Iron Homeostasis and Environmental Responses in Cyanobacteria: Regulatory Networks Involving Fur

2016 ◽  
pp. 1065-1078 ◽  
Author(s):  
María Luisa Peleato ◽  
María Teresa Bes ◽  
María F. Fillat
Keyword(s):  
Regulatory Networks ◽  
Iron Homeostasis ◽  
Environmental Responses

scholarly journals Omics Approaches for Understanding Grapevine Berry Development: Regulatory Networks Associated with Endogenous Processes and Environmental Responses

2017 ◽  
Vol 8 ◽  
Author(s):  
Alejandra Serrano ◽  
Carmen Espinoza ◽  
Grace Armijo ◽  
Claudio Inostroza-Blancheteau ◽  
Evelyn Poblete ◽  
...  
Keyword(s):  
Regulatory Networks ◽  
Berry Development ◽  
Grapevine Berry ◽  
Environmental Responses

scholarly journals Construction of gene causal regulatory networks using microarray data with the coefficient of intrinsic dependence

2019 ◽  
Vol 60 (1) ◽  
Author(s):  
Li-yu Daisy Liu ◽  
Ya-Chun Hsiao ◽  
Hung-Chi Chen ◽  
Yun-Wei Yang ◽  
Men-Chi Chang
Keyword(s):  
Microarray Data ◽  
Regulatory Networks ◽  
Predictive Power ◽  
Iron Homeostasis ◽  
Crop Improvement ◽  
Gene Expressions ◽  
Regulatory Pathways ◽  
Gene Signatures ◽  
Practical Applications ◽  
Gene Regulatory

Abstract Background In the past two decades, biologists have been able to identify the gene signatures associated with various phenotypes through the monitoring of gene expressions with high-throughput biotechnologies. These gene signatures have in turn been successfully applied to drug development, disease prevention, crop improvement, etc. However, ignoring the interactions among genes has weakened the predictive power of gene signatures in practical applications. Gene regulatory networks, in which genes are represented by nodes and the associations between genes are represented by edges, are typically constructed to analyze and visualize such gene interactions. More specifically, the present study sought to measure gene–gene associations by using the coefficient of intrinsic dependence (CID) to capture more nonlinear as well as cause-effect gene relationships. Results A stepwise procedure using the CID along with the partial coefficient of intrinsic dependence (pCID) was demonstrated for the rebuilding of simulated networks and the well-known CBF-COR pathway under cold stress using Arabidopsis microarray data. The procedure was also applied to the construction of bHLH gene regulatory pathways under abiotic stresses using rice microarray data, in which OsbHLH104, a putative phytochrome-interacting factor (OsPIF14), and OsbHLH060, a positive regulator of iron homeostasis (OsPRI1) were inferred as the most affiliated genes. The inferred regulatory pathways were verified through literature reviews. Conclusions The proposed method can efficiently decipher gene regulatory pathways and may assist in achieving higher predictive power in practical applications. The lack of any mention in the literature of some of the regulatory event may have been due to the high complexity of the regulatory systems in the plant transcription, a possibility which could potentially be confirmed in the near future given ongoing rapid developments in bio-technology.

Description and Analysis of Switchlike Regulatory Networks Exemplified by a Model of Cellular Iron Homeostasis

1998 ◽  
Vol 195 (3) ◽  
pp. 339-350 ◽  
Author(s):  
Stig W. Omholt ◽  
Xiang Kefang ◽  
Øivind Andersen ◽  
Erik Plahte
Keyword(s):  
Regulatory Networks ◽  
Iron Homeostasis ◽  
Cellular Iron ◽  
Cellular Iron Homeostasis

scholarly journals Identification of a Salmonella ancillary copper detoxification mechanism by a comparative analysis of the genome-wide transcriptional response to copper and zinc excess

Microbiology ◽  
2014 ◽  
Vol 160 (8) ◽  
pp. 1659-1669 ◽  
Author(s):  
Lucas B. Pontel ◽  
Nadia L. Scampoli ◽  
Steffen Porwollik ◽  
Susana K. Checa ◽  
Michael McClelland ◽  
...  
Keyword(s):  
Metal Ions ◽  
Stress Responses ◽  
Regulatory Networks ◽  
Iron Homeostasis ◽  
Transcriptional Response ◽  
Zinc Excess ◽  
Copper And Zinc ◽  
Genome Wide ◽  
Copper Excess ◽  
Upregulated Genes

Copper and zinc are essential metal ions, but toxic in excess. Bacteria have evolved different strategies to control their intracellular concentrations, ensuring proper supply while avoiding toxicity, including the induction of metal-specific as well as non-specific mechanisms. We compared the transcriptional profiles of Salmonella Typhimurium after exposure to either copper or zinc ions in both rich and minimal media. Besides metal-specific regulatory networks many global stress-response pathways react to an excess of either of these metal ions. Copper excess affects both zinc and iron homeostasis by inducing transcription of these metal-specific regulons. In addition to the control of zinc-specific regulons, zinc excess affects the Cpx regulon and the σE envelope-stress responses. Finally, novel metal-specific upregulated genes were detected including a new copper-detoxification pathway that involves the siderophore enterobactin and the outer-membrane protein TolC. This work sheds light onto the transcriptional landscape of Salmonella after copper or zinc overload, and discloses a new mechanism of copper detoxification.

