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 Quantitative mapping of mRNA 3’ ends in Pseudomonas aeruginosa reveals putative riboregulators and a pervasive role for transcription termination in response to azithromycin

2020 ◽  
Author(s):  
Salini Konikkat ◽  
Michelle R. Scribner ◽  
Rory Eutsey ◽  
N. Luisa Hiller ◽  
Vaughn S. Cooper ◽  
...  
Keyword(s):  
Cystic Fibrosis ◽  
Stress Responses ◽  
Biofilm Formation ◽  
Molecular Mechanisms ◽  
Transcription Termination ◽  
Transcriptional Response ◽  
Chronic Infections ◽  
Biofilm Growth ◽  
Persistent Infections ◽  
Upregulated Genes

ABSTRACTP. aeruginosa produces serious chronic infections in hospitalized patients and immunocompromised individuals, including cystic fibrosis patients. The molecular mechanisms by which P. aeruginosa responds to antibiotics and other stresses to promote persistent infections may provide new avenues for therapeutic intervention. Azithromycin (AZM), an antibiotic frequently used in cystic fibrosis treatment, is thought to improve clinical outcomes through a number of mechanisms including impaired biofilm growth and QS. The mechanisms underlying the transcriptional response to AZM remain unclear. Here, we interrogated the P. aeruginosa transcriptional response to AZM using an improved genome-wide approach to quantitate RNA 3’-ends (3pMap). We also identified hundreds of P. aeruginosa genes subject to premature transcription termination in their transcript leaders using 3pMap. AZM treatment of planktonic and biofilm cultures alters the expression of hundreds of genes, including those involved in QS, biofilm formation, and virulence. Strikingly, most genes downregulated by AZM in biofilms had increased levels of intragenic 3’-ends indicating premature transcription termination or pausing. Reciprocally, AZM reduced premature transcription termination in many upregulated genes. Most notably, reduced termination accompanied robust induction of obgE, a GTPase involved in persister formation in P. aeruginosa. Our results support a model in which AZM-induced premature transcription termination downregulates expression of central transcriptional regulators, which in turn both impairs QS and biofilm formation, and stress responses, while upregulating genes associated with persistence.

scholarly journals The SIN3A histone deacetylase complex is required for a complete transcriptional response to hypoxia

2017 ◽  
Author(s):  
Maria Tiana ◽  
Barbara Acosta-Iborra ◽  
Laura Puente-Santamaría ◽  
Pablo Hernansanz-Agustin ◽  
Rebecca Worsley-Hunt ◽  
...  
Keyword(s):  
Histone Deacetylase ◽  
Environmental Changes ◽  
Transcriptional Response ◽  
Specific Gene ◽  
Transcriptional Level ◽  
Genome Wide ◽  
Repressor Complex ◽  
Nascent Transcripts ◽  
Upregulated Genes ◽  
Transcriptional Output

ABSTRACTCells adapt to environmental changes, including fluctuations in oxygen levels, through the induction of specific gene expression programs. To identify genes regulated by hypoxia at the transcriptional level, we pulse-labeled HUVEC cells with 4-thiouridine and sequenced nascent transcripts. Then, we searched genome-wide binding profiles from the ENCODE project for factors that correlated with changes in transcription and identified binding of several components of the Sin3A co-repressor complex, including SIN3A, SAP30 and HDAC1/2, proximal to genes repressed by hypoxia.SIN3Ainterference revealed that it participates in the downregulation of 75% of the hypoxia-repressed genes in endothelial cells. Unexpectedly, it also blunted the induction of 47% of the upregulated genes, suggesting a role for this corepressor in gene induction. In agreement, ChIP-seq experiments showed that SIN3A preferentially localizes to the promoter region of actively transcribed genes and that SIN3A signal was enriched in hypoxia-repressed genes, prior exposure to the stimulus. Importantly, SINA3 occupancy was not altered by hypoxia in spite of changes in H3K27ac signal. In summary, our results reveal a prominent role for SIN3A in the transcriptional response to hypoxia and suggest a model where modulation of the associated histone deacetylase activity, rather than its recruitment, determines the transcriptional output.

scholarly journals Genome-wide profiling of long noncoding RNAs involved in wheat spike development

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Pei Cao ◽  
Wenjuan Fan ◽  
Pengjia Li ◽  
Yuxin Hu
Keyword(s):  
Stress Responses ◽  
Regulatory Networks ◽  
Developmental Stages ◽  
Genetic Manipulation ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Differentially Expressed ◽  
Genome Wide ◽  
Spike Development ◽  
Wheat Spike

