scholarly journals The MarR-type regulator MalR is involved in stress-responsive cell envelope remodeling inCorynebacterium glutamicum

2019 ◽  
Author(s):  
Max Hünnefeld ◽  
Marcus Persicke ◽  
Jörn Kalinowski ◽  
Julia Frunzke
Keyword(s):  
Gene Expression ◽  
Antibiotic Treatment ◽  
Target Genes ◽  
Cell Envelope ◽  
Affinity Purification ◽  
Stress Protein ◽  
Bacterial Cells ◽  
Phage Gene ◽  
A Genome ◽  
Target Promoters

1AbstractIt is the enormous adaptive capacity of microorganisms, which is key to their competitive success in nature, but also challenges antibiotic treatment of human diseases. To deal with a diverse set of stresses, bacteria are able to reprogram gene expression using a wide variety of transcription factors. Here, we focused on the MarR-type regulator MalR conserved in theCorynebacterineae, including the prominent pathogensCorynebacterium diphtheriaeandMycobacterium tuberculosis. In several corynebacterial species, themalRgene forms an operon with a gene encoding a universal stress protein (uspA). Chromatin-affinity purification and sequencing (ChAP-Seq) analysis revealed that MalR binds more than 60 target promoters in theC. glutamicumgenome as well as in the large cryptic prophage CGP3. Overproduction of MalR caused severe growth defects and an elongated cell morphology. ChAP-Seq data combined with a global transcriptome analysis of themalRoverexpression strain emphasized a central role of MalR in cell envelope remodeling in response to environmental stresses. Prominent MalR targets are for example involved in peptidoglycan biosynthesis and synthesis of branched-chain fatty acids. Phenotypic microarrays suggest an altered sensitivity of a ΔmalRmutant towards several β-lactam antibiotics. We furthermore revealed MalR as a repressor of several prophage genes suggesting that MalR may be involved in the control of stress-responsive induction of the large CGP3 element. In conclusion, our results emphasize MalR as a regulator involved in stress-responsive remodeling of the cell envelope ofC. glutamicumand suggest a link between cell envelope stress and the control of phage gene expression.ImportanceBacteria live in changing environments that force the cells to be highly adaptive. The cell envelope represents both, a barrier against harsh external conditions and an interaction interface. The dynamic remodeling of the cell envelope as a response towards, e.g. antibiotic treatment represents a major challenge in the treatment of diseases. Members of the MarR family of regulators are known to contribute to an adaptation of bacterial cells towards antibiotic stress. However, our knowledge on this adaptive response was so far restricted to a small number of well-described target genes. In this study, we performed a genome-wide profiling of DNA-binding of the MarR-type regulator MalR ofC. glutamicum, which is conserved in several coryne- and mycobacterial species. By binding to more than 60 different target promoters, MalR is shaping a global reprogramming of gene expression conferring a remodeling of the cell envelope in response to stress.

scholarly journals Genome-Wide Analysis of Glucocorticoid-Responsive Transcripts in the Hypothalamic Paraventricular Region of Male Rats

Endocrinology ◽  
2018 ◽  
Vol 160 (1) ◽  
pp. 38-54 ◽  
Author(s):  
Keiichi Itoi ◽  
Ikuko Motoike ◽  
Ying Liu ◽  
Sam Clokie ◽  
Yasumasa Iwasaki ◽  
...  
Keyword(s):  
Gene Expression ◽  
Target Genes ◽  
Receptor Gene ◽  
Male Rats ◽  
Regulatory Mechanisms ◽  
High Dose ◽  
Sequencing Analysis ◽  
Reverse Transcription Pcr ◽  
Genome Wide ◽  
A Genome