scholarly journals A fluorescence-based genetic screen reveals diverse mechanisms silencing small RNA signaling in E. coli

2021 ◽  
Vol 118 (27) ◽  
pp. e2106964118
Author(s):  
Jiandong Chen ◽  
Leann To ◽  
Francois de Mets ◽  
Xing Luo ◽  
Nadim Majdalani ◽  
...  
Keyword(s):  
Small Rna ◽  
Messenger Rna ◽  
Regulatory Networks ◽  
Iron Homeostasis ◽  
Mrna Translation ◽  
Genetic Screen ◽  
Phenotypic Traits ◽  
E Coli ◽  
Small Regulatory Rnas ◽  
Screen System

As key players of gene regulation in many bacteria, small regulatory RNAs (sRNAs) associated with the RNA chaperone Hfq shape numerous phenotypic traits, including metabolism, stress response and adaptation, as well as virulence. sRNAs can alter target messenger RNA (mRNA) translation and stability via base pairing. sRNA synthesis is generally under tight transcriptional regulation, but other levels of regulation of sRNA signaling are less well understood. Here we used a fluorescence-based functional screen to identify regulators that can quench sRNA signaling of the iron-responsive sRNA RyhB in Escherichia coli. The identified regulators fell into two classes, general regulators (affecting signaling by many sRNAs) and RyhB-specific regulators; we focused on the specific ones here. General regulators include three Hfq-interacting sRNAs, CyaR, ChiX, and McaS, previously found to act through Hfq competition, RNase T, a 3′ to 5′ exonuclease not previously implicated in sRNA degradation, and YhbS, a putative GCN5-related N-acetyltransferase (GNAT). Two specific regulators were identified. AspX, a 3′end-derived small RNA, specifically represses RyhB signaling via an RNA sponging mechanism. YicC, a previously uncharacterized but widely conserved protein, triggers rapid RyhB degradation via collaboration with the exoribonuclease PNPase. These findings greatly expand our knowledge of regulation of bacterial sRNA signaling and suggest complex regulatory networks for controlling iron homeostasis in bacteria. The fluorescence-based genetic screen system described here is a powerful tool expected to accelerate the discovery of novel regulators of sRNA signaling in many bacteria.

scholarly journals mSphere of Influence: Decoding Transcriptional Regulatory Networks To Illuminate the Mechanisms of Microbial Pathogenicity

mSphere ◽  
2020 ◽  
Vol 5 (1) ◽  
Author(s):  
Sadri Znaidi
Keyword(s):  
Candida Albicans ◽  
Functional Genomics ◽  
Regulatory Networks ◽  
Iron Homeostasis ◽  
Transcriptional Regulatory Networks ◽  
Content Type ◽  
Host Environment ◽  
Regulatory Circuit ◽  
Transcriptional Regulatory ◽  
Cell Host Microbe

ABSTRACT Sadri Znaidi works in the field of molecular mycology with a focus on functional genomics in Candida albicans. In this mSphere of Influence article, he reflects on how the paper “An iron homeostasis regulatory circuit with reciprocal roles in Candida albicans commensalism and pathogenesis” by Chen et al. (C. Chen, K. Pande, S. D. French, B. B. Tuch, and S. M. Noble, Cell Host Microbe 10:118–135, 2011, https://doi.org/10.1016/j.chom.2011.07.005) made an impact on his research on how transcriptional regulatory networks function to control C. albicans’ ability to efficiently interact with the host environment.

scholarly journals Transcriptional integration of plant responses to iron availability

2020 ◽  
Author(s):  
Fei Gao ◽  
Christian Dubos
Keyword(s):  
Transcription Factors ◽  
Regulatory Networks ◽  
Iron Homeostasis ◽  
Future Research ◽  
Plant Responses ◽  
Transcriptional Regulatory Networks ◽  
Helix Loop Helix ◽  
Regulatory Cascade ◽  
Transcriptional Regulatory ◽  
Electron Transport Chains

Abstract Iron is one of the most important micronutrients for plant growth and development. It functions as the enzyme cofactor or component of electron transport chains in various vital metabolic processes, including photosynthesis, respiration, and amino acid biosynthesis. To maintain iron homeostasis, and therefore prevent any deficiency or excess that could be detrimental, plants have evolved complex transcriptional regulatory networks to tightly control iron uptake, translocation, assimilation, and storage. These regulatory networks are composed of various transcription factors; among them, members of the basic helix-loop-helix (bHLH) family play an essential role. Here, we first review recent advances in understanding the roles of bHLH transcription factors involved in the regulatory cascade controlling iron homeostasis in the model plant Arabidopsis, and extend this understanding to rice and other plant species. The importance of other classes of transcription factors will also be discussed. Second, we elaborate on the post-translational mechanisms involved in the regulation of these regulatory networks. Finally, we provide some perspectives on future research that should be conducted in order to precisely understand how plants control the homeostasis of this micronutrient.

Regulatory networks for the control of body iron homeostasis and their dysregulation in HFE mediated hemochromatosis

2005 ◽  
Vol 204 (2) ◽  
pp. 489-499 ◽  
Author(s):  
Susanne Ludwiczek ◽  
Igor Theurl ◽  
Siamak Bahram ◽  
Klaus Schümann ◽  
Günter Weiss
Keyword(s):  
Regulatory Networks ◽  
Iron Homeostasis ◽  
Body Iron
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