Abstract Background Long noncoding RNAs (lncRNAs) have been shown to play important roles in the regulation of plant growth and development. Recent transcriptomic analyses have revealed the gene expression profiling in wheat spike development, however, the possible regulatory roles of lncRNAs in wheat spike morphogenesis remain largely unclear. Results Here, we analyzed the genome-wide profiling of lncRNAs during wheat spike development at six stages, and identified a total of 8,889 expressed lncRNAs, among which 2,753 were differentially expressed lncRNAs (DE lncRNAs) at various developmental stages. Three hundred fifteen differentially expressed cis- and trans-regulatory lncRNA-mRNA pairs comprised of 205 lncRNAs and 279 genes were predicted, which were found to be mainly involved in the stress responses, transcriptional and enzymatic regulations. Moreover, the 145 DE lncRNAs were predicted as putative precursors or target mimics of miRNAs. Finally, we identified the important lncRNAs that participate in spike development by potentially targeting stress response genes, TF genes or miRNAs. Conclusions This study outlines an overall view of lncRNAs and their possible regulatory networks during wheat spike development, which also provides an alternative resource for genetic manipulation of wheat spike architecture and thus yield.

scholarly journals The Role of OsWRKY Genes in Rice When Faced with Single and Multiple Abiotic Stresses

Agronomy ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 1301
Author(s):  
Rajendran Jeyasri ◽  
Pandiyan Muthuramalingam ◽  
Lakkakula Satish ◽  
Sivakumar Adarshan ◽  
Muthukannan Aishwarya Lakshmi ◽  
...  
Keyword(s):  
Stress Responses ◽  
In Silico ◽  
Regulatory Networks ◽  
Oryza Sativa L ◽  
Family Interactions ◽  
Transcriptional Reprogramming ◽  
Genome Wide ◽  
A Genome ◽  
Spatio Temporal

The WRKY genes are one of the largest families of transcription factors (TFs) and play a crucial role in certain processes in plants including stress signaling, regulation of transcriptional reprogramming associated with stress responses, and other regulatory networks. This study aims to investigate the WRKY gene family in the C3 model plant, Oryza sativa L., using a genome-wide in silico expression analysis. Firstly, 104 WRKY TF family members were identified, and then their molecular properties and expression signatures were analyzed systematically. In silico spatio-temporal and hormonal expression profiling revealed the roles of OsWRKY genes and their dynamism in diverse developmental tissues and hormones, respectively. Comparative mapping between OsWRKY genes and their synteny with C4 panicoid genomes showed the evolutionary insights of the WRKY TF family. Interactions of OsWRKY coding gene sequences represented the complexity of abiotic stress (AbS) and their molecular cross-talks. The expression signature of 26 novel candidate genes in response to stresses exhibited the putative involvement of individual and combined AbS (CAbS) responses. These novel findings unravel the in-depth insights into OsWRKY TF genes and delineate the plant developmental metabolisms and their functional regulations in individual and CAbS conditions.

scholarly journals X chromosome-dependent disruption of placental regulatory networks in hybrid dwarf hamsters

Genetics ◽  
2021 ◽  
Author(s):  
Thomas D Brekke ◽  
Emily C Moore ◽  
Shane C Campbell-Staton ◽  
Colin M Callahan ◽  
Zachary A Cheviron ◽  
...  
Keyword(s):  
Gene Expression ◽  
X Chromosome ◽  
Regulatory Networks ◽  
Mammalian Species ◽  
Strongly Correlated ◽  
Placental Development ◽  
Substitution Lines ◽  
Genome Wide ◽  
Highly Sensitive ◽  
First And Second Generation

AbstractEmbryonic development in mammals is highly sensitive to changes in gene expression within the placenta. The placenta is also highly enriched for genes showing parent-of-origin or imprinted expression, which is predicted to evolve rapidly in response to parental conflict. However, little is known about the evolution of placental gene expression, or if divergence of placental gene expression plays an important role in mammalian speciation. We used crosses between two species of dwarf hamsters (Phodopus sungorus and Phodopus campbelli) to examine the genetic and regulatory underpinnings of severe placental overgrowth in their hybrids. Using quantitative genetic mapping and mitochondrial substitution lines, we show that overgrowth of hybrid placentas was primarily caused by genetic differences on the maternally inherited P. sungorus X chromosome. Mitochondrial interactions did not contribute to abnormal hybrid placental development, and there was only weak correspondence between placental disruption and embryonic growth. Genome-wide analyses of placental transcriptomes from the parental species and first- and second-generation hybrids revealed a central group of co-expressed X-linked and autosomal genes that were highly enriched for maternally biased expression. Expression of this gene network was strongly correlated with placental size and showed widespread misexpression dependent on epistatic interactions with X-linked hybrid incompatibilities. Collectively, our results indicate that the X chromosome is likely to play a prominent role in the evolution of placental gene expression and the accumulation of hybrid developmental barriers between mammalian species.

scholarly journals High-throughput single-cell chromatin accessibility CRISPR screens enable unbiased identification of regulatory networks in cancer