Abstract Glucocorticoids (GCs) are essential for stress adaptation, acting centrally and in the periphery. Corticotropin-releasing factor (CRF), a major regulator of adrenal GC synthesis, is produced in the paraventricular nucleus of the hypothalamus (PVH), which contains multiple neuroendocrine and preautonomic neurons. GCs may be involved in diverse regulatory mechanisms in the PVH, but the target genes of GCs are largely unexplored except for the CRF gene (Crh), a well-known target for GC negative feedback. Using a genome-wide RNA-sequencing analysis, we identified transcripts that changed in response to either high-dose corticosterone (Cort) exposure for 12 days (12-day high Cort), corticoid deprivation for 7 days (7-day ADX), or acute Cort administration. Among others, canonical GC target genes were upregulated prominently by 12-day high Cort. Crh was upregulated or downregulated most prominently by either 7-day ADX or 12-day high Cort, emphasizing the recognized feedback effects of GC on the hypothalamic-pituitary-adrenal (HPA) axis. Concomitant changes in vasopressin and apelin receptor gene expression are likely to contribute to HPA repression. In keeping with the pleotropic cellular actions of GCs, 7-day ADX downregulated numerous genes of a broad functional spectrum. The transcriptome response signature differed markedly between acute Cort injection and 12-day high Cort. Remarkably, six immediate early genes were upregulated 1 hour after Cort injection, which was confirmed by quantitative reverse transcription PCR and semiquantitative in situ hybridization. This study may provide a useful database for studying the regulatory mechanisms of GC-dependent gene expression and repression in the PVH.

New insights into promoter–enhancer communication mechanisms revealed by dynamic single-molecule imaging

2021 ◽  
Author(s):  
Jieru Li ◽  
Alexandros Pertsinidis
Keyword(s):  
Gene Expression ◽  
Single Molecule ◽  
Target Genes ◽  
Regulatory Elements ◽  
Specific Gene ◽  
Single Molecule Imaging ◽  
Cell Type ◽  
Regulatory Information ◽  
Cell Type Specific ◽  
Target Promoters

Establishing cell-type-specific gene expression programs relies on the action of distal enhancers, cis-regulatory elements that can activate target genes over large genomic distances — up to Mega-bases away. How distal enhancers physically relay regulatory information to target promoters has remained a mystery. Here, we review the latest developments and insights into promoter–enhancer communication mechanisms revealed by live-cell, real-time single-molecule imaging approaches.

scholarly journals The TEA Transcription Factor Tec1 Confers Promoter-Specific Gene Regulation by Ste12-Dependent and -Independent Mechanisms

2010 ◽  
Vol 9 (4) ◽  
pp. 514-531 ◽  
Author(s):  
Barbara Heise ◽  
Julia van der Felden ◽  
Sandra Kern ◽  
Mario Malcher ◽  
Stefan Brückner ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Transcriptional Activation ◽  
Binding Sites ◽  
Target Genes ◽  
Specific Gene ◽  
Dependent Manner ◽  
A Genome ◽  
Regulated Gene Expression

ABSTRACT In Saccharomyces cerevisiae, the TEA transcription factor Tec1 is known to regulate target genes together with a second transcription factor, Ste12. Tec1-Ste12 complexes can activate transcription through Tec1 binding sites (TCSs), which can be further combined with Ste12 binding sites (PREs) for cooperative DNA binding. However, previous studies have hinted that Tec1 might regulate transcription also without Ste12. Here, we show that in vivo, physiological amounts of Tec1 are sufficient to stimulate TCS-mediated gene expression and transcription of the FLO11 gene in the absence of Ste12. In vitro, Tec1 is able to bind TCS elements with high affinity and specificity without Ste12. Furthermore, Tec1 contains a C-terminal transcriptional activation domain that confers Ste12-independent activation of TCS-regulated gene expression. On a genome-wide scale, we identified 302 Tec1 target genes that constitute two distinct classes. A first class of 254 genes is regulated by Tec1 in a Ste12-dependent manner and is enriched for genes that are bound by Tec1 and Ste12 in vivo. In contrast, a second class of 48 genes can be regulated by Tec1 independently of Ste12 and is enriched for genes that are bound by the stress transcription factors Yap6, Nrg1, Cin5, Skn7, Hsf1, and Msn4. Finally, we find that combinatorial control by Tec1-Ste12 complexes stabilizes Tec1 against degradation. Our study suggests that Tec1 is able to regulate TCS-mediated gene expression by Ste12-dependent and Ste12-independent mechanisms that enable promoter-specific transcriptional control.

scholarly journals Dissection of Combinatorial Control by the Met4 Transcriptional Complex

