scholarly journals Identification of the PhoB Regulon and Role of PhoU in the Phosphate Starvation Response of Caulobacter crescentus

2015 ◽  
Vol 198 (1) ◽  
pp. 187-200 ◽  
Author(s):  
Emma A. Lubin ◽  
Jonathan T. Henry ◽  
Aretha Fiebig ◽  
Sean Crosson ◽  
Michael T. Laub
Keyword(s):  
Target Genes ◽  
Caulobacter Crescentus ◽  
Phosphate Limitation ◽  
Transcriptional Responses ◽  
Content Type ◽  
Phosphate Starvation Response ◽  
Genome Wide ◽  
Intracellular Phosphate ◽  
Sense And Respond

ABSTRACTAn ability to sense and respond to changes in extracellular phosphate is critical for the survival of most bacteria. ForCaulobacter crescentus, which typically lives in phosphate-limited environments, this process is especially crucial. Like many bacteria,Caulobacterresponds to phosphate limitation through a conserved two-component signaling pathway called PhoR-PhoB, but the direct regulon of PhoB in this organism is unknown. Here we used chromatin immunoprecipitation-DNA sequencing (ChIP-Seq) to map the global binding patterns of the phosphate-responsive transcriptional regulator PhoB under phosphate-limited and -replete conditions. Combined with genome-wide expression profiling, our work demonstrates that PhoB is induced to regulate nearly 50 genes under phosphate-starved conditions. The PhoB regulon is comprised primarily of genes known or predicted to helpCaulobacterscavenge for and import inorganic phosphate, including 15 different membrane transporters. We also investigated the regulatory role of PhoU, a widely conserved protein proposed to coordinate phosphate import with expression of the PhoB regulon by directly modulating the histidine kinase PhoR. However, our studies show that it likely does not play such a role inCaulobacter, as PhoU depletion has no significant effect on PhoB-dependent gene expression. Instead, cells lacking PhoU exhibit striking accumulation of large polyphosphate granules, suggesting that PhoU participates in controlling intracellular phosphate metabolism.IMPORTANCEThe transcription factor PhoB is widely conserved throughout the bacterial kingdom, where it helps organisms respond to phosphate limitation by driving the expression of a battery of genes. Most of what is known about PhoB and its target genes is derived from studies ofEscherichia coli. Our work documents the PhoB regulon inCaulobacter crescentus, and comparison to the regulon inE. colireveals significant differences, highlighting the evolutionary plasticity of transcriptional responses driven by highly conserved transcription factors. We also demonstrated that the conserved protein PhoU, which is implicated in bacterial persistence, does not regulate PhoB activity, as previously suggested. Instead, our results favor a model in which PhoU affects intracellular phosphate accumulation, possibly through the high-affinity phosphate transporter.

scholarly journals Genome-wide miRNA analysis and integrated network for flavonoid biosynthesis in Osmanthus fragrans

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yong Shi ◽  
Heng Xia ◽  
Xiaoting Cheng ◽  
Libin Zhang
Keyword(s):  
Secondary Metabolites ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Expression Profiles ◽  
Flavonoid Biosynthesis ◽  
Integrated Network ◽  
Osmanthus Fragrans ◽  
Flavonoid Synthesis ◽  
Genome Wide

AbstractBackgroundOsmanthus fragransis an important economical plant containing multiple secondary metabolites including flavonoids and anthocyanins. During the past years, the roles of miRNAs in regulating the biosynthesis of secondary metabolites in plants have been widely investigated. However, few studies on miRNA expression profiles and the potential roles in regulating flavonoid biosynthesis have been reported inO. fragrans.ResultsIn this study, we used high-throughput sequencing technology to analyze the expression profiles of miRNAs in leaf and flower tissues ofO. fragrans. As a result, 106 conserved miRNAs distributed in 47 families and 88 novel miRNAs were identified. Further analysis showed there were 133 miRNAs differentially expressed in leaves and flowers. Additionally, the potential target genes of miRNAs as well as the related metabolic pathways were predicted. In the end, flavonoid content was measured in flower and leaf tissues and potential role of miR858 in regulating flavonoid synthesis was illustrated inO. fragrans.ConclusionsThis study not only provided the genome-wide miRNA profiles in the flower and leaf tissue ofO. fragrans, but also investigated the potential regulatory role of miR858a in flavonoid synthesis inO. fragrans. The results specifically indicated the connection of miRNAs to the regulation of secondary metabolite biosynthesis in non-model economical plant.

