Escherichia coli glycogen metabolism is controlled by the PhoP-PhoQ regulatory system at submillimolar environmental Mg2+ concentrations, and is highly interconnected with a wide variety of cellular processes

2009 ◽  
Vol 424 (1) ◽  
pp. 129-141 ◽  
Author(s):  
Manuel Montero ◽  
Gustavo Eydallin ◽  
Alejandro M. Viale ◽  
Goizeder Almagro ◽  
Francisco J. Muñoz ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Stress Responses ◽  
Regulatory System ◽  
Glycogen Metabolism ◽  
Metabolic Model ◽  
Knock Out ◽  
Cellular Processes ◽  
Genome Wide ◽  
A Genome ◽  
Keio Collection

Using the Keio collection of gene-disrupted mutants of Escherichia coli, we have recently carried out a genome-wide screening of the genes affecting glycogen metabolism. Among the mutants identified in the study, ΔmgtA, ΔphoP and ΔphoQ cells, all lacking genes that are induced under low extracellular Mg2+ conditions, displayed glycogen-deficient phenotypes. In this work we show that these mutants accumulated normal glycogen levels when the culture medium was supplemented with submillimolar Mg2+ concentrations. Expression analyses conducted in wild-type, ΔphoP and ΔphoQ cells showed that the glgCAP operon is under PhoP-PhoQ control in the submillimolar Mg2+ concentration range. Subsequent screening of the Keio collection under non-limiting Mg2+ allowed the identification of 183 knock-out mutants with altered glycogen levels. The stringent and general stress responses, end-turnover of tRNA, intracellular AMP levels, and metabolism of amino acids, iron, carbon and sulfur were major determinants of glycogen levels. glgC::lacZY expression analyses using mutants representing different functional categories revealed that the glgCAP operon belongs to the RelA regulon. We propose an integrated metabolic model wherein glycogen metabolism is (a) tightly controlled by the energy and nutritional status of the cell and (b) finely regulated by changes in environmental Mg2+ occurring at the submillimolar concentration range.

scholarly journals Network analysis links genome-wide phenotypic and transcriptional stress responses in a bacterial pathogen with a large pan-genome

2016 ◽  
Author(s):  
Paul A. Jensen ◽  
Zeyu Zhu ◽  
Tim van Opijnen
Keyword(s):  
Gene Expression ◽  
Stress Responses ◽  
Meta Analysis ◽  
Bacterial Pathogen ◽  
Metabolic Model ◽  
Genetic Network ◽  
Rna Seq ◽  
Genome Wide ◽  
A Genome ◽  
Response To Stress

ABSTRACTBackgroundBacteria modulate subcellular processes to handle stressful environments. Genome-wide profiling of gene expression (RNA-Seq) and fitness (Tn-Seq) allows two views of the same genetic network underlying these responses. However, it remains unclear how they combine, enabling a bacterium to overcome a perturbation.ResultsHere we generate RNA-Seq and Tn-Seq profiles in three strains of S. pneumoniae in response to stress defined by different levels of nutrient depletion. These profiles show that genes that change their expression and/or become phenotypically important come from a diverse set of functional categories, and genes that are phenotypically important tend to be highly expressed. Surprisingly, we find that expression and fitness changes rarely occur on the same gene, which we confirmed by over 140 validation experiments. To rationalize these unexpected results we built the first genome-scale metabolic model of S. pneumoniae showing that differential expression and phenotypic importance actually correlate between nearest neighbors, although they are distinctly partitioned into small subnetworks. Moreover, a meta-analysis of 234 S. pneumoniae gene expression studies reveals that essential genes and phenotypically important subnetworks rarely change expression, indicating that they are shielded from transcriptional fluctuations and that a clear distinction exists between transcriptional and phenotypic response networks.ConclusionsWe present a genome-wide computational/experimental approach that contextualizes changes that occur on transcriptomic and phenomic levels in response to stress. Importantly, this highlights the need to connect disparate response networks, for instance in antibiotic target identification, where preferred targets are phenotypically important genes that would be overlooked by transcriptomic analyses alone.

scholarly journals Genome-wide analysis of Escherichia coli fitness determinants in a cross-feeding mutualism with Rhodopseudomonas palustris

