scholarly journals Plastidial (p)ppGpp synthesis by the Ca2+-dependent RelA-SpoT homolog regulates the adaptation of chloroplast gene expression to darkness in Arabidopsis

2019 ◽  
Author(s):  
Sumire Ono ◽  
Sae Suzuki ◽  
Doshun Ito ◽  
Shota Tagawa ◽  
Takashi Shiina ◽  
...  
Keyword(s):  
Gene Expression ◽  
Nutrient Deficiency ◽  
Stringent Response ◽  
Transient Increase ◽  
Specific Gene ◽  
Mrna Levels ◽  
Knockout Mutant ◽  
Chloroplast Gene Expression ◽  
Hydrolytic Activities ◽  
In The Wild

AbstractIn bacteria, the hyper-phosphorylated nucleotides, guanosine 5’-diphosphate 3’-diphosphate (ppGpp) and guanosine 5’-triphosphate 3’-diphosphate (pppGpp), function as secondary messengers in the regulation of various metabolic processes of the cell, including transcription, translation, and enzymatic activities, especially under nutrient deficiency. The activity carried out by these nucleotide messengers is known as the stringent response. (p)ppGpp levels are controlled by two distinct enzymes, namely, RelA and SpoT, in Escherichia coli. RelA-SpoT homologs (RSHs) are also conserved in plants and algae where they function in the plastids. The model plant Arabidopsis thaliana contains four RSHs: RSH1, RSH2, RSH3, and Ca2+-dependent RSH (CRSH). Genetic characterizations of RSH1, RSH2, and RSH3 were undertaken, which showed that the (p)ppGpp-dependent plastidial stringent response significantly influences plant growth and stress acclimation. However, the physiological significance of CRSH-dependent (p)ppGpp synthesis remains unclear, as no crsh-null mutant has been available. Here to investigate the function of CRSH, a crsh-knockout mutant of Arabidopsis was constructed using a site-specific gene-editing technique, and its phenotype was characterized. A transient increase of ppGpp was observed for 30 min in the wild type (WT) after light-to-dark transition, but this increase was not observed in the crsh mutant. Similar analyzes were performed with the rsh2rsh3 double and rsh1rsh2rsh3 triple mutants of Arabidopsis and showed that the transient increments of ppGpp in the mutants were higher than those in the WT. The increase of (p)ppGpp in the WT and rsh2rsh3 accompanied decrements in the mRNA levels of psbD transcribed by the plastid-encoded plastid RNA polymerase. These results indicated that the transient increase of intracellular ppGpp at night is due to CRSH-dependent ppGpp synthesis and the (p)ppGpp level is maintained by the hydrolytic activities of RSH1, RSH2, and RSH3 to accustom plastidial gene expression to darkness.

scholarly journals Plastidial (p)ppGpp Synthesis by the Ca2+-Dependent RelA–SpoT Homolog Regulates the Adaptation of Chloroplast Gene Expression to Darkness in Arabidopsis

2020 ◽  
Author(s):  
Sumire Ono ◽  
Sae Suzuki ◽  
Doshun Ito ◽  
Shota Tagawa ◽  
Takashi Shiina ◽  
...  
Keyword(s):  
Gene Expression ◽  
Stringent Response ◽  
Transient Increase ◽  
Specific Gene ◽  
Mrna Levels ◽  
Knockout Mutant ◽  
Chloroplast Gene Expression ◽  
Secondary Messenger ◽  
Hydrolytic Activities ◽  
In The Wild

Abstract In bacteria, the hyper-phosphorylated nucleotide, guanosine 3′,5′-bis(pyrophosphate) (ppGpp), functions as a secondary messenger under stringent conditions. ppGpp levels are controlled by two distinct enzymes, namely RelA and SpoT, in Escherichia coli. RelA–SpoT homologs (RSHs) are also conserved in plants where they function in the plastids. The model plant Arabidopsis thaliana contains four RSHs: RSH1, RSH2, RSH3 and Ca2+-dependent RSH (CRSH). Genetic characterizations of RSH1, RSH2 and RSH3 were undertaken, which showed that the ppGpp-dependent plastidial stringent response significantly influences plant growth and stress acclimation. However, the physiological significance of CRSH-dependent ppGpp synthesis remains unclear, as no crsh-null mutant has been available. Here, to investigate the function of CRSH, a crsh-knockout mutant of Arabidopsis was constructed using a site-specific gene-editing technique, and its phenotype was characterized. A transient increase in ppGpp was observed for 30 min in the wild type (WT) after the light-to-dark transition, but this increase was not observed in the crsh mutant. Similar analyses were performed with the rsh2-rsh3 double and rsh1-rsh2-rsh3 triple mutants and showed that the transient increments of ppGpp in the mutants were higher than those in the WT. The increase in ppGpp in the WT and rsh2 rsh3 accompanied decrements in the mRNA levels of some plastidial genes transcribed by the plastid-encoded plastid RNA polymerase. These results indicate that the transient increase in ppGpp at night is due to CRSH-dependent ppGpp synthesis and that the ppGpp level is maintained by the hydrolytic activities of RSH1, RSH2 and RSH3 to accustom plastidial gene expression to darkness.