2010 ◽  
Vol 21 (3) ◽  
pp. 456-469 ◽  
Author(s):  
Traci A. Lee ◽  
Paul Jorgensen ◽  
Andrew L. Bognar ◽  
Caroline Peyraud ◽  
Dominique Thomas ◽  
...  
Keyword(s):  
Dna Binding ◽  
Metabolic Network ◽  
Target Genes ◽  
A Genome ◽  
Wide Scale ◽  
Combinatorial System ◽  
Transcriptional Complex ◽  
Differential Transcription ◽  
Target Promoters

Met4 is the transcriptional activator of the sulfur metabolic network in Saccharomyces cerevisiae. Lacking DNA-binding ability, Met4 must interact with proteins called Met4 cofactors to target promoters for transcription. Two types of DNA-binding cofactors (Cbf1 and Met31/Met32) recruit Met4 to promoters and one cofactor (Met28) stabilizes the DNA-bound Met4 complexes. To dissect this combinatorial system, we systematically deleted each category of cofactor(s) and analyzed Met4-activated transcription on a genome-wide scale. We defined a core regulon for Met4, consisting of 45 target genes. Deletion of both Met31 and Met32 eliminated activation of the core regulon, whereas loss of Met28 or Cbf1 interfered with only a subset of targets that map to distinct sectors of the sulfur metabolic network. These transcriptional dependencies roughly correlated with the presence of Cbf1 promoter motifs. Quantitative analysis of in vivo promoter binding properties indicated varying levels of cooperativity and interdependency exists between members of this combinatorial system. Cbf1 was the only cofactor to remain fully bound to target promoters under all conditions, whereas other factors exhibited different degrees of regulated binding in a promoter-specific fashion. Taken together, Met4 cofactors use a variety of mechanisms to allow differential transcription of target genes in response to various cues.

scholarly journals Genome-Wide Phylogenetic Analysis, Expression Pattern, and Transcriptional Regulatory Network of the Pig C/EBP Gene Family

2021 ◽  
Vol 17 ◽  
pp. 117693432110413
Author(s):  
Chaoxin Zhang ◽  
Tao Wang ◽  
Tongyan Cui ◽  
Shengwei Liu ◽  
Bing Zhang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Phylogenetic Analysis ◽  
Regulatory Network ◽  
Target Genes ◽  
Transcriptional Regulatory Network ◽  
Expression Patterns ◽  
Enrichment Analysis ◽  
Functional Enrichment ◽  
Genome Wide ◽  
A Genome

The CCAAT/enhancer binding protein (C/EBP) transcription factors (TFs) regulate many important biological processes, such as energy metabolism, inflammation, cell proliferation etc. A genome-wide gene identification revealed the presence of a total of 99 C/EBP genes in pig and 19 eukaryote genomes. Phylogenetic analysis showed that all C/EBP TFs were classified into 6 subgroups named C/EBPα, C/EBPβ, C/EBPδ, C/EBPε, C/EBPγ, and C/EBPζ. Gene expression analysis showed that the C/EBPα, C/EBPβ, C/EBPδ, C/EBPγ, and C/EBPζ genes were expressed ubiquitously with inconsistent expression patterns in various pig tissues. Moreover, a pig C/EBP regulatory network was constructed, including C/EBP genes, TFs and miRNAs. A total of 27 feed-forward loop (FFL) motifs were detected in the pig C/EBP regulatory network. Based on the RNA-seq data, gene expression patterns related to FFL sub-network were analyzed in 27 adult pig tissues. Certain FFL motifs may be tissue specific. Functional enrichment analysis indicated that C/EBP and its target genes are involved in many important biological pathways. These results provide valuable information that clarifies the evolutionary relationships of the C/EBP family and contributes to the understanding of the biological function of C/EBP genes.

scholarly journals The Influence of 3′UTRs on MicroRNA Function Inferred from Human SNP Data

2011 ◽  
Vol 2011 ◽  
pp. 1-9 ◽  
Author(s):  
Zihua Hu ◽  
Andrew E. Bruno
Keyword(s):  
Gene Expression ◽  
Mirna Target ◽  
Target Genes ◽  
Nucleotide Polymorphisms ◽  
Snp Data ◽  
A Genome ◽  
Local Sequence ◽  
Target Sites ◽  
Sequence Region ◽  
Microrna Function

