Restoring Global Gene Regulation through Experimental Evolution Uncovers a NAP (Nucleoid-Associated Protein)-Like Behavior of Crp/Cap

Here we report that mutations in the topA gene compensate for loss of cAMP, showing that the interplay between Crp and the supercoiling status of promoters is key to global stress response. Furthermore, we observed an effect of apoCrp on gene expression in the absence of its effector cAMP. This provides support for the proposed NAP-like role for Crp, suggesting that it represents an intermediate point in the evolution of a ligand-controlled TF from a NAP.

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Computational modelling unravels the precise clockwork of cyanobacteria

Interface Focus ◽

10.1098/rsfs.2018.0038 ◽

2018 ◽

Vol 8 (6) ◽

pp. 20180038 ◽

Cited By ~ 4

Author(s):

Nicolas M. Schmelling ◽

Ilka M. Axmann

Keyword(s):

Gene Expression ◽

Gene Regulation ◽

Circadian Clock ◽

Environmental Changes ◽

Regulation Of Gene Expression ◽

Computational Modelling ◽

Circadian Clocks ◽

Fitness Advantage ◽

Fundamental Part ◽

Global Gene Regulation

Precisely timing the regulation of gene expression by anticipating recurring environmental changes is a fundamental part of global gene regulation. Circadian clocks are one form of this regulation, which is found in both eukaryotes and prokaryotes, providing a fitness advantage for these organisms. Whereas many different eukaryotic groups harbour circadian clocks, cyanobacteria are the only known oxygenic phototrophic prokaryotes to regulate large parts of their genes in a circadian fashion. A decade of intensive research on the mechanisms and functionality using computational and mathematical approaches in addition to the detailed biochemical and biophysical understanding make this the best understood circadian clock. Here, we summarize the findings and insights into various parts of the cyanobacterial circadian clock made by mathematical modelling. These findings have implications for eukaryotic circadian research as well as synthetic biology harnessing the power and efficiency of global gene regulation.

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Faculty Opinions recommendation of Restoring Global Gene Regulation through Experimental Evolution Uncovers a NAP (Nucleoid-Associated Protein)-Like Behavior of Crp/Cap.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.741056639.793589446 ◽

2021 ◽

Author(s):

Charles Dorman

Keyword(s):

Gene Regulation ◽

Experimental Evolution ◽

Global Gene Regulation

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Faculty Opinions recommendation of Defects in dosage compensation impact global gene regulation in the mouse trophoblast.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.727785295.793569993 ◽

2020 ◽

Author(s):

Anton Wutz

Keyword(s):

Gene Regulation ◽

Dosage Compensation ◽

Global Gene Regulation

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Stress-induced differential gene expression in cardiac tissue

Scientific Reports ◽

10.1038/s41598-021-88267-8 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Ana Elisa T. S. de Carvalho ◽

Marco A. Cordeiro ◽

Luana S. Rodrigues ◽

Daniela Ortolani ◽

Regina C. Spadari

Keyword(s):

Gene Expression ◽

Stress Response ◽

Left Ventricle ◽

Differential Gene Expression ◽

Cardiac Tissue ◽

Stressful Situation ◽

Adaptive Mechanism ◽

Number Of Genes ◽

Differential Gene ◽

Shock Stress

AbstractThe stress response is adaptive and aims to guarantee survival. However, the persistence of a stressor can culminate in pathology. Catecholamines released as part of the stress response over activate beta adrenoceptors (β-AR) in the heart. Whether and how stress affects the expression of components of the intracellular environment in the heart is still, however, unknown. This paper used microarray to analyze the gene expression in the left ventricle wall of rats submitted to foot shock stress, treated or not treated with the selective β2-AR antagonist ICI118,551 (ICI), compared to those of non-stressed rats also treated or not with ICI, respectively. The main findings were that stress induces changes in gene expression in the heart and that β2-AR plays a role in this process. The vast majority of genes disregulated by stress were exclusive for only one of the comparisons, indicating that, in the same stressful situation, the profile of gene expression in the heart is substantially different when the β2-AR is active or when it is blocked. Stress induced alterations in the expression of such a large number of genes seems to be part of stress-induced adaptive mechanism.