scholarly journals Positive Regulation of Leptospira interrogans kdp Expression by KdpE as Demonstrated with a Novel β-Galactosidase Reporter in Leptospira biflexa

2012 ◽  
Vol 78 (16) ◽  
pp. 5699-5707 ◽  
Author(s):  
James Matsunaga ◽  
Mariana L. Coutinho
Keyword(s):  
Gene Expression ◽  
Response Regulator ◽  
Regulation Of Gene Expression ◽  
Leptospira Interrogans ◽  
Mrna Levels ◽  
Genetic Circuits ◽  
Positive Regulation ◽  
Content Type ◽  
Novel Approach ◽  
In The Wild

ABSTRACTLeptospirosis is a potentially deadly zoonotic disease that afflicts humans and animals.Leptospira interrogans, the predominant agent of leptospirosis, encounters diverse conditions as it proceeds through its life cycle, which includes stages inside and outside the host. Unfortunately, the number of genetic tools available for examining the regulation of gene expression inL. interrogansis limited. Consequently, little is known about the genetic circuits that control gene expression inLeptospira. To better understand the regulation of leptospiral gene expression, theL. interrogans kdplocus, encoding homologs of the P-type ATPase KdpABC potassium transporter with their KdpD sensors and KdpE response regulators, was selected for analysis. We showed that akdpEmutation inL. interrogansprevented the increase inkdpABCmRNA levels observed in the wild-typeL. interrogansstrain when external potassium levels were low. To confirm that KdpE was a positive regulator ofkdpABCtranscription, we developed a novel approach for constructing chromosomal genetic fusions to the endogenousbgaL(β-galactosidase) gene of the nonpathogenLeptospira biflexa. We demonstrated positive regulation of akdpA′-bgaLfusion inL. biflexaby theL. interrogansKdpE response regulator. A controllipL32′-bgaLfusion was not regulated by KdpE. These results demonstrate the utility of genetic fusions to thebgaLgene ofL. biflexafor examining leptospiral gene regulation.

scholarly journals Transcriptional and posttranscriptional control of c-fos gene expression in human monocytes.

1988 ◽  
Vol 8 (1) ◽  
pp. 340-346 ◽  
Author(s):  
E Sariban ◽  
R Luebbers ◽  
D Kufe
Keyword(s):  
Gene Expression ◽  
Protein Synthesis ◽  
Phorbol Ester ◽  
Fold Increase ◽  
Transient Increase ◽  
Mrna Levels ◽  
Human Monocytes ◽  
Posttranscriptional Control ◽  
Sense Strand ◽  
The Stability

We examined the mechanisms that are responsible for the regulation of c-fos gene expression in human monocytes. Levels of c-fos mRNA were low or undetectable in resting monocytes. Results of run-on transcription assays, however, demonstrated that both the first two and last two exons of the c-fos gene were transcribed at similar rates, and that only the sense strand of this gene was transcribed. These findings suggest that the level of c-fos transcripts in resting human monocytes is controlled at a posttranscriptional level. Activation of resting monocytes with phorbol ester was associated with a rapid and transient increase in c-fos mRNA levels. This increase in c-fos transcripts was related to an enhanced rate of c-fos transcription. Moreover, exposure of resting monocytes to inhibitors of protein synthesis induced (i) a rapid and marked (300-fold) increase in c-fos mRNA levels, despite only a 9-fold increase in c-fos transcription, and (ii) a prolongation of the half-life of c-fos mRNA. Thus, while posttranscriptional control was responsible for the down-regulation of c-fos transcripts in both resting and activated human monocytes, transcriptional mechanisms were responsible for the transient increase in c-fos expression induced by phorbol ester. Furthermore, the marked increases in c-fos mRNA associated with inhibition of protein synthesis were regulated by both transcriptional and posttranscriptional mechanisms. These findings may be related to recent observations which indicate that both positive and negative factors transcriptionally regulate c-fos gene expression and that sequences found in the 3'-untranslated region of the c-fos mRNA are responsible for the stability of this transcript.

scholarly journals Translation quality control is critical for bacterial responses to amino acid stress