MicroRNAs (miRNAs) regulate gene expression posttranscriptionally. Although previous efforts have demonstrated the functional importance of target sites on miRNAs, little is known about the influence of the rest of 3′ untranslated regions (3′UTRs) of target genes on microRNA function. We conducted a genome-wide study and found that the entire 3′UTR sequences could also play important roles on miRNA function in addition to miRNA target sites. This was evidenced by the fact that human single nucleotide polymorphisms (SNPs) on both seed target region and the rest of 3′UTRs of miRNA target genes were under significantly stronger negative selection, when compared to non-miRNA target genes. We also discovered that the flanking nucleotides on both sides of miRNA target sites were subject to moderate strong selection. A local sequence region of ~67 nucleotides with symmetric structure is herein defined. Additionally, from gene expression analysis, we found that SNPs and miRNA target sites on target sequences may interactively affect gene expression.

scholarly journals Possible differences in efficiency of guide RNA with different spacer sequence in CRISPR knock-down or knock-out of particular gene

2019 ◽  
Author(s):  
Wenfa Ng
Keyword(s):  
Gene Expression ◽  
Genome Editing ◽  
Target Gene ◽  
Target Genes ◽  
Fluorescent Protein ◽  
Bacterial Cells ◽  
Fluorescent Intensity ◽  
Guide Rna ◽  
Targeting Efficiency ◽  
Template Dna

Cluster regularly interspersed short palindromic repeats (CRISPR) mediated genome editing has emerged as the dominant technique for modulating the expression of target genes. Specifically, when coupled with different effectors, CRISPR could be utilized to either activate or repress gene expression. Specificity of the CRISPR gene editing method arises from the unique spacer sequence in guide RNA that mediates the specific localization of Cas9 endonuclease to particular stretches of DNA. However, complementary base pairing between the guide RNA and template DNA depends critically on existence of protospacer adjacent motif (PAM) sequence immediately downstream of the spacer sequence. Such three nucleotide PAM sequence could be present at multiple loci in a given gene, which meant that different spacer sequence could be incorporated in guide RNA design to target the same gene. Given that different spacer sequences have different binding affinities to template DNA, differences could exist in the efficiency in which CRISPR-Cas9 could be guided to generate a double strand break in a particular gene locus. Using green fluorescent protein (GFP) reporter gene expressed in recombinant Escherichia coli as experimental system, this study sought to understand if differences in targeting efficiency exist between guide RNA with different spacer sequence that could target the same gene. Fluorescent intensity of cells at the population level would serve as readout of the targeting efficiency. For example, spacer sequence in guide RNA that could better activate the endonuclease activity of Cas9 would result in lower fluorescent intensity of GFP. To check for the effect of expression mode on targeting efficiency of guide RNA, GFP gene would be expressed on a plasmid in E. coli as well as integrated into the genome of the bacterium. Doing so would provide critical information on whether the CRISPR-Cas9 system has differentiated efficacy in generating double strand breaks in genomic versus plasmid DNA. Such information would inform future experimental design involving CRISPR-Cas9 genome editing technology as well as hold implications on how CRISPR evolved as an adaptive immune system in defending bacterial cells against foreign DNA. Given the goal of the study to understand the relative extent in which a target gene would be disrupted by CRISPR-Cas9 guided by different spacer sequence on guide RNA, no repair module for the target gene would be provided. Collectively, multiple occurrence of PAM sequence in a target gene meant that different spacer sequences could be used in CRISPR-Cas9 to downregulate gene expression. Relative efficacies of different spacer sequence in guide RNA in achieving targeted gene inactivation remain poorly understood and constitutes the basis of this study, which hopefully would provide guidance on the selection of specific spacer sequence that would yield the most efficacious disruption of gene expression at the genome and plasmid level.

scholarly journals Transcriptomic Analysis of Sinorhizobium meliloti and Medicago truncatula Symbiosis Using Nitrogen Fixation–Deficient Nodules

2015 ◽  
Vol 28 (8) ◽  
pp. 856-868 ◽  
Author(s):  
Claus Lang ◽  
Sharon R. Long
Keyword(s):  
Gene Expression ◽  
Nitrogen Fixation ◽  
Bacterial Infection ◽  
Medicago Truncatula ◽  
Sinorhizobium Meliloti ◽  
Cell Envelope ◽  
Root Nodules ◽  
Bacterial Cells ◽  
Nitrogen Fixing ◽  
Bacterial Genes