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Deuterium Oxide (D2O) Induces Early Stress Response Gene Expression and Impairs Growth and Metastasis of Experimental Malignant Melanoma

Cancers ◽

10.3390/cancers13040605 ◽

2021 ◽

Vol 13 (4) ◽

pp. 605

Author(s):

Jana Jandova ◽

Anh B. Hua ◽

Jocelyn Fimbres ◽

Georg T. Wondrak

Keyword(s):

Gene Expression ◽

Stress Response ◽

Malignant Melanoma ◽

Tumor Growth ◽

Deuterium Oxide ◽

Human Melanoma ◽

Pharmacological Intervention ◽

Melanoma Metastasis ◽

Response Gene ◽

Stress Response Gene

There are two stable isotopes of hydrogen, protium (1H) and deuterium (2H; D). Cellular stress response dysregulation in cancer represents both a major pathological driving force and a promising therapeutic target, but the molecular consequences and potential therapeutic impact of deuterium (2H)-stress on cancer cells remain largely unexplored. We have examined the anti-proliferative and apoptogenic effects of deuterium oxide (D2O; ‘heavy water’) together with stress response gene expression profiling in panels of malignant melanoma (A375V600E, A375NRAS, G361, LOX-IMVI), and pancreatic ductal adenocarcinoma (PANC-1, Capan-2, or MIA PaCa-2) cells with inclusion of human diploid Hs27 skin fibroblasts. Moreover, we have examined the efficacy of D2O-based pharmacological intervention in murine models of human melanoma tumor growth and metastasis. D2O-induction of apoptosis was substantiated by AV-PI flow cytometry, immunodetection of PARP-1, and pro-caspase 3 cleavage, and rescue by pan-caspase inhibition. Differential array analysis revealed early modulation of stress response gene expression in both A375 melanoma and PANC-1 adenocarcinoma cells elicited by D2O (90%; ≤6 h) (upregulated: CDKN1A, DDIT3, EGR1, GADD45A, HMOX1, NFKBIA, or SOD2 (up to 9-fold; p < 0.01)) confirmed by independent RT-qPCR analysis. Immunoblot analysis revealed rapid onset of D2O-induced stress response phospho-protein activation (p-ERK, p-JNK, p-eIF2α, or p-H2AX) or attenuation (p-AKT). Feasibility of D2O-based chemotherapeutic intervention (drinking water (30% w/w)) was demonstrated in a severe combined immunodeficiency (SCID) mouse melanoma metastasis model using luciferase-expressing A375-Luc2 cells. Lung tumor burden (visualized by bioluminescence imaging) was attenuated by D2O, and inhibition of invasiveness was also confirmed in an in vitro Matrigel transwell invasion assay. D2O supplementation also suppressed tumor growth in a murine xenograft model of human melanoma, and median survival was significantly increased without causing adverse effects. These data demonstrate for the first time that systemic D2O administration impairs growth and metastasis of malignant melanoma through the pharmacological induction of deuterium (2H)-stress.

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Base-Pair Opening Dynamics Study of Fluoride Riboswitch in the Bacillus cereus CrcB Gene

International Journal of Molecular Sciences ◽

10.3390/ijms22063234 ◽

2021 ◽

Vol 22 (6) ◽

pp. 3234

Author(s):

Juhyun Lee ◽

Si-Eun Sung ◽

Janghyun Lee ◽

Jin Young Kang ◽

Joon-Hwa Lee ◽

...

Keyword(s):

Gene Expression ◽

Gene Regulation ◽

Nmr Spectroscopy ◽

Bacillus Cereus ◽

Base Pair ◽

Noncoding Rna ◽

Hydrogen Exchange ◽

Magnesium Ion ◽

Fluoride Ion ◽

Base Pair Opening

Riboswitches are segments of noncoding RNA that bind with metabolites, resulting in a change in gene expression. To understand the molecular mechanism of gene regulation in a fluoride riboswitch, a base-pair opening dynamics study was performed with and without ligands using the Bacillus cereus fluoride riboswitch. We demonstrate that the structural stability of the fluoride riboswitch is caused by two steps depending on ligands. Upon binding of a magnesium ion, significant changes in a conformation of the riboswitch occur, resulting in the greatest increase in their stability and changes in dynamics by a fluoride ion. Examining hydrogen exchange dynamics through NMR spectroscopy, we reveal that the stabilization of the U45·A37 base-pair due to the binding of the fluoride ion, by changing the dynamics while maintaining the structure, results in transcription regulation. Our results demonstrate that the opening dynamics and stabilities of a fluoride riboswitch in different ion states are essential for the genetic switching mechanism.