scholarly journals Identification of Genes That Contribute to the Pathogenesis of Invasive Pneumococcal Disease byIn VivoTranscriptomic Analysis

2012 ◽  
Vol 80 (9) ◽  
pp. 3268-3278 ◽  
Author(s):  
Abiodun D. Ogunniyi ◽  
Layla K. Mahdi ◽  
Claudia Trappetti ◽  
Nadine Verhoeven ◽  
Daphne Mermans ◽  
...  
Keyword(s):  
Invasive Pneumococcal Disease ◽  
Pneumococcal Disease ◽  
Targeted Mutagenesis ◽  
Content Type ◽  
Genome Wide ◽  
Blood Relative ◽  
High Level ◽  
Upregulated Genes

ABSTRACTStreptococcus pneumoniae(the pneumococcus) continues to be responsible for a high level of global morbidity and mortality resulting from pneumonia, bacteremia, meningitis, and otitis media. Here we have used a novel technique involving niche-specific, genome-widein vivotranscriptomic analyses to identify genes upregulated in distinct niches during pathogenesis after intranasal infection of mice with serotype 4 or 6A pneumococci. The analyses yielded 28 common, significantly upregulated genes in the lungs relative to those in the nasopharynx and 25 significantly upregulated genes in the blood relative to those in the lungs in both strains, some of which were previously unrecognized. The role of five upregulated genes from either the lungs or the blood in pneumococcal pathogenesis and virulence was then evaluated by targeted mutagenesis. One of the mutants (ΔmalX) was significantly attenuated for virulence in the lungs, two (ΔaliAand ΔilvH) were significantly attenuated for virulence in the blood relative to the wild type, and two others (ΔcbiOand ΔpiuA) were completely avirulent in a mouse intranasal challenge model. We also show that the products ofaliA,malX, andpiuAare promising candidates for incorporation into multicomponent protein-based pneumococcal vaccines currently under development. Importantly, we suggest that this new approach is a viable complement to existing strategies for the discovery of genes critical to the distinct stages of invasive pneumococcal disease and potentially has broad application for novel protein antigen discovery in other pathogens such asS. pyogenes,Haemophilus influenzaetype b, andNeisseria meningitidis.

Molecular network of chromatin immunoprecipitation followed by deep sequencing-based vitamin D receptor target genes

2013 ◽  
Vol 19 (8) ◽  
pp. 1035-1045 ◽  
Author(s):  
Jun-ichi Satoh ◽  
Hiroko Tabunoki
Keyword(s):  
Multiple Sclerosis ◽  
Vitamin D ◽  
Vitamin D Receptor ◽  
Deep Sequencing ◽  
Immune Cells ◽  
Chromatin Immunoprecipitation ◽  
Target Genes ◽  
Molecular Network ◽  
Genome Wide

Background: Vitamin D is a liposoluble vitamin essential for calcium metabolism. The ligand-bound vitamin D receptor (VDR), heterodimerized with retinoid X receptor, interacts with vitamin D response elements (VDREs) to regulate gene expression. Vitamin D deficiency due to insufficient sunlight exposure confers an increased risk for multiple sclerosis (MS). Objective: To study a protective role of vitamin D in multiple sclerosis (MS), it is important to characterize the global molecular network of VDR target genes (VDRTGs) in immune cells. Methods: We identified genome-wide VDRTGs collectively from two distinct chromatin immunoprecipitation followed by deep sequencing (ChIP-Seq) datasets of VDR-binding sites derived from calcitriol-treated human cells of B cell and monocyte origins. We mapped short reads of next generation sequencing (NGS) data on hg19 with Bowtie, detected the peaks with Model-based Analysis of ChIP-Seq (MACS), and identified genomic locations by GenomeJack, a novel genome viewer for NGS platforms. Results: We found 2997 stringent peaks distributed on protein-coding genes, chiefly located in the promoter and the intron on VDRE DR3 sequences. However, the corresponding transcriptome data verified calcitriol-induced upregulation of only a small set of VDRTGs. The molecular network of 1541 calcitriol-responsive VDRTGs showed a significant relationship with leukocyte transendothelial migration, Fcγ receptor-mediated phagocytosis, and transcriptional regulation by VDR, suggesting a pivotal role of genome-wide VDRTGs in immune regulation. Conclusion: These results suggest the working hypothesis that persistent deficiency of vitamin D might perturb the complex network of VDRTGs in immune cells, being responsible for induction of an autoimmune response causative for MS.

