2.3) Lrp
LRP, the Leucine-responsive Regulatory Protein (18 kDa), is a
widely conserved global transcription factor that can activate or
repress gene expression (Table 1 ) (Ziegler and Freddolino,
2021). Combined Chromatin-Immunoprecipitation sequencing (ChIP-seq) and
RNA sequencing (RNA-seq) under different nutrient availability
conditions revealed that Lrp regulates one third of E. coli via direct, cooperative and indirect routes, but little is known about the
precise mechanism by which Lrp regulates its target genes (Kroner, Wolfe
and Freddolino, 2019). Lrp regulates genes involved in metabolism, such
as those involved in amino acid biosynthesis, nutrient transport,
motility, virulence, stress response and antibiotic resistance (Ziegler
and Freddolino, 2021). In E.coli, this protein is commonly
referred to as a feast/famine regulatory protein due to its response to
nutrient levels. Lrp is a highly expressed protein with 2,500 molecules
per cell in the exponential phase in rich medium, and three-to-fourfold
higher in minimal medium (Ali Azam et al. , 1999). Lrp is composed
of a helix-turn-helix DNA-binding domain and a regulator of amino acid
metabolism (RAM) domain (De Los Rios and Perona, 2007), which binds
effector molecules and modulates oligomerisation. Under starvation
conditions, Lrp forms hexadecamers through oligomerisation. Conversely,
in conditions of feast, it dissociates into octamers via leucine-induced mechanisms (Chen et al. , 2001). While
oligomerisation beyond dimers is required for Lrp’s regulatory activity,
exogenous leucine modulates Lrp activity at its target promoters
exclusively by inhibiting Lrp binding to DNA (Ziegler and Freddolino,
2023). Lrp is also a DNA-organising protein, but the binding motifs
remain difficult to elucidate. Those proposed since its discovery share
a central AT-rich stretch flanked by 5’-CAG-3’ and/or 5’-CTG-3’ (Ziegler
and Freddolino, 2021). Furthermore, there is evidence that E.
coli Lrp favours DNA wrapping (Pollak and Reich, 2015) and also loops
DNA over length scales of multiple kilobases (Ziegler and Freddolino,
2023), demonstrating its ability to organise bacterial DNA. Finally, it
is worth noting that while Lrp from Vibrio vulnificus, Neisseria
meningitidis, Mycobacterium tuberculosis, Clostridium difficile, andStreptomyces spiramyceticus have been identified as global
regulators. However, the set of regulated genes is partially distinct
between species (Ren et al. , 2007; Reddy et al. , 2008;
Song et al. , 2016; Ho et al. , 2017; Chen et al. ,
2019; Lu et al. , 2019).