scholarly journals Diverse Stress-Inducing Treatments cause Distinct Aberrant Body Morphologies in the Chlamydia-Related Bacterium, Waddlia chondrophila

2020 ◽  
Vol 8 (1) ◽  
pp. 89 ◽  
Author(s):  
Aurélie Scherler ◽  
Nicolas Jacquier ◽  
Carole Kebbi-Beghdadi ◽  
Gilbert Greub
Keyword(s):  
Gene Expression ◽  
Mammalian Cells ◽  
Chlamydia Pneumoniae ◽  
Expression Patterns ◽  
Dna Gyrase ◽  
Morphological Characterization ◽  
Chronic Infections ◽  
Reverse Transcription Pcr ◽  
Related Bacterium ◽  
First Time

Chlamydiae, such as Chlamydia trachomatis and Chlamydia pneumoniae, can cause chronic infections. It is believed that persistent forms called aberrant bodies (ABs) might be involved in this process. AB formation seems to be a common trait of all members of the Chlamydiales order and is caused by distinct stress stimuli, such as β-lactam antibiotics or nutrient starvation. While the diverse stimuli inducing ABs are well described, no comprehensive morphological characterization has been performed in Chlamydiales up to now. We thus infected mammalian cells with the Chlamydia-related bacterium Waddlia chondrophila and induced AB formation using different stimuli. Their morphology, differences in DNA content and in gene expression were assessed by immunofluorescence, quantitative PCR, and reverse transcription PCR, respectively. All stimuli induced AB formation. Interestingly, we show here for the first time that the DNA gyrase inhibitor novobiocin also caused appearance of ABs. Two distinct patterns of ABs could be defined, according to their morphology and number: (i) small and multiple ABs versus (ii) large and rare ABs. DNA replication of W. chondrophila was generally not affected by the different treatments. Finally, no correlation could be observed between specific types of ABs and expression patterns of mreB and rodZ genes.

scholarly journals First-Choice Antibiotics at Subinhibitory Concentrations Induce Persistence of Chlamydia pneumoniae

2004 ◽  
Vol 48 (4) ◽  
pp. 1402-1405 ◽  
Author(s):  
Jens Gieffers ◽  
Jan Rupp ◽  
Andreas Gebert ◽  
Werner Solbach ◽  
Matthias Klinger
Keyword(s):  
Gene Expression ◽  
Membrane Proteins ◽  
Chlamydia Pneumoniae ◽  
Growth Forms ◽  
Chronic Infections ◽  
First Line ◽  
First Choice ◽  
Subinhibitory Concentrations

ABSTRACT Persistent growth forms of Chlamydia pneumoniae have been associated with chronic infections in vivo. We investigated the effects of first-line therapeutics on the induction of persistence by monitoring recoverable organisms, gene expression of membrane proteins, and morphology. We found that all of the antibiotics tested have distinct and subinhibitory concentrations at which they induce persistence.

scholarly journals Posttranscriptional gene regulation by RNA-binding proteins during oxidative stress: implications for cellular senescence

2008 ◽  
Vol 389 (3) ◽  
pp. 243-255 ◽  
Author(s):  
Kotb Abdelmohsen ◽  
Yuki Kuwano ◽  
Hyeon Ho Kim ◽  
Myriam Gorospe
Keyword(s):  
Oxidative Stress ◽  
Gene Expression ◽  
Cellular Senescence ◽  
Mammalian Cells ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Oxidant Damage ◽  
Regulated Gene Expression

AbstractTo respond adequately to oxidative stress, mammalian cells elicit rapid and tightly controlled changes in gene expression patterns. Besides alterations in the subsets of transcribed genes, two posttranscriptional processes prominently influence the oxidant-triggered gene expression programs: mRNA turnover and translation. Here, we review recent progress in our knowledge of theturnover andtranslationregulatory (TTR) mRNA-bindingproteins (RBPs) that influence gene expression in response to oxidative damage. Specifically, we identify oxidant damage-regulated mRNAs that are targets of TTR-RBPs, we review the oxidant-triggered signaling pathways that govern TTR-RBP function, and we examine emerging evidence that TTR-RBP activity is altered with senescence and aging. Given the potent influence of TTR-RBPs upon oxidant-regulated gene expression profiles, we propose that the senescence-associated changes in TTR-RBPs directly contribute to the impaired responses to oxidant damage that characterize cellular senescence and advancing age.