scholarly journals Mutations of the Listeria monocytogenes PeptidoglycanN-Deacetylase andO-Acetylase Result in Enhanced Lysozyme Sensitivity, Bacteriolysis, and Hyperinduction of Innate Immune Pathways

2011 ◽  
Vol 79 (9) ◽  
pp. 3596-3606 ◽  
Author(s):  
Chris S. Rae ◽  
Aimee Geissler ◽  
Paul C. Adamson ◽  
Daniel A. Portnoy
Keyword(s):  
Listeria Monocytogenes ◽  
Transcriptional Responses ◽  
Gram Positive ◽  
Content Type ◽  
Growth Defects ◽  
Gram Positive Bacteria ◽  
Host Cell Death

ABSTRACTListeria monocytogenesis a Gram-positive intracellular pathogen that is naturally resistant to lysozyme. Recently, it was shown that peptidoglycan modification by N-deacetylation or O-acetylation confers resistance to lysozyme in various Gram-positive bacteria, includingL. monocytogenes.L. monocytogenespeptidoglycan is deacetylated by the action ofN-acetylglucosamine deacetylase (Pgd) and acetylated byO-acetylmuramic acid transferase (Oat). We characterized Pgd−, Oat−, and double mutants to determine the specific role ofL. monocytogenespeptidoglycan acetylation in conferring lysozyme sensitivity during infection of macrophages and mice. Pgd−and Pgd−Oat−double mutants were attenuated approximately 2 and 3.5 logs, respectively,in vivo. In bone-marrow derived macrophages, the mutants demonstrated intracellular growth defects and increased induction of cytokine transcriptional responses that emanated from a phagosome and the cytosol. Lysozyme-sensitive mutants underwent bacteriolysis in the macrophage cytosol, resulting in AIM2-dependent pyroptosis. Each of thein vitrophenotypes was rescued upon infection of LysM−macrophages. The addition of extracellular lysozyme to LysM−macrophages restored cytokine induction, host cell death, andL. monocytogenesgrowth inhibition. This surprising observation suggests that extracellular lysozyme can access the macrophage cytosol and act on intracellular lysozyme-sensitive bacteria.

scholarly journals Investigating the Function of Ddr48p in Candida albicans

2012 ◽  
Vol 11 (6) ◽  
pp. 718-724 ◽  
Author(s):  
I. A. Cleary ◽  
N. B. MacGregor ◽  
S. P. Saville ◽  
D. P. Thomas
Keyword(s):  
Candida Albicans ◽  
Biofilm Formation ◽  
The United States ◽  
Pathogenic Potential ◽  
Content Type ◽  
General Stress Response ◽  
Damage Response ◽  
Sense And Respond ◽  
Immune Defects

ABSTRACTCandidiasis now represents the fourth most frequent nosocomial infection both in the United States and worldwide.Candida albicansis an increasingly common threat to human health as a consequence of AIDS, steroid therapy, organ and tissue transplantation, cancer therapy, broad-spectrum antibiotics, and other immune defects. The pathogenic potential ofC. albicansis intimately related to certain key processes, including biofilm formation and filamentation. Ddr48p is a damage response protein that is significantly upregulated during both biofilm formation and filamentation, but its actual function is unknown. Previous studies have indicated that this protein may be essential inC. albicansbut notSaccharomyces cerevisiae. Here we examined the function of Ddr48p and investigated the role of this protein in biofilm formation and filamentation. We demonstrated that this protein is not essential inC. albicansand appears to be dispensable for filamentation. However,DDR48is required for the flocculation response stimulated by 3-aminotriazole-induced amino acid starvation. Furthermore, we examined the response of this deletion strain to a wide variety of environmental stressors and antifungal compounds. We observed several mild sensitivity or resistance phenotypes and also found that Ddr48p contributes to the DNA damage response ofC. albicans. The results of this study reveal that the role of this highly expressed protein goes beyond a general stress response and impinges on a key facet of pathogenesis, namely, the ability to sense and respond to changes in the host environment.

scholarly journals Global Gene Expression Profile for Swarming Bacillus cereus Bacteria