2020 ◽  
Author(s):  
Breah LaSarre ◽  
Adam M. Deutschbauer ◽  
Crystal E. Love ◽  
James B. McKinlay
Keyword(s):  
Escherichia Coli ◽  
Microbial Communities ◽  
Rhodopseudomonas Palustris ◽  
Microbial Interactions ◽  
Dependent Manner ◽  
Fermentation Products ◽  
E Coli ◽  
Cellular Processes ◽  
Genome Wide ◽  
A Genome

ABSTRACTMicrobial interactions abound in natural ecosystems and shape community structure and function. Substantial attention has been given to cataloging mechanisms by which microbes interact, but there is a limited understanding of the genetic landscapes that promote or hinder microbial interactions. We previously developed a mutualistic coculture pairing Escherichia coli and Rhodopseudomonas palustris, wherein E. coli provides carbon to R. palustris in the form of glucose fermentation products and R. palustris fixes N2 gas and provides nitrogen to E. coli in the form of NH4+. The stable coexistence and reproducible trends exhibited by this coculture make it ideal for interrogating the genetic underpinnings of a cross-feeding mutualism. Here, we used random barcode transposon sequencing (RB-TnSeq) to conduct a genome-wide search for E. coli genes that influence fitness during cooperative growth with R. palustris. RB-TnSeq revealed hundreds of genes that increased or decreased E. coli fitness in a mutualism-dependent manner. Some identified genes were involved in nitrogen sensing and assimilation, as expected given the coculture design. The other identified genes were involved in diverse cellular processes, including energy production and cell wall and membrane biogenesis. Additionally, we discovered unexpected purine cross-feeding from R. palustris to E. coli, with coculture rescuing growth of an E. coli purine auxotroph. Our data provide insight into the genes and gene networks that can influence a cross-feeding mutualism and underscore that microbial interactions are not necessarily predictable a priori.IMPORTANCEMicrobial communities impact life on earth in profound ways, including driving global nutrient cycles and influencing human health and disease. These community functions depend on the interactions that resident microbes have with the environment and each other. Thus, identifying genes that influence these interactions will aid the management of natural communities and the use of microbial consortia as biotechnology. Here, we identified genes that influenced Escherichia coli fitness during cooperative growth with a mutualistic partner, Rhodospeudomonas palustris. Although this mutualism centers on the bidirectional exchange of essential carbon and nitrogen, E. coli fitness was positively and negatively affected by genes involved in diverse cellular processes. Furthermore, we discovered an unexpected purine cross-feeding interaction. These results contribute knowledge on the genetic foundation of a microbial cross-feeding interaction and highlight that unanticipated interactions can occur even within engineered microbial communities.

BIOM-32. ENDOPLASMIC RETICULUM PROTEIN SSR3 DETERMINES AND PREDICTS RESPONSE TO PACLITAXEL IN BREAST CANCER AND GLIOBLASTOMA

2021 ◽  
Vol 23 (Supplement_6) ◽  
pp. vi17-vi18
Author(s):  
Crismita Dmello ◽  
Aarón Sonabend ◽  
Víctor Arrieta ◽  
Daniel Zhang ◽  
Deepak Kanojia ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Endoplasmic Reticulum ◽  
Glioma Cells ◽  
Predictive Biomarkers ◽  
Predictive Biomarker ◽  
Precision Oncology ◽  
Patient Response ◽  
Knock Out ◽  
Genome Wide ◽  
A Genome

Abstract Paclitaxel (PTX) is one the most potent and commonly used chemotherapies for breast and pancreatic cancer. Given the potency of this drug for glioblastomas (GBM) several ongoing clinical trials are investigating means of enhancing delivery of PTX across the blood-brain barrier for this disease. In spite of the efficacy of PTX, individual tumors exhibit variable susceptibility to this drug, with response rate in the range of 30%-60%. To identify predictive biomarkers for response to PTX, we performed a genome-wide CRISPR knock-out screen using human glioma cells. The most enriched genes in the CRISPR screen underwent further selection based on their correlation with survival in the breast cancer patient cohorts treated with PTX and not in patients treated with other chemotherapies, a finding that was validated on a second independent patient cohort. This led to the discovery of endoplasmic reticulum (ER) protein SSR3 as a putative predictive biomarker for PTX. SSR3 protein levels showed positive correlation with response to PTX in breast cancer cells, glioma cells, in multiple intracranial glioma xenografts and in GBM patient derived explant cultures. Knockout of SSR3 turned the cells resistant to PTX while its overexpression sensitized the cells to PTX. In gliomas, SSR3-mediated susceptibility to PTX relates to modulation of phosphorylation of ER stress sensor IRE1α. Thus, by using genome-wide screen combined with patient response data, we discovered a biomarker that demonstrates causal and correlative relationship with response to PTX in breast cancer and GBM. Prospective validation of this biomarker is warranted for its broad implementation for precision oncology.

