study elucidates the role of alarmone ppGpp in induction of ydcI gene expression and the role of YdcI possibly acting as an H-NS antagonist for its target, iraP. Hence, this work highights the potential role of YdcI in E. coli in regulating the carbon flux in the TCA cycle in response to stress. Taken together, the findings of this work are of relevance to understand and decipher the complex regulatory network and potential functional implications of the partially characterized LTTRs in E. coli.

Item Type:	Thesis (PhD thesis)
Creators:	Creators Email ORCID ORCID Put Code Roy, Ria Basu riabasuroy3@gmail.com UNSPECIFIED UNSPECIFIED
URN:	urn:nbn:de:hbz:38-788757
Date:	2025
Language:	English
Faculty:	Faculty of Mathematics and Natural Sciences
Divisions:	Faculty of Mathematics and Natural Sciences > Department of Biology > Institute for Genetics
Subjects:	Life sciences
Uncontrolled Keywords:	Keywords Language Bacterial genetics UNSPECIFIED Transcription regulation UNSPECIFIED Escherichia coli UNSPECIFIED
Date of oral exam:	17 June 2025
Referee:	Name Academic Title Gehring, Niels Prof. Dr. Dohmen, Jürgen Prof. Dr.
Refereed:	Yes
URI:	http://kups.ub.uni-koeln.de/id/eprint/78875