2011 ◽  
Vol 77 (15) ◽  
pp. 5149-5156 ◽  
Author(s):  
Sara Salvetti ◽  
Karoline Faegri ◽  
Emilia Ghelardi ◽  
Anne-Brit Kolstø ◽  
Sonia Senesi
Keyword(s):  
Bacillus Cereus ◽  
Transcriptional Response ◽  
Global Gene Expression ◽  
Solid Surfaces ◽  
Content Type ◽  
Reverse Transcription Pcr ◽  
Genome Wide ◽  
Genes Encoding ◽  
Hemolysin Bl

ABSTRACTBacillus cereuscan use swarming to move over and colonize solid surfaces in different environments. This kind of motility is a collective behavior accompanied by the production of long and hyperflagellate swarm cells. In this study, the genome-wide transcriptional response ofB. cereusATCC 14579 during swarming was analyzed. Swarming was shown to trigger the differential expression (>2-fold change) of 118 genes. Downregulated genes included those required for basic cellular metabolism. In accordance with the hyperflagellate phenotype of the swarm cell, genes encoding flagellin were overexpressed. Some genes associated with K+transport, phBC6A51 phage genes, and the binding component of the enterotoxin hemolysin BL (HBL) were also induced. Quantitative reverse transcription-PCR (qRT-PCR) experiments indicated an almost 2-fold upregulation of the entirehbloperon during swarming. Finally, BC1435 and BC1436, orthologs ofliaI-liaHthat are known to be involved in the resistance ofBacillus subtilisto daptomycin, were upregulated under swarming conditions. Accordingly, phenotypic assays showed reduced susceptibility of swarmingB. cereuscells to daptomycin, and Pspac-induced hyper-expression of these genes in liquid medium highlighted the role of BC1435 and BC1436 in the response ofB. cereusto daptomycin.

scholarly journals Genome-wide identification and functional prediction of salt- stress related long non-coding RNAs (lncRNAs) in chickpea (Cicer arietinum L.)

2021 ◽  
Author(s):  
Neeraj Kumar ◽  
Chellapilla Bharadwaj ◽  
Sarika Sahu ◽  
Aalok Shiv ◽  
Abhishek Kumar Shrivastava ◽  
...  
Keyword(s):  
Salt Stress ◽  
Stress Response ◽  
Target Genes ◽  
Salt Stress Response ◽  
Rna Molecules ◽  
Transporter Family ◽  
Genome Wide ◽  
New Generation ◽  
In Cis

AbstractLncRNAs (long noncoding RNAs) are 200 bp length crucial RNA molecules, lacking coding potential and having important roles in regulating gene expression, particularly in response to abiotic stresses. In this study, we identified salt stress-induced lncRNAs in chickpea roots and predicted their intricate regulatory roles. A total of 3452 novel lncRNAs were identified to be distributed across all 08 chickpea chromosomes. On comparing salt-tolerant (ICCV 10, JG 11) and salt-sensitive cultivars (DCP 92–3, Pusa 256), 4446 differentially expressed lncRNAs were detected under various salt  treatments. We predicted 3373 lncRNAs to be regulating their target genes in cis regulating manner and 80 unique lncRNAs were observed as interacting with 136 different miRNAs, as eTMs (endogenous target mimic) targets of miRNAs and implicated them in the regulatory network of salt stress response. Functional analysis of these lncRNA revealed their association in targeting salt stress response-related genes like potassium transporter, transporter family genes, serine/threonine-protein kinase, aquaporins like TIP1-2, PIP2-5 and transcription factors like, AP2, NAC, bZIP, ERF, MYB and WRKY. Furthermore, about 614 lncRNA-SSRs (simple sequence repeats) were identified as a new generation of molecular markers with higher efficiency and specificity in chickpea. Overall, these findings will pave the understanding of comprehensive functional role of potential lncRNAs, which can help in providing insight into the molecular mechanism of salt tolerance in chickpea.

scholarly journals Genome-Wide Transcriptional Responses to Carbon Starvation in Nongrowing Lactococcus lactis

2015 ◽  
Vol 81 (7) ◽  
pp. 2554-2561 ◽  
Author(s):  
Onur Ercan ◽  
Michiel Wels ◽  
Eddy J. Smid ◽  
Michiel Kleerebezem
Keyword(s):  
Lactococcus Lactis ◽  
Natural Transformation ◽  
Recovery Period ◽  
Transcriptional Responses ◽  
Content Type ◽  
Gene Set ◽  
Expression Of Genes ◽  
Genome Wide ◽  
Elevated Expression ◽  
Branched Chain