scholarly journals Correction to: Morphological Characterization and Gene Expression Patterns for Melanin Pigmentation in Rex Rabbit

2019 ◽  
Vol 57 (5) ◽  
pp. 746-746
Author(s):  
Shuaishuai Hu ◽  
Pin Zhai ◽  
Yang Chen ◽  
Bohao Zhao ◽  
Naisu Yang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Patterns ◽  
Morphological Characterization ◽  
Gene Expression Patterns ◽  
Melanin Pigmentation ◽  
Rex Rabbit

Diurnal rhythms (DR) in gene expression in human oral mucosa: Implications for gender differences in toxicity, response and survival and optimal timing of targeted therapy (Rx)

2007 ◽  
Vol 25 (18_suppl) ◽  
pp. 2507-2507 ◽  
Author(s):  
G. A. Bjarnason ◽  
A. Seth ◽  
Z. Wang ◽  
N. Blanas ◽  
M. Straume ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gender Differences ◽  
Oral Mucosa ◽  
Clock Genes ◽  
Expression Patterns ◽  
Diurnal Rhythms ◽  
Optimal Timing ◽  
Rna Expression ◽  
Toxicity Response ◽  
First Time

2507 Background: DR in processes relevant to oncology, including cell cycle, apoptosis, and angiogenesis, have been demonstrated (Nat Rev Cancer 3:350, Cancer Res 63:7277). In rodents, 10–20% of the genome has a 24-hour (h) rhythm in RNA expression (Cell 109:307). A molecular clock consisting of transcription/translation feedback loops of clock-genes controls this rhythmicity (Nat Rev Neurosci 4:649). We studied, for the first time, daily whole genome RNA expression patterning in healthy human volunteers. Methods: RNA samples extracted from oral mucosa biopsies (bx) obtained every 4h over 24h (6 bx) from 5 males (M) and 5 females (F) were subjected to microarray analysis (Affymetrix HG_U133_Plus2 chip, 54,679 transcripts). COSOPT, designed for circadian microarray time series analysis (Methods Enzymol 383: 149) was used to detect genes with significant rhythms (pMMC-Beta = 0.1). Expression patterns were visualized in GeneSpring GX7.3 (Agilent) and validated by real-time PCR and ANOVA. Results: There were 801 and 810 rhythmic genes in M and F respectively, with most genes peaking at 4AM or 4PM in M but at 6AM or 11AM in F. Only 90 rhythmic genes (including core clock-genes and clock controlled genes) were common to M and F, with over 700 genes only rhythmic in M and not in F and vice versa. The profiles of clock- genes and clock-controlled genes were inverted relative to the nocturnal rodent data. There were 75 and 67 rhythmic transcription factor genes in M and F respectively, with 28 common to both M and F. There were 71 rhythmic human cancer genes (Nat Rev Cancer 4:177) with significant gender differences. This group includes rhythmic gene products involved in signaling pathways currently targeted for cancer Rx. Conclusions: We show for the first time a significant gender specific DR in gene expression involving multiple genes of interest in oncology. This may contribute to the documented gender differences in toxicity, response and survival (J Clin Onc 24: 3562, NEJM 353:133), and can inform future trials of optimal timing of antisense Rx and other targeted Rx. The inverted DR in rodents vs. humans has implications for translating rodent data to human Rx trials. No significant financial relationships to disclose.

scholarly journals DNA Methylation and Chromatin: Role(s) of Methyl-CpG-Binding Protein ZBTB38

2018 ◽  
Vol 11 ◽  
pp. 251686571881111 ◽  
Author(s):  
Maud de Dieuleveult ◽  
Benoit Miotto
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Transcription Factors ◽  
Dna Sequences ◽  
Mammalian Cells ◽  
Expression Patterns ◽  
Control Of Gene Expression ◽  
Methylated Dna

