scholarly journals Genome-wide analysis of cell-gene interactions

2017 ◽  
Author(s):  
S. Cardinale
Keyword(s):  
Single Gene ◽  
Rna Stability ◽  
Cellular Functions ◽  
Synthetic Genes ◽  
E Coli ◽  
Cell Functions ◽  
Specific Effects ◽  
Genome Wide ◽  
Cell Gene ◽  
Single Gene Deletion

AbstractThe study presents an analysis of how different cellular functions link cell size to the expression of synthetic genes inE. coli. The Size-Expression interaction was mapped with a two-gene genetic probe across 3800 single-gene deletion strains. Through regression analysis, expression-specific effects and gene-specific effects were derived from size effects and generic expression effects, respectively. The entire compendium of cell functions broadly mapped to four systems of distinct primary influence on the Size-Expression map. Specifically, membrane structural components primarily affected size, whereas protein and RNA stability primarily affected gene expression. In addition, major Size-Expression shifts showed no substantial gene-specific effects unless they were mediated by key components of the protein synthesis apparatus.Subject Category:Synthetic Biology

Behavioural phenotyping of C. elegans on UV-killed E. coli mutants v1

2021 ◽  
Author(s):  
Saul Moore
Keyword(s):  
Caenorhabditis Elegans ◽  
Gene Deletion ◽  
Uv Light ◽  
Single Gene ◽  
Deletion Mutants ◽  
E Coli ◽  
C Elegans ◽  
Behavioural Phenotyping ◽  
Keio Collection ◽  
Single Gene Deletion

Protocol for screening candidate behaviour-modifying E. coli BW25113 single-gene deletion mutants from the 'Keio Collection', to investigate their effects on Caenorhabditis elegans behaviour when killed by ultraviolet (UV) light

scholarly journals Hox Targets and Cellular Functions

Scientifica ◽  
2013 ◽  
Vol 2013 ◽  
pp. 1-26 ◽  
Author(s):  
Ernesto Sánchez-Herrero
Keyword(s):  
Drosophila Melanogaster ◽  
Hox Genes ◽  
The Body ◽  
Cell Behavior ◽  
Cellular Functions ◽  
Cell Functions ◽  
Genome Wide ◽  
Homologous Structure ◽  
Direct Regulation ◽  
Do So

Hox genes are a group of genes that specify structures along the anteroposterior axis in bilaterians. Although in many cases they do so by modifying a homologous structure with a different (or no) Hox input, there are also examples of Hox genes constructing new organs with no homology in other regions of the body. Hox genes determine structures though the regulation of targets implementing cellular functions and by coordinating cell behavior. The genetic organization to construct or modify a certain organ involves both a genetic cascade through intermediate transcription factors and a direct regulation of targets carrying out cellular functions. In this review I discuss new data from genome-wide techniques, as well as previous genetic and developmental information, to describe some examples of Hox regulation of different cell functions. I also discuss the organization of genetic cascades leading to the development of new organs, mainly usingDrosophila melanogasteras the model to analyze Hox function.

scholarly journals Image based annotation of Chemogenomic Libraries for Phenotypic Screening

2022 ◽  
Author(s):  
Amelie Tjaden ◽  
Apirat Chaikuad ◽  
Eric Kowarz ◽  
Rolf Marschalek ◽  
Stefan Knapp ◽  
...  
Keyword(s):  
Small Molecules ◽  
Cellular Responses ◽  
Chemical Probes ◽  
Cellular Functions ◽  
Single Experiment ◽  
Cell Functions ◽  
Specific Effects ◽  
Apoptosis And Necrosis ◽  
Comprehensive Characterization

Phenotypical screening is a widely used approach in drug discovery for the identification of small molecules with cellular activities. However, functional annotation of identified hits often poses a challenge. The development of small molecules with narrow or exclusive target selectivity such as chemical probes and chemogenomic (CG) libraries, greatly diminishes this challenge, but non-specific effects caused by compound toxicity or interference with basic cellular functions still poses a problem to associate phenotypic readouts with molecular targets. Hence, each compound should ideally be comprehensively characterized regarding its effects on general cell functions. Here, we report an optimized live-cell multiplexed assay that classifies cells based on nuclear morphology, presenting an excellent indicator for cellular responses such as early apoptosis and necrosis. This basic readout in combination with the detection of other general cell damaging activities of small molecules such as changes in cytoskeletal morphology, cell cycle and mitochondrial health provides a comprehensive time-dependent characterization of the effect of small molecules on cellular health in a single experiment. The developed high-content assay offers multi-dimensional comprehensive characterization that can be used to delineate generic effects regarding cell functions and cell viability, allowing an assessment of compound suitability for subsequent detailed phenotypic and mechanistic studies.

scholarly journals Transcriptome Profiling of Cellular Response to Kanamycin B in E.coli

