A systems approach discovers the role and characteristics of seven LysR type transcription factors in Escherichia coli

Abstract

Although Escherichia coli K-12 strains represent perhaps the best known model bacteria, we do not know the identity or functions of all of their transcription factors (TFs). It is now possible to systematically discover the physiological function of TFs in E. coli BW25113 using a set of synergistic methods; including ChIP-exo, growth phenotyping, conserved gene clustering, and transcriptome analysis. Among 47 LysR-type TFs (LTFs) found on the E. coli K-12 genome, many regulate nitrogen source utilization or amino acid metabolism. However, 19 LTFs remain unknown. In this study, we elucidated the regulation of seven of these 19 LTFs: YbdO, YbeF, YcaN, YbhD, YgfI, YiaU, YneJ. We show that: (1) YbdO (tentatively re-named CitR) regulation has an effect on bacterial growth at low pH with citrate supplementation. CitR is a repressor of the ybdNM operon and is implicated in the regulation of citrate lyase genes (citCDEFG); (2) YgfI (tentatively re-named DhfA) activates the dhaKLM operon that encodes the phosphotransferase system, DhfA is involved in formate, glycerol and dihydroxyacetone utilization; (3) YiaU (tentatively re-named LpsR) regulates the yiaT gene encoding an outer membrane protein, and waaPSBOJYZU operon is also important in determining cell density at the stationary phase and resistance to oxacillin microaerobically; (4) YneJ, re-named here as PtrR, directly regulates the expression of the succinate-semialdehyde dehydrogenase, Sad (also known as YneI), and is a predicted regulator of fnrS (a small RNA molecule). PtrR is important for bacterial growth in the presence of l-glutamate and putrescine as nitrogen/energy sources; and (5) YbhD and YcaN regulate adjacent y-genes on the genome. We have thus established the functions for four LTFs and identified the target genes for three LTFs.

In vitrotranscription-based biosensing of glycolate for prototyping of a complex enzyme cascade

“…Today, only a few of allosteric transcription factors are sufficiently characterized and collected in curated databases such as GroovDB 37 . However, systems-biology approaches have proven powerful in identifying the role of aTFs in vivo [38][39][40][41][42] , and are complemented recently through computational approaches that were able to successfully predict new aTF-operator pairs [43][44][45][46] and enzymes converting non-detectable metabolites into detectable ones 47,48 . At the same time, efforts to engineer aTFs for new effector specificities and enhanced properties are increasing 42,[49][50][51] , which will hopefully increase the repertoire and availability of aTFs to construct new IVT biosensors in the future.…”

High-Throughput Evolution Unravels Landscapes of High-Level Antibiotic Resistance Induced by Low-Level Antibiotic Exposure

“…We, therefore, identified a set of core mutant PRGs ( n = 131) contributing to high-level resistance evolution through the phenotype-genotype atlas. In addition to the well-characterized ARGs, e.g., pdeR involved in biofilm formation 38 , ycjV involved in efflux pump 35,39 , MJ1187 involved in drug inactivation 40 , yafK involved in target bypass 41,42 , and yjiR involved in transcriptional reprogramming 43 , others may confer high-level resistance via unreported mechanisms, e.g., metH , ynfB , ulaG , ftsK , rtcR , and hflK . By locating these understudied core mutant PRGs in the gene co-fitness interaction network and analyzing the functions of interacted genes, their resistance mechanisms were proposed.…”

Versatility and Complexity: Common and Uncommon Facets of LysR-Type Transcriptional Regulators

“…However, the entire complement of genes regulated by any specific LTTR cannot be revealed solely by genetic context. The evaluation of LTTR function is improved by methods of systems biology and gene cluster analysis integrated with phylogenetic footprinting, which evaluates conservation among diverse microbes (61,(105)(106)(107). One study investigated seven Escherichia coli LTTRs of unknown function (106).…”

“…The evaluation of LTTR function is improved by methods of systems biology and gene cluster analysis integrated with phylogenetic footprinting, which evaluates conservation among diverse microbes (61,(105)(106)(107). One study investigated seven Escherichia coli LTTRs of unknown function (106). The workflow combined information from transcriptomics (110), determination of DNA-binding sites with an in vivo chromatin immunoprecipitation method (41), and mutants lacking specific LTTRs.…”