DNA methylation plays an essential role in the control of gene expression during early stages of development as well as in disease. Although many transcription factors are sensitive to this modification of the DNA, we still do not clearly understand how it contributes to the establishment of proper gene expression patterns. We discuss here the recent findings regarding the biological and molecular function(s) of the transcription factor ZBTB38 that binds methylated DNA sequences in vitro and in cells. We speculate how these findings may help understand the role of DNA methylation and DNA methylation–sensitive transcription factors in mammalian cells.

scholarly journals Network rewiring: physiological consequences of reciprocally exchanging the physical locations and growth-phase-dependent expression patterns of the Salmonella fis and dps genes

2020 ◽  
Author(s):  
Marina M Bogue ◽  
Aalap Mogre ◽  
Michael C Beckett ◽  
Nicholas R Thomson ◽  
Charles J Dorman
Keyword(s):  
Gene Expression ◽  
Protein Binding ◽  
Stationary Phase ◽  
Growth Phase ◽  
Regulatory Network ◽  
Mammalian Cells ◽  
Expression Patterns ◽  
Virulence Gene ◽  
Exponential Phase ◽  
Virulence Gene Expression

ABSTRACTThe Fis nucleoid-associated protein controls the expression of a large and diverse regulon of genes in Gram-negative bacteria. Fis production is normally maximal in bacteria during the early exponential phase of batch culture growth, becoming almost undetectable by the onset of stationary phase. We tested the effect on the Fis regulatory network in Salmonella of moving the complete fis gene from its usual location near the origin of chromosomal replication to the position normally occupied by the dps gene in the Right macrodomain of the chromosome, and vice versa, creating the strain GX. In a parallel experiment, we tested the effect of rewiring the Fis regulatory network by placing the fis open reading frame under the control of the stationary-phase-activated dps promoter at the dps genetic location within Ter, and vice versa, creating the strain OX. ChIP-seq was used to measure global Fis protein binding and gene expression patterns. Strain GX showed few changes when compared with the wild type, although we did detect increased Fis binding at Ter, accompanied by reduced binding at Ori. Strain OX displayed a more pronounced version of this distorted Fis protein-binding pattern together with numerous alterations in the expression of genes in the Fis regulon. OX, but not GX, had a reduced ability to infect cultured mammalian cells. These findings illustrate the inherent robustness of the Fis regulatory network to rewiring based on gene repositioning alone and emphasise the importance of fis expression signals in phenotypic determination.IMPORTANCEWe assessed the impacts on Salmonella physiology of reciprocally translocating the genes encoding the Fis and Dps nucleoid-associated proteins (NAPs), and of inverting their growth phase production patterns such that Fis is produced in stationary phase (like Dps) and Dps is produced in exponential phase (like Fis). Changes to peak binding of Fis were detected by ChIP-seq on the chromosome, as were widespread impacts on the transcriptome, especially when Fis production mimicked Dps. Virulence gene expression and the expression of a virulence phenotype were altered. Overall, these radical changes to NAP gene expression were well tolerated, revealing the robust and well-buffered nature of global gene regulation networks in the bacterium.

scholarly journals A family of viral satellites manipulates invading virus gene expression and affects cholera toxin mobilization

2020 ◽  
Author(s):  
Zachary K Barth ◽  
Zoe Netter ◽  
Angus Angermeyer ◽  
Pooja Bhardwaj ◽  
Kimberley D Seed
Keyword(s):  
Gene Expression ◽  
Cholera Toxin ◽  
Expression Patterns ◽  
Rna Seq ◽  
Time Resolved ◽  
Enhanced Resolution ◽  
Infected Cells ◽  
Time Courses ◽  
Host Metabolism ◽  
First Time

