Yilmaz, Cihan
(2022).
Molecular genetic and genomic analyses of the dual-function transcription regulator PdeL in E. coli.
PhD thesis, Universität zu Köln.
Abstract
PdeL is a transcription regulator and one of 13 phosphodiesterases in Escherichia coli K-12.
Phosphodiesterases hydrolyze the ubiquitous bacterial second messenger cyclic-di-GMP and
contribute to its signaling involving bacterial lifestyle and other processes. PdeL is characterized
by the presence of an N-terminal FixJ/NarL-type DNA-binding domain linked to a catalytically
active, cyclic-di-GMP specific, EAL-type phosphodiesterase (PDE) domain. PdeL has been shown
to positively autoregulate its own expression. No further loci have yet been shown to be
regulated by PdeL.
In this work, I characterized PdeL as a transcriptional regulator of different loci, including the
flagellar class 2 operon fliFGHIJK and sslE, encoding an extracellular metalloprotease.
Repression of fliFGHIJK operon inhibits the expression of flagellar subunits needed in the early
phase of flagella synthesis. As a result of repression of transcription by PdeL motility is
inhibited. The DNA-binding site of PdeL at the regulatory region of fliFGHIJK overlaps with DNAbinding
sites of flagellar master regulator FlhD4C2 and transcription regulator CsgD indicating
that PdeL could be repressing fliFGHIJK transcription by inhibiting its activation. The expression
of sslE is activated by PdeL. The metalloprotease SslE is important for infection of epithelial cells
by E. coli. Regulation of sslE by PdeL indicates a role of PdeL in virulence. In addition, I describe
a finding that overexpression of PdeL and other transcription regulators cause changes in
nucleoid structure and affect cell division presumably by unspecific binding throughout the
nucleoid. This finding is of particular relevance for the characterization of transcription
regulators when physiological conditions under which they are expressed and active are yet
poorly understood and plasmidic expression systems are employed.
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