2021 ◽  
Author(s):  
Yaowen Chang ◽  
Xuhui Zhang ◽  
Alastair I.H. Murchie ◽  
Dongrong Chen
Keyword(s):  
Cellular Response ◽  
Transcriptome Profiling ◽  
Cellular Functions ◽  
E Coli ◽  
Genome Wide ◽  
Component Systems ◽  
Two Component Systems ◽  
Profiling Analysis ◽  
Genome Wide Study

Abstract Background: Aminoglycosides are not only antibiotics but also have wider and diverse non-antibiotic cellular functions. No genome-wide study focusing on the changes of gene expression by aminoglycosides in E.coli has been reported. Here, we report transcriptome-profiling analysis of E.coli with or without Kanamycin B to elucidate the understanding of non-antibiotic cellular functions. Results: The differentially expressed genes (DEGs) at two given concentrations of Kanamycin B were identified. The results indicated that Kanamycin B does not affect the expression of the majority of the genes. Functional classification of the DEGs revealed that they were mainly related to microbial metabolism including two-component systems, biofilm formation, oxidative phosphorylation and nitrogen metabolism in diverse environments. Conclusions: Kanamycin B treatment causes diverse changes in the transcriptional profile of E. coli JM109, that are not directly associated with the antibiotic activity of Kanamycin B.

scholarly journals Genome-Wide Analysis Identifies MYND-Domain Protein Mub1 as an Essential Factor for Rpn4 Ubiquitylation

2007 ◽  
Vol 28 (4) ◽  
pp. 1404-1412 ◽  
Author(s):  
Donghong Ju ◽  
Xiaogang Wang ◽  
Haiming Xu ◽  
Youming Xie
Keyword(s):  
Ubiquitin Ligase ◽  
Single Gene ◽  
Genome Wide ◽  
Entire Collection ◽  
In Vitro Reconstitution ◽  
Negative Feedback Circuit ◽  
E2 Enzymes ◽  
Yeast Mutants ◽  
Single Gene Deletion

ABSTRACT The proteasome homeostasis in Saccharomyces cerevisiae is regulated by a negative feedback circuit in which the Rpn4 transcription factor upregulates the proteasome genes and is rapidly degraded by the proteasome. Previous work has identified Ubr2 and Rad6 as the cognate E3 and E2 enzymes for Rpn4 ubiquitylation. However, our recent attempts to ubiquitylate Rpn4 using purified Ubr2 and Rad6 proteins in a reconstitution system have been unsuccessful, suggesting that an additional factor is required for Rpn4 ubiquitylation. Here, we screened the entire collection of the single-gene-deletion yeast mutants generated by the Saccharomyces Genome Deletion Project and identified the mub1Δ mutant defective in ubiquitin-dependent degradation of Rpn4. An in vitro reconstitution ubiquitylation assay confirms that Mub1 is the missing factor for Rpn4 ubiquitylation. We further show that Mub1 directly interacts with Ubr2 and Rpn4. The MYND domain of Mub1 may play an important role in Rpn4 ubiquitylation. Interestingly, Mub1 itself is a short-lived protein and its degradation is dependent on the Ubr2/Rad6 ubiquitin ligase. Together, these data suggest that Mub1 and Ubr2 cooperate to transfer ubiquitin to Rpn4 from Rad6 and that Mub1 may switch from a partner to a substrate of the Ubr2/Rad6 ubiquitin ligase.

Antioxidant rescue of C. elegans behaviour on Keio E. coli mutants v1

2021 ◽  
Author(s):  
Saul Moore
Keyword(s):  
Caenorhabditis Elegans ◽  
Gene Deletion ◽  
Single Gene ◽  
Deletion Mutants ◽  
E Coli ◽  
C Elegans ◽  
Keio Collection ◽  
Single Gene Deletion

Protocol for screening candidate behaviour-modifying E. coli BW25113 single-gene deletion mutants from the 'Keio Collection', to investigate their effects on Caenorhabditis elegans behaviour in the presence of antioxidants.

scholarly journals Transcriptional and Post-Transcriptional Polar Effects in Bacterial Gene Deletion Libraries

mSystems ◽  
2021 ◽  
Author(s):  
André Mateus ◽  
Malay Shah ◽  
Johannes Hevler ◽  
Nils Kurzawa ◽  
Jacob Bobonis ◽  
...  
Keyword(s):  
Gene Function ◽  
Gene Deletion ◽  
Single Gene ◽  
Bacterial Gene ◽  
Genome Wide ◽  
Single Gene Deletion ◽  
Deletion Libraries

Single-gene deletion libraries have allowed genome-wide characterization of gene function and interactions. While each mutant intends to disrupt the function of a single gene, it can unintentionally target other genes, such as those located in the same operon as the deletion.

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