ABSTRACTThis paper describes the transcriptional adaptations of nongrowing, retentostat cultures ofLactococcus lactisto starvation. Near-zero-growth cultures (μ = 0.0001 h−1) obtained by extended retentostat cultivation were exposed to starvation by termination of the medium supply for 24 h, followed by a recovery period of another 24 h by reinitiating the medium supply to the retentostat culture. During starvation, the viability of the culture was largely retained, and the expression of genes involved in transcription and translational machineries, cell division, and cell membrane energy metabolism was strongly repressed. Expression of these genes was largely recovered following the reinitiation of the medium supply. Starvation triggered the elevated expression of genes associated with synthesis of branched-chain amino acids, histidine, purine, and riboflavin. The expression of these biosynthesis genes was found to remain at an elevated level after reinitiation of the medium supply. In addition, starvation induced the complete gene set predicted to be involved in natural competence inL. lactisKF147, and the elevated expression of these genes was sustained during the subsequent recovery period, but our attempts to experimentally demonstrate natural transformation in these cells failed. Mining the starvation response gene set identified a conservedcis-acting element that resembles the lactococcal CodY motif in the upstream regions of genes associated with transcription and translational machineries, purine biosynthesis, and natural transformation inL. lactis, suggesting a role for CodY in the observed transcriptome adaptations to starvation in nongrowing cells.

scholarly journals The Intestinal Microbiota Interferes with the microRNA Response upon Oral Listeria Infection

mBio ◽  
2013 ◽  
Vol 4 (6) ◽  
Author(s):  
Cristel Archambaud ◽  
Odile Sismeiro ◽  
Joern Toedling ◽  
Guillaume Soubigou ◽  
Christophe Bécavin ◽  
...  
Keyword(s):  
Bacterial Infection ◽  
Intestinal Microbiota ◽  
Mirna Expression ◽  
Target Genes ◽  
Host Protein ◽  
Protein Coding ◽  
Content Type ◽  
Protein Coding Genes ◽  
The Impact

ABSTRACT The intestinal tract is the largest reservoir of microbes in the human body. The intestinal microbiota is thought to be able to modulate alterations of the gut induced by enteropathogens, thereby maintaining homeostasis. Listeria monocytogenes is the agent of listeriosis, an infection transmitted to humans upon ingestion of contaminated food. Crossing of the intestinal barrier is a critical step of the infection before dissemination into deeper organs. Here, we investigated the role of the intestinal microbiota in the regulation of host protein-coding genes and microRNA (miRNA or miR) expression during Listeria infection. We first established the intestinal miRNA signatures corresponding to the 10 most highly expressed miRNAs in the murine ileum of conventional and germfree mice, noninfected and infected with Listeria. Next, we identified 6 miRNAs whose expression decreased upon Listeria infection in conventional mice. Strikingly, five of these miRNA expression variations (in miR-143, miR-148a, miR-200b, miR-200c, and miR-378) were dependent on the presence of the microbiota. In addition, as is already known, protein-coding genes were highly affected by infection in both conventional and germfree mice. By crossing bioinformatically the predicted targets of the miRNAs to our whole-genome transcriptomic data, we revealed an miRNA-mRNA network that suggested miRNA-mediated global regulation during intestinal infection. Other recent studies have revealed an miRNA response to either bacterial pathogens or commensal bacteria. In contrast, our work provides an unprecedented insight into the impact of the intestinal microbiota on host transcriptional reprogramming during infection by a human pathogen. IMPORTANCE While the crucial role of miRNAs in regulating the host response to bacterial infection is increasingly recognized, the involvement of the intestinal microbiota in the regulation of miRNA expression has not been explored in detail. Here, we investigated the impact of the intestinal microbiota on the regulation of protein-coding genes and miRNA expression in a host infected by L. monocytogenes, a food-borne pathogen. We show that the microbiota interferes with the microRNA response upon oral Listeria infection and identify several protein-coding target genes whose expression correlates inversely with that of the miRNA. Further investigations of the regulatory networks involving miR-143, miR-148a, miR-200b, miR-200c, and miR-378 will provide new insights into the impact of the intestinal microbiota on the host upon bacterial infection.

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