scholarly journals A Genome-Wide Assay Specifies Only GreA as a Transcription Fidelity Factor in Escherichia coli

2018 ◽  
Vol 8 (7) ◽  
pp. 2257-2264 ◽  
Author(s):  
Charles C. Traverse ◽  
Howard Ochman
Keyword(s):  
Escherichia Coli ◽  
Genome Wide ◽  
A Genome

scholarly journals Chromatin architectural proteins regulate flowering time by precluding gene looping

2021 ◽  
Vol 7 (24) ◽  
pp. eabg3097
Author(s):  
Bo Zhao ◽  
Yanpeng Xi ◽  
Junghyun Kim ◽  
Sibum Sung
Keyword(s):  
Chromatin Structure ◽  
Cellular Processes ◽  
Genome Wide ◽  
A Genome ◽  
Evolutionarily Conserved ◽  
Architectural Proteins ◽  
Floral Repressor ◽  
Flanking Regions ◽  
Genome Wide Study

Chromatin structure is critical for gene expression and many other cellular processes. In Arabidopsis thaliana, the floral repressor FLC adopts a self-loop chromatin structure via bridging of its flanking regions. This local gene loop is necessary for active FLC expression. However, the molecular mechanism underlying the formation of this class of gene loops is unknown. Here, we report the characterization of a group of linker histone-like proteins, named the GH1-HMGA family in Arabidopsis, which act as chromatin architecture modulators. We demonstrate that these family members redundantly promote the floral transition through the repression of FLC. A genome-wide study revealed that this family preferentially binds to the 5′ and 3′ ends of gene bodies. The loss of this binding increases FLC expression by stabilizing the FLC 5′ to 3′ gene looping. Our study provides mechanistic insights into how a family of evolutionarily conserved proteins regulates the formation of local gene loops.

scholarly journals Comprehensive Genome-Wide Analysis of The Catalase Enzyme Toolbox In Potato (Solanum Tuberosum L.)

2021 ◽  
Author(s):  
Rania Jbir Koubaa ◽  
Mariem Ayadi ◽  
Mohamed Najib Saidi ◽  
Safa Charfeddine ◽  
Radhia Gargouri Bouzid ◽  
...  
Keyword(s):  
Stress Responses ◽  
Expression Profiling ◽  
Phylogenetic Trees ◽  
Solanum Tuberosum L ◽  
Potato Cultivar ◽  
Promoter Sequence ◽  
3D Protein Structure ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
A Genome

Abstract As antioxidant enzymes, catalase (CAT) protects organisms from oxidative stress via the production of reactive oxygen species (ROS). These enzymes play important roles in diverse biological processes. However, little is known about the CAT genes in potato plants despite its important economical rank of this crop in the world. Yet, abiotic and biotic stresses severely hinder growth and development of the plants which affects the production and quality of the crop. To define the possible roles of CAT genes under various stresses, a genome-wide analysis of CAT gene family has been performed in potato plant.In this study, the StCAT gene’s structure, secondary and 3D protein structure, physicochemical properties, synteny analysis, phylogenetic tree and also expression profiling under various developmental and environmental cues were predicted using bioinformatics tools. The expression analysis by RT-PCR was performed using commercial potato cultivar. Three genes encoding StCAT that code for three proteins each of size 492 aa, interrupted by seven introns have been identified in potatoes. StCAT proteins were found to be localized in the peroxisome which is judged as the main H2O2 cell production site during different processes. Many regulating cis-elements related to stress responses and plant hormones signaling were found in the promoter sequence of each gene. The analysis of motifs and phylogenetic trees showed that StCAT are closer to their homologous in S. lycopersicum and share a 41% – 95% identity with other plants’ CATs. Expression profiling revealed that StCAT1 is the constitutively expressive member; while StCAT2 and StCAT3 are the stress-responsive members.