2016 ◽  
Vol 113 (8) ◽  
pp. 2252-2257 ◽  
Author(s):  
Tammy J. Bullwinkle ◽  
Michael Ibba
Keyword(s):  
Gene Expression ◽  
Quality Control ◽  
Amino Acid ◽  
Acid Stress ◽  
Stringent Response ◽  
Growth Conditions ◽  
Leader Peptide ◽  
Transcriptional Responses ◽  
Translation Quality ◽  
In The Wild

Gene expression relies on quality control for accurate transmission of genetic information. One mechanism that prevents amino acid misincorporation errors during translation is editing of misacylated tRNAs by aminoacyl-tRNA synthetases. In the absence of editing, growth is limited upon exposure to excess noncognate amino acid substrates and other stresses, but whether these physiological effects result solely from mistranslation remains unclear. To explore if translation quality control influences cellular processes other than protein synthesis, an Escherichia coli strain defective in Tyr-tRNAPhe editing was used. In the absence of editing, cellular levels of aminoacylated tRNAPhe were elevated during amino acid stress, whereas in the wild-type strain these levels declined under the same growth conditions. In the editing-defective strain, increased levels of aminoacylated tRNAPhe led to continued synthesis of the PheL leader peptide and attenuation of pheA transcription under amino acid stress. Consequently, in the absence of editing, activation of the phenylalanine biosynthetic operon becomes less responsive to phenylalanine limitation. In addition to raising aminoacylated tRNA levels, the absence of editing lowered the amount of deacylated tRNAPhe in the cell. This reduction in deacylated tRNA was accompanied by decreased synthesis of the second messenger guanosine tetraphosphate and limited induction of stringent response-dependent gene expression in editing-defective cells during amino acid stress. These data show that a single quality-control mechanism, the editing of misacylated aminoacyl-tRNAs, provides a critical checkpoint both for maintaining the accuracy of translation and for determining the sensitivity of transcriptional responses to amino acid stress.

Transcriptional and posttranscriptional control of c-fos gene expression in human monocytes

1988 ◽  
Vol 8 (1) ◽  
pp. 340-346
Author(s):  
E Sariban ◽  
R Luebbers ◽  
D Kufe
Keyword(s):  
Gene Expression ◽  
Protein Synthesis ◽  
Phorbol Ester ◽  
Fold Increase ◽  
Transient Increase ◽  
Mrna Levels ◽  
Human Monocytes ◽  
Posttranscriptional Control ◽  
Sense Strand ◽  
The Stability

We examined the mechanisms that are responsible for the regulation of c-fos gene expression in human monocytes. Levels of c-fos mRNA were low or undetectable in resting monocytes. Results of run-on transcription assays, however, demonstrated that both the first two and last two exons of the c-fos gene were transcribed at similar rates, and that only the sense strand of this gene was transcribed. These findings suggest that the level of c-fos transcripts in resting human monocytes is controlled at a posttranscriptional level. Activation of resting monocytes with phorbol ester was associated with a rapid and transient increase in c-fos mRNA levels. This increase in c-fos transcripts was related to an enhanced rate of c-fos transcription. Moreover, exposure of resting monocytes to inhibitors of protein synthesis induced (i) a rapid and marked (300-fold) increase in c-fos mRNA levels, despite only a 9-fold increase in c-fos transcription, and (ii) a prolongation of the half-life of c-fos mRNA. Thus, while posttranscriptional control was responsible for the down-regulation of c-fos transcripts in both resting and activated human monocytes, transcriptional mechanisms were responsible for the transient increase in c-fos expression induced by phorbol ester. Furthermore, the marked increases in c-fos mRNA associated with inhibition of protein synthesis were regulated by both transcriptional and posttranscriptional mechanisms. These findings may be related to recent observations which indicate that both positive and negative factors transcriptionally regulate c-fos gene expression and that sequences found in the 3'-untranslated region of the c-fos mRNA are responsible for the stability of this transcript.

Maturation Stage-Specific Regulation of Megakaryocytic Genes by Pointed-Domain Ets Proteins.

Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 1737-1737
Author(s):  
Liyan Pang ◽  
Xun Wang ◽  
Yuhuan Wang ◽  
Gerd Blobel ◽  
Mortimer Poncz
Keyword(s):  
Gene Expression ◽  
Fetal Liver ◽  
Critical Role ◽  
Regulatory Region ◽  
Maturation Stage ◽  
Specific Gene ◽  
Mrna Levels ◽  
Specific Regulation

Abstract The pointed-domain Ets transcription factor Fli-1 has a critical role during megakaryocyte-specific gene expression. Previously, we demonstrated that Fli-1 occupies the early megakaryocyte-specific gene αIIb in vivo. Moreover, our work suggested a mechanism for Fli-1 function