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Sarah E. Pierce ◽  
Jeffrey M. Granja ◽  
William J. Greenleaf
Keyword(s):  
Transcription Factor ◽  
Single Cell ◽  
Cancer Cells ◽  
High Throughput ◽  
Regulatory Networks ◽  
Temporal Dynamics ◽  
Chromatin Accessibility ◽  
Regulatory Regions ◽  
Factor Binding ◽  
Genome Wide

AbstractChromatin accessibility profiling can identify putative regulatory regions genome wide; however, pooled single-cell methods for assessing the effects of regulatory perturbations on accessibility are limited. Here, we report a modified droplet-based single-cell ATAC-seq protocol for perturbing and evaluating dynamic single-cell epigenetic states. This method (Spear-ATAC) enables simultaneous read-out of chromatin accessibility profiles and integrated sgRNA spacer sequences from thousands of individual cells at once. Spear-ATAC profiling of 104,592 cells representing 414 sgRNA knock-down populations reveals the temporal dynamics of epigenetic responses to regulatory perturbations in cancer cells and the associations between transcription factor binding profiles.

scholarly journals Genome-Wide Analysis of the Trihelix Gene Family and Their Response to Cold Stress in Dendrobium officinale

2021 ◽  
Vol 13 (5) ◽  
pp. 2826
Author(s):  
Yan Tong ◽  
Hui Huang ◽  
YuHua Wang
Keyword(s):  
Stress Responses ◽  
Cold Treatment ◽  
Dendrobium Officinale ◽  
Functional Domain ◽  
Cis Elements ◽  
Genome Wide Analysis ◽  
Functional Studies ◽  
Genome Wide ◽  
Growth Development ◽  
Chinese Medicinal Plant

Trihelix transcription factors play important roles in plant growth, development and various stress responses. In this study, we identified 32 trihelix family genes (DoGT) in the important Chinese medicinal plant Dendrobium officinale. These trihelix genes could be classified into five different subgroups. The gene structure and conserved functional domain of these trihelix genes were similar in the same subfamily but diverged between different subfamilies. Various stresses responsive cis-elements presented in the promoters of DoGT genes, suggesting that the trihelix genes might respond to the environmental stresses. Expressional changes of DoGT genes in three tissues and under cold treatment suggested that trihelix genes were involved in diverse functions during D. officinale development and cold tolerance. This study provides novel insights into the phylogenetic relationships and functions of the D. officinaletrihelix genes, which will aid future functional studies investigating the divergent roles of trihelix genes belonging to other species.

scholarly journals Contrasting roles of GmNAC065 and GmNAC085 in natural senescence, plant development, multiple stresses and cell death responses

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Bruno Paes Melo ◽  
Isabela Tristan Lourenço-Tessutti ◽  
Otto Teixeira Fraga ◽  
Luanna Bezerra Pinheiro ◽  
Camila Barrozo de Jesus Lins ◽  
...  
Keyword(s):  
Cell Death ◽  
Plant Development ◽  
Stress Responses ◽  
Regulatory Networks ◽  
Lower Stress ◽  
Multiple Stresses ◽  
Gene Sets ◽  
Ros Accumulation ◽  
Stress Dependent ◽  
Senescence Associated Genes

AbstractNACs are plant-specific transcription factors involved in controlling plant development, stress responses, and senescence. As senescence-associated genes (SAGs), NACs integrate age- and stress-dependent pathways that converge to programmed cell death (PCD). In Arabidopsis, NAC-SAGs belong to well-characterized regulatory networks, poorly understood in soybean. Here, we interrogated the soybean genome and provided a comprehensive analysis of senescence-associated Glycine max (Gm) NACs. To functionally examine GmNAC-SAGs, we selected GmNAC065, a putative ortholog of Arabidopsis ANAC083/VNI2 SAG, and the cell death-promoting GmNAC085, an ANAC072 SAG putative ortholog, for analyses. Expression analysis of GmNAC065 and GmNAC085 in soybean demonstrated (i) these cell death-promoting GmNACs display contrasting expression changes during age- and stress-induced senescence; (ii) they are co-expressed with functionally different gene sets involved in stress and PCD, and (iii) are differentially induced by PCD inducers. Furthermore, we demonstrated GmNAC065 expression delays senescence in Arabidopsis, a phenotype associated with enhanced oxidative performance under multiple stresses, higher chlorophyll, carotenoid and sugar contents, and lower stress-induced PCD compared to wild-type. In contrast, GmNAC085 accelerated stress-induced senescence, causing enhanced chlorophyll loss, ROS accumulation and cell death, decreased antioxidative system expression and activity. Accordingly, GmNAC065 and GmNAC085 targeted functionally contrasting sets of downstream AtSAGs, further indicating that GmNAC85 and GmNAC065 regulators function inversely in developmental and environmental PCD.

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