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Rox3 and Rts1 Function in the Global Stress Response Pathway in Baker's Yeast

Genetics ◽

10.1093/genetics/142.4.1083 ◽

1996 ◽

Vol 142 (4) ◽

pp. 1083-1093 ◽

Cited By ~ 8

Author(s):

Carlos C Evangelista ◽

Ana M Rodriguez Torres ◽

M Paullin Limbach ◽

Richard S Zitomer

Keyword(s):

Stress Response ◽

Heat Shock ◽

Osmotic Stress ◽

Regulatory Element ◽

Regulatory Region ◽

Mitogen Activated Protein Kinase ◽

Regulatory Subunit ◽

Temperature Sensitive ◽

Global Stress ◽

Rna Accumulation

Abstract Yeast respond to a variety of stresses through a global stress response that is mediated by a number of signal transduction pathways and the cis-acting STRE DNA sequence. The CYC7 gene, encoding iso-2-cytochrome c, has been demonstrated to respond to heat shock, glucose starvation, approach-to-stationary phase, and, as we demonstrate here, to osmotic stress. This response was delayed in a the hogl-Δ1 strain implicating the Hog1 mitogen-activated protein kinase cascade, a known component of the global stress response. Deletion analysis of the CYC7 regulatory region suggested that three STRE elements were each capable of inducing the stress response. Mutations in the ROX3 gene prevented CYC7 RNA accumulation during heat shock and osmotic stress. ROX3 RNA levels were shown to be induced by stress through a novel regulatory element. A selection for high-copy suppressors of a ROX3 temperature-sensitive allele resulted in the isolation of RTS1, encoding a protein with homology to the B′ regulatory subunit of protein phosphatase 2A0. Deletion of RTS1 caused temperature and osmotic sensitivity and increased accumulation of CYC7 RNA under all conditions. Over-expression of this gene caused increased CYC7 RNA accumulation in rox3 mutants but not in wild-type cells.

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CFTR Cooperative Cis-Regulatory Elements in Intestinal Cells

International Journal of Molecular Sciences ◽

10.3390/ijms22052599 ◽

2021 ◽

Vol 22 (5) ◽

pp. 2599

Author(s):

Mégane Collobert ◽

Ozvan Bocher ◽

Anaïs Le Nabec ◽

Emmanuelle Génin ◽

Claude Férec ◽

...

Keyword(s):

Gene Expression ◽

Cystic Fibrosis ◽

Gene Regulation ◽

Genetic Diseases ◽

Regulatory Elements ◽

Cftr Gene ◽

Intestinal Cells ◽

Cooperative Effects ◽

Cis Acting ◽

Study Techniques

About 8% of the human genome is covered with candidate cis-regulatory elements (cCREs). Disruptions of CREs, described as “cis-ruptions” have been identified as being involved in various genetic diseases. Thanks to the development of chromatin conformation study techniques, several long-range cystic fibrosis transmembrane conductance regulator (CFTR) regulatory elements were identified, but the regulatory mechanisms of the CFTR gene have yet to be fully elucidated. The aim of this work is to improve our knowledge of the CFTR gene regulation, and to identity factors that could impact the CFTR gene expression, and potentially account for the variability of the clinical presentation of cystic fibrosis as well as CFTR-related disorders. Here, we apply the robust GWAS3D score to determine which of the CFTR introns could be involved in gene regulation. This approach highlights four particular CFTR introns of interest. Using reporter gene constructs in intestinal cells, we show that two new introns display strong cooperative effects in intestinal cells. Chromatin immunoprecipitation analyses further demonstrate fixation of transcription factors network. These results provide new insights into our understanding of the CFTR gene regulation and allow us to suggest a 3D CFTR locus structure in intestinal cells. A better understand of regulation mechanisms of the CFTR gene could elucidate cases of patients where the phenotype is not yet explained by the genotype. This would thus help in better diagnosis and therefore better management. These cis-acting regions may be a therapeutic challenge that could lead to the development of specific molecules capable of modulating gene expression in the future.

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