Redefining fundamental concepts of transcription initiation in bacteria
Despite enormous progress in understanding the fundamentals of bacterial gene regulation,
our knowledge remains limited when compared with the number of bacterial genomes and …
our knowledge remains limited when compared with the number of bacterial genomes and …
RegulonDB 11.0: Comprehensive high-throughput datasets on transcriptional regulation in Escherichia coli K-12
Genomics has set the basis for a variety of methodologies that produce high-throughput
datasets identifying the different players that define gene regulation, particularly regulation …
datasets identifying the different players that define gene regulation, particularly regulation …
RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond
S Gama-Castro, H Salgado… - Nucleic acids …, 2016 - academic.oup.com
Abstract RegulonDB (http://regulondb. ccg. unam. mx) is one of the most useful and
important resources on bacterial gene regulation, as it integrates the scattered scientific …
important resources on bacterial gene regulation, as it integrates the scattered scientific …
Recent advances in constraint and machine learning-based metabolic modeling by leveraging stoichiometric balances, thermodynamic feasibility and kinetic law …
Understanding the governing principles behind organisms' metabolism and growth
underpins their effective deployment as bioproduction chassis. A central objective of …
underpins their effective deployment as bioproduction chassis. A central objective of …
An acid-tolerance response system protecting exponentially growing Escherichia coli
Y Xu, Z Zhao, W Tong, Y Ding, B Liu, Y Shi… - Nature …, 2020 - nature.com
The ability to grow at moderate acidic conditions (pH 4.0–5.0) is important to Escherichia coli
colonization of the host's intestine. Several regulatory systems are known to control acid …
colonization of the host's intestine. Several regulatory systems are known to control acid …
Genome-wide reconstruction of OxyR and SoxRS transcriptional regulatory networks under oxidative stress in Escherichia coli K-12 MG1655
Summary Three transcription factors (TFs), OxyR, SoxR, and SoxS, play a critical role in
transcriptional regulation of the defense system for oxidative stress in bacteria. However …
transcriptional regulation of the defense system for oxidative stress in bacteria. However …
Genome-wide promoter responses to CRISPR perturbations of regulators reveal regulatory networks in Escherichia coli
Elucidating genome-scale regulatory networks requires a comprehensive collection of gene
expression profiles, yet measuring gene expression responses for every transcription factor …
expression profiles, yet measuring gene expression responses for every transcription factor …
tRNA queuosine modification is involved in biofilm formation and virulence in bacteria
J Díaz-Rullo, JE González-Pastor - Nucleic Acids Research, 2023 - academic.oup.com
Abstract tRNA modifications are crucial for fine-tuning of protein translation. Queuosine (Q)
modification of tRNAs is thought to modulate the translation rate of NAU codons, but its …
modification of tRNAs is thought to modulate the translation rate of NAU codons, but its …
A heritable iron memory enables decision-making in Escherichia coli
S Bhattacharyya, N Bhattarai… - Proceedings of the …, 2023 - National Acad Sciences
The importance of memory in bacterial decision-making is relatively unexplored. We show
here that a prior experience of swarming is remembered when Escherichia coli encounters a …
here that a prior experience of swarming is remembered when Escherichia coli encounters a …
Global transcriptional regulatory network for Escherichia coli robustly connects gene expression to transcription factor activities
Transcriptional regulatory networks (TRNs) have been studied intensely for> 25 y. Yet, even
for the Escherichia coli TRN—probably the best characterized TRN—several questions …
for the Escherichia coli TRN—probably the best characterized TRN—several questions …