The bacterium Sinorhizobium meliloti interacts symbiotically with legume plant hosts such as Medicago truncatula to form nitrogen-fixing root nodules. During symbiosis, plant and bacterial cells differentiate in a coordinated manner, resulting in specialized plant cells that contain nitrogen-fixing bacteroids. Both plant and bacterial genes are required at each developmental stage of symbiosis. We analyzed gene expression in nodules formed by wild-type bacteria on six plant mutants with defects in nitrogen fixation. We observed differential expression of 482 S. meliloti genes with functions in cell envelope homeostasis, cell division, stress response, energy metabolism, and nitrogen fixation. We simultaneously analyzed gene expression in M. truncatula and observed differential regulation of host processes that may trigger bacteroid differentiation and control bacterial infection. Our analyses of developmentally arrested plant mutants indicate that plants use distinct means to control bacterial infection during early and late symbiotic stages.

scholarly journals Mechanisms of enhancer action: the known and the unknown

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Anil Panigrahi ◽  
Bert W. O’Malley
Keyword(s):  
Gene Expression ◽  
Differential Gene Expression ◽  
Transcriptional Activation ◽  
Target Genes ◽  
Cell Types ◽  
Regulatory Sequences ◽  
Quantitative Expression ◽  
Full Complement ◽  
Differential Gene ◽  
Target Promoters

AbstractDifferential gene expression mechanisms ensure cellular differentiation and plasticity to shape ontogenetic and phylogenetic diversity of cell types. A key regulator of differential gene expression programs are the enhancers, the gene-distal cis-regulatory sequences that govern spatiotemporal and quantitative expression dynamics of target genes. Enhancers are widely believed to physically contact the target promoters to effect transcriptional activation. However, our understanding of the full complement of regulatory proteins and the definitive mechanics of enhancer action is incomplete. Here, we review recent findings to present some emerging concepts on enhancer action and also outline a set of outstanding questions.

scholarly journals The Mettl3 epitranscriptomic writer amplifies p53 stress responses

2021 ◽  
Author(s):  
Nitin Raj ◽  
Mengxiong Wang ◽  
Jose A Seoane ◽  
Nancie A Moonie ◽  
Janos Demeter ◽  
...  
Keyword(s):  
Gene Expression ◽  
Stress Responses ◽  
Target Genes ◽  
Human Cancer ◽  
Affinity Purification ◽  
P53 Protein ◽  
Critical Role ◽  
Protein Stabilization ◽  
Negative Regulator ◽  
P53 Target Genes

The p53 transcription factor, encoded by the most frequently mutated gene in human cancer, plays a critical role in tissue homeostasis in response to stress signals. The mechanisms through which p53 promotes downstream tumor suppressive gene expression programs remain, however, only superficially understood. Here, we used tandem affinity purification and mass spectrometry to reveal new components of the p53 response. This approach uncovered Mettl3, a component of the m6A RNA methyltransferase complex (MTC), as a p53-interacting protein. Analysis of Mettl3-deficient cells revealed that Mettl3 promotes p53 protein stabilization and target gene expression in response to DNA damage. Mettl3 acts in part by competing with the p53 negative regulator, Mdm2, for binding to the p53 transactivation domains to promote methyltransferase-independent stabilization of p53. In addition, Mettl3 relies on its catalytic activity to augment p53 responses, with p53 recruiting Mettl3 to p53 target genes to co-transcriptionally direct m6A modification of p53 pathway transcripts to enhance their expression. Mettl3 also promotes p53 activity downstream of oncogenic signals in vivo, in both allograft and autochthonous lung adenocarcinoma models, suggesting cooperative action of p53 and Mettl3 in tumor suppression. Accordingly, we found in diverse human cancers that mutations in MTC components perturb expression of p53 target genes and that MTC mutations are mutually exclusive with TP53 mutations, suggesting that the MTC enhances the p53 transcriptional program in human cancer. Together, these studies reveal a fundamental role for Mettl3 in amplifying p53 signaling through protein stabilization and epitranscriptome regulation.

Sign in / Sign up

Export Citation Format

Share Document