Metabolic remodeling in Escherichia coli   MG 1655. A prophage e14‐encoded small RNA ,  co293 , post‐transcriptionally regulates transcription factors HcaR and FadR

FEBS Journal ◽  
2020 ◽  
Vol 287 (21) ◽  
pp. 4767-4782
Author(s):  
Ashok Kumar Madikonda ◽  
Akbarpasha Shaikh ◽  
Sonali Khanra ◽  
Harshita Yakkala ◽  
Sailu Yellaboina ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Transcription Factors ◽  
Small Rna ◽  
Metabolic Remodeling

The functional landscape bound to the transcription factors of Escherichia coli K-12

2015 ◽  
Vol 58 ◽  
pp. 93-103 ◽  
Author(s):  
Ernesto Pérez-Rueda ◽  
Silvia Tenorio-Salgado ◽  
Alejandro Huerta-Saquero ◽  
Yalbi I. Balderas-Martínez ◽  
Gabriel Moreno-Hagelsieb
Keyword(s):  
Escherichia Coli ◽  
Transcription Factors ◽  
K 12

scholarly journals Systematic characterization of artificial small RNA-mediated inhibition of Escherichia coli growth

RNA Biology ◽  
2017 ◽  
Vol 14 (2) ◽  
pp. 206-218 ◽  
Author(s):  
Emiko Noro ◽  
Masaru Mori ◽  
Gakuto Makino ◽  
Yuki Takai ◽  
Sumiko Ohnuma ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Small Rna ◽  
Coli Growth

scholarly journals Transcriptomic, Protein-DNA Interaction, and Metabolomic Studies of VosA, VelB, and WetA in Aspergillus nidulans Asexual Spores

mBio ◽  
2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Ming-Yueh Wu ◽  
Matthew E. Mead ◽  
Mi-Kyung Lee ◽  
George F. Neuhaus ◽  
Donovon A. Adpressa ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Secondary Metabolism ◽  
Aspergillus Nidulans ◽  
Filamentous Fungi ◽  
Genetic Regulatory Networks ◽  
Asexual Development ◽  
Morphological Development ◽  
Vast Number ◽  
Content Type ◽  
Metabolic Remodeling

ABSTRACT In filamentous fungi, asexual development involves cellular differentiation and metabolic remodeling leading to the formation of intact asexual spores. The development of asexual spores (conidia) in Aspergillus is precisely coordinated by multiple transcription factors (TFs), including VosA, VelB, and WetA. Notably, these three TFs are essential for the structural and metabolic integrity, i.e., proper maturation, of conidia in the model fungus Aspergillus nidulans. To gain mechanistic insight into the complex regulatory and interdependent roles of these TFs in asexual sporogenesis, we carried out multi-omics studies on the transcriptome, protein-DNA interactions, and primary and secondary metabolism employing A. nidulans conidia. RNA sequencing and chromatin immunoprecipitation sequencing analyses have revealed that the three TFs directly or indirectly regulate the expression of genes associated with heterotrimeric G-protein signal transduction, mitogen-activated protein (MAP) kinases, spore wall formation and structural integrity, asexual development, and primary/secondary metabolism. In addition, metabolomics analyses of wild-type and individual mutant conidia indicate that these three TFs regulate a diverse array of primary metabolites, including those in the tricarboxylic acid (TCA) cycle, certain amino acids, and trehalose, and secondary metabolites such as sterigmatocystin, emericellamide, austinol, and dehydroaustinol. In summary, WetA, VosA, and VelB play interdependent, overlapping, and distinct roles in governing morphological development and primary/secondary metabolic remodeling in Aspergillus conidia, leading to the production of vital conidia suitable for fungal proliferation and dissemination. IMPORTANCE Filamentous fungi produce a vast number of asexual spores that act as efficient propagules. Due to their infectious and/or allergenic nature, fungal spores affect our daily life. Aspergillus species produce asexual spores called conidia; their formation involves morphological development and metabolic changes, and the associated regulatory systems are coordinated by multiple transcription factors (TFs). To understand the underlying global regulatory programs and cellular outcomes associated with conidium formation, genomic and metabolomic analyses were performed in the model fungus Aspergillus nidulans. Our results show that the fungus-specific WetA/VosA/VelB TFs govern the coordination of morphological and chemical developments during sporogenesis. The results of this study provide insights into the interdependent, overlapping, or distinct genetic regulatory networks necessary to produce intact asexual spores. The findings are relevant for other Aspergillus species such as the major human pathogen Aspergillus fumigatus and the aflatoxin producer Aspergillus flavus.