scholarly journals A genome-wide screen in the mouse liver reveals sex-specific and cell non-autonomous regulation of cell fitness

2021 ◽  
Author(s):  
Heather R. Keys ◽  
Kristin A. Knouse
Keyword(s):  
Functional Genomics ◽  
High Throughput ◽  
Mouse Liver ◽  
Ex Vivo ◽  
Screening Method ◽  
Living Organism ◽  
Cellular Processes ◽  
Autonomous Regulation ◽  
Genome Wide ◽  
A Genome

ABSTRACTOur ability to understand and modulate mammalian physiology and disease requires knowing how all genes contribute to any given phenotype in the organism. Genome-wide screening using CRISPR-Cas9 has emerged as a powerful method for the genetic dissection of cellular processes1,2, but the need to stably deliver single guide RNAs to millions of cells has restricted its implementation to ex vivo systems. These ex vivo systems cannot reproduce all of the cellular phenotypes observed in vivo nor can they recapitulate all of the factors that influence these phenotypes. There thus remains a pressing need for high-throughput functional genomics in a living organism. Here, we establish accessible genome-wide screening in the mouse liver and use this approach to uncover the complete regulation of cellular fitness in a living organism. We discover novel sex-specific and cell non-autonomous regulation of cell growth and viability. In particular, we find that the class I major histocompatibility complex is essential for preventing immune-mediated clearance of hepatocytes. Our approach provides the first comprehensive picture of cell fitness in a living organism and highlights the importance of investigating cellular phenomena in their native context. Our screening method is robust, scalable, and easily adapted to examine diverse cellular processes using any CRISPR application. We have hereby established a foundation for high-throughput functional genomics in a living mammal, enabling unprecedented insight into mammalian physiology and disease.

scholarly journals Genome-wide identification and analysis of cystatin family genes in Sorghum (Sorghum bicolor (L.) Moench)

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10617
Author(s):  
Jie Li ◽  
Xinhao Liu ◽  
Qingmei Wang ◽  
Junyan Sun ◽  
Dexian He
Keyword(s):  
Gene Family ◽  
Seed Development ◽  
Stress Responses ◽  
Abiotic Stresses ◽  
Expression Profiles ◽  
Seed Formation ◽  
Aphid Infestation ◽  
Genome Wide ◽  
A Genome ◽  
Cystatin Family

To set a systematic study of the Sorghum cystatins (SbCys) gene family, a genome-wide analysis of the SbCys family genes was performed by bioinformatics-based methods. In total, 18 SbCys genes were identified in Sorghum, which were distributed unevenly on chromosomes, and two genes were involved in a tandem duplication event. All SbCys genes had similar exon/intron structure and motifs, indicating their high evolutionary conservation. Transcriptome analysis showed that 16 SbCys genes were expressed in different tissues, and most genes displayed higher expression levels in reproductive tissues than in vegetative tissues, indicating that the SbCys genes participated in the regulation of seed formation. Furthermore, the expression profiles of the SbCys genes revealed that seven cystatin family genes were induced during Bipolaris sorghicola infection and only two genes were responsive to aphid infestation. In addition, quantitative real-time polymerase chain reaction (qRT-PCR) confirmed that 17 SbCys genes were induced by one or two abiotic stresses (dehydration, salt, and ABA stresses). The interaction network indicated that SbCys proteins were associated with several biological processes, including seed development and stress responses. Notably, the expression of SbCys4 was up-regulated under biotic and abiotic stresses, suggesting its potential roles in mediating the responses of Sorghum to adverse environmental impact. Our results provide new insights into the structural and functional characteristics of the SbCys gene family, which lay the foundation for better understanding the roles and regulatory mechanism of Sorghum cystatins in seed development and responses to different stress conditions.

scholarly journals Correction: A Genome-Wide Analysis of Promoter-Mediated Phenotypic Noise in Escherichia coli

PLoS Genetics ◽  
2012 ◽  
Vol 8 (5) ◽  
Author(s):  
Olin K. Silander ◽  
Nela Nikolic ◽  
Alon Zaslaver ◽  
Anat Bren ◽  
Ilya Kikoin ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
A Genome
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