Mechanisms and evolution of control logic in prokaryotic transcriptional regulation

SAFT van Hijum, MH Medema… - … and Molecular Biology …, 2009 - Am Soc Microbiol
SUMMARY A major part of organismal complexity and versatility of prokaryotes resides in
their ability to fine-tune gene expression to adequately respond to internal and external …

Glucose Transport in Escherichia coli: From Basics to Transport Engineering

OE Carreón-Rodríguez, G Gosset, A Escalante… - Microorganisms, 2023 - mdpi.com
Escherichia coli is the best-known model for the biotechnological production of many
biotechnological products, including housekeeping and heterologous primary and …

Regulatory activity revealed by dynamic correlations in gene expression noise

MJ Dunlop, RS Cox III, JH Levine, RM Murray… - Nature …, 2008 - nature.com
Gene regulatory interactions are context dependent, active in some cellular states but not in
others. Stochastic fluctuations, or'noise', in gene expression propagate through active, but …

Metabolic engineering of Escherichia coli for production of L-aspartate and its derivative β-alanine with high stoichiometric yield

X Piao, L Wang, B Lin, H Chen, W Liu, Y Tao - Metabolic engineering, 2019 - Elsevier
L-aspartate is an important 4-carbon platform compound that can be used as the precursor
of numerous chemical products. The bioproduction of L-aspartate directly from biomass …

The incoherent feed‐forward loop can generate non‐monotonic input functions for genes

S Kaplan, A Bren, E Dekel, U Alon - Molecular systems biology, 2008 - embopress.org
Gene regulation networks contain recurring circuit patterns called network motifs. One of the
most common network motif is the incoherent type 1 feed‐forward loop (I1‐FFL), in which an …

Glucose transport in Escherichia coli mutant strains with defects in sugar transport systems

S Steinsiek, K Bettenbrock - Journal of bacteriology, 2012 - Am Soc Microbiol
In Escherichia coli, several systems are known to transport glucose into the cytoplasm. The
main glucose uptake system under batch conditions is the glucose phosphoenolpyruvate …

Deciphering the transcriptional regulatory logic of amino acid metabolism

BK Cho, S Federowicz, YS Park, K Zengler… - Nature chemical …, 2012 - nature.com
Although metabolic networks have been reconstructed on a genome scale, the
corresponding reconstruction and integration of governing transcriptional regulatory …

Identification of stress‐related proteins in Escherichia coli using the pollutant cis‐dichloroethylene

J Lee, SR Hiibel, KF Reardon… - Journal of applied …, 2010 - academic.oup.com
Aims: To complement our proteome study, whole‐transcriptome analyses were utilized here
to identify proteins related to degrading cis‐1, 2‐dichloroethylene (cis‐DCE). Methods and …

Gene dispensability in Escherichia coli grown in thirty different carbon environments

M Tong, S French, SS El Zahed, WK Ong, PD Karp… - MBio, 2020 - Am Soc Microbiol
Central metabolism is a topic that has been studied for decades, and yet, this process is still
not fully understood in Escherichia coli, perhaps the most amenable and well-studied model …

Simplified models of biological networks

K Sneppen, S Krishna, S Semsey - Annual review of biophysics, 2010 - annualreviews.org
The function of living cells is controlled by complex regulatory networks that are built of a
wide diversity of interacting molecular components. The sheer size and intricacy of …