Overproduction and purification of the Escherichia coli transcription factors “toxic” to a bacterial cell

2019 ◽  
Vol 161 ◽  
pp. 70-77
Author(s):  
Tatiana A. Bessonova ◽  
Natalia V. Lekontseva ◽  
Uliana S. Shvyreva ◽  
Alexey D. Nikulin ◽  
Maria N. Tutukina ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Transcription Factors ◽  
Bacterial Cell

scholarly journals Transcriptional Cross Talk within themar-sox-robRegulon in Escherichia coli Is Limited to therobandmarRABOperons

2012 ◽  
Vol 194 (18) ◽  
pp. 4867-4875 ◽  
Author(s):  
Lon M. Chubiz ◽  
George D. Glekas ◽  
Christopher V. Rao
Keyword(s):  
Escherichia Coli ◽  
Transcription Factors ◽  
Cross Talk ◽  
Antimicrobial Compounds ◽  
Enteric Bacterium ◽  
Unknown Mechanism ◽  
Content Type ◽  
Physiological Conditions

ABSTRACTBacteria possess multiple mechanisms to survive exposure to various chemical stresses and antimicrobial compounds. In the enteric bacteriumEscherichia coli, three homologous transcription factors—MarA, SoxS, and Rob—play a central role in coordinating this response. Three separate systems are known to regulate the expression and activities of MarA, SoxS, and Rob. However, a number of studies have shown that the three do not function in isolation but rather are coregulated through transcriptional cross talk. In this work, we systematically investigated the extent of transcriptional cross talk in themar-sox-robregulon. While the three transcription factors were found to have the potential to regulate each other's expression when ectopically expressed, the only significant interactions observed under physiological conditions were betweenmarandrobsystems. MarA, SoxS, and Rob all activate themarRABpromoter, more so when they are induced by their respective inducers: salicylate, paraquat, and decanoate. None of the three proteins affects thesoxSpromoter, though unexpectedly, it was mildly repressed by decanoate by an unknown mechanism. SoxS is the only one of the three proteins to repress therobpromoter. Surprisingly, salicylate somewhat activates transcription ofrob, while decanoate represses it a bit. Rob, in turn, activates not only its downstream promoters in response to salicylate but also themarRABpromoter. These results demonstrate that themarandrobsystems function together in response to salicylate.

scholarly journals RyhB small RNA modulates the free intracellular iron pool and is essential for normal growth during iron limitation in Escherichia coli

2006 ◽  
Vol 62 (4) ◽  
pp. 1181-1190 ◽  
Author(s):  
Jean-François Jacques ◽  
Soojin Jang ◽  
Karine Prévost ◽  
Guillaume Desnoyers ◽  
Maxime Desmarais ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Small Rna ◽  
Normal Growth ◽  
Iron Limitation ◽  
Intracellular Iron ◽  
Iron Pool

scholarly journals The small RNA GlmY acts upstream of the sRNA GlmZ in the activation of glmS expression and is subject to regulation by polyadenylation in Escherichia coli

2008 ◽  
Vol 36 (8) ◽  
pp. 2570-2580 ◽  
Author(s):  
Birte Reichenbach ◽  
Alexandre Maes ◽  
Falk Kalamorz ◽  
Eliane Hajnsdorf ◽  
Boris Görke
Keyword(s):  
Escherichia Coli ◽  
Small Rna

scholarly journals Investigation of Transcription Repression and Small-Molecule Responsiveness by TetR-Like Transcription Factors Using a Heterologous Escherichia coli-Based Assay

2007 ◽  
Vol 189 (18) ◽  
pp. 6655-6664 ◽  
Author(s):  
Sang Kyun Ahn ◽  
Kapil Tahlan ◽  
Zhou Yu ◽  
Justin Nodwell
Keyword(s):  
Escherichia Coli ◽  
Transcription Factors ◽  
Small Molecule ◽  
Target Genes ◽  
Streptomyces Coelicolor ◽  
Targeted Mutagenesis ◽  
E Coli ◽  
Small Molecule Ligands

ABSTRACT The SCO7222 protein and ActR are two of ∼150 TetR-like transcription factors encoded in the Streptomyces coelicolor genome. Using bioluminescence as a readout, we have developed Escherichia coli-based biosensors that accurately report the regulatory activity of these proteins and used it to investigate their interactions with DNA and small-molecule ligands. We found that the SCO7222 protein and ActR repress the expression of their putative target genes, SCO7223 and actII-ORF2 (actA), respectively, by interacting with operator sequence in the promoters. The operators recognized by the two proteins are related such that O 7223 (an operator for SCO7223) could be bound by both the SCO7222 protein and ActR with similar affinities. In contrast, Oact (an operator for actII-ORF2) was bound tightly by ActR and more weakly by the SCO7222 protein. We demonstrated ligand specificity of these proteins by showing that while TetR (but not ActR or the SCO7222 protein) interacts with tetracyclines, ActR (but not TetR or the SCO7222 protein) interacts with actinorhodin and related molecules. Through operator-targeted mutagenesis, we found that at least two nucleotide changes in O 7223 were required to disrupt its interaction with SCO7222 protein, while ActR was more sensitive to changes on Oact . Most importantly, we found that the interaction of each protein with wild-type and mutant operator sequences in vivo and in vitro correlated perfectly. Our data suggest that E. coli-based biosensors of this type should be broadly applicable to TetR-like transcription factors.

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