AbstractMany viruses possess temporally unfolding gene expression patterns aimed at subverting host defenses, commandeering host metabolism, and ultimately producing a large number of progeny virions. High throughput -omics tools, such as RNA-seq, have dramatically enhanced resolution of expression patterns during infection. Less studied have been viral satellites, mobile genomes that parasitize viruses and have far reaching effects on host-cell fitness. By performing RNA-seq on infection time courses, we have obtained the first time-resolved transcriptomes for bacteriophage satellites during lytic infection. Specifically, we have acquired transcriptomes for the lytic Vibrio cholerae phage ICP1 and all five known variants of ICP1’s parasite, the Phage Inducible Chromosomal Island-Like Elements (PLEs). PLEs rely on ICP1 for both DNA replication and mobilization, and abolish production of ICP1 progeny in infected cells. We investigated PLEs impact on ICP1 gene expression and found that PLEs did not broadly restrict or reduce ICP1 gene expression. A major exception occurred in ICP1’s capsid morphogenesis operon, which was downregulated by each of the PLE variants. This transcriptional manipulation, conserved among PLEs, has also evolved independently in at least one other phage satellite, suggesting that viral satellites may be under strong selective pressure to reduce the capsid expression of their larger host viruses. Surprisingly, PLEs were also found to alter the gene expression of CTXϕ, the integrative phage that encodes cholera toxin and is necessary for virulence of toxigenic V. cholerae. One PLE, PLE1, upregulated CTXϕ genes involved in replication and integration, and boosted CTXϕ mobility following induction of the SOS response. Our data show that PLEs exhibit conserved manipulation of their host-phage’s gene expression, but divergent effects on CTXϕ, revealing that PLEs can influence both their hosts’ resistance to phage and the mobility of virulence encoding elements.

Morphological Characterization and Gene Expression Patterns for Melanin Pigmentation in Rex Rabbit

2019 ◽  
Vol 57 (5) ◽  
pp. 734-744 ◽  
Author(s):  
Shuaishuai Hu ◽  
Pin Zhai ◽  
Yang Chen ◽  
Bohao Zhao ◽  
Naisu Yang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Patterns ◽  
Morphological Characterization ◽  
Gene Expression Patterns ◽  
Melanin Pigmentation ◽  
Rex Rabbit

scholarly journals Transcription of Virulence Factors in Staphylococcus aureus Small-Colony Variants Isolated from Cystic Fibrosis Patients Is Influenced by SigB

2006 ◽  
Vol 188 (1) ◽  
pp. 64-76 ◽  
Author(s):  
Hélène Moisan ◽  
Eric Brouillette ◽  
Christian Lebeau Jacob ◽  
Philippe Langlois-Bégin ◽  
Sophie Michaud ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cystic Fibrosis ◽  
Staphylococcus Aureus ◽  
Mammalian Cells ◽  
Positive Control ◽  
Minor Role ◽  
Chronic Infections ◽  
Small Colony Variants ◽  
Transcriptional Signature ◽  
Small Colony

ABSTRACT Staphylococcus aureus small-colony variants (SCVs) are believed to account in part for the persistence of S. aureus during chronic infections. Little is understood about the gene expression profile that may explain the phenotype and distinguish SCVs from prototype S. aureus strains. In this study, DNA array transcriptional profiles of clinical SCVs isolated from the airways of cystic fibrosis patients were obtained and compared to those obtained from a laboratory-derived SCV strain (i.e., a respiratory-deficient hemB mutant) and prototype S. aureus strains. The genes commonly up-regulated in both hemB and clinical SCVs were found to be implicated in fermentation and glycolysis pathways. The well-known virulence regulator agr was not activated in SCVs, and such strains had low levels of alpha-toxin (hla) gene expression. Clinical SCVs also had a transcriptional signature of their own. Of striking interest is that many genes, most of them under the positive control of the alternate sigma factor SigB, were specifically up-regulated and differed in that way from that seen in prototype S. aureus and the hemB mutant. Since SigB influences up-regulation of adhesin type genes while indirectly down-regulating exoproteins and toxins, we evaluated the internalization and persistence of SCVs in mammalian cells. Results showed that clinical SCVs persisted much more efficiently in cells than the hemB and prototype strains and that a sigB mutant was a poor persister. Thus, it appears that the agr locus plays a minor role in the regulation of the virulon of SCVs, unlike SigB, which may have a key role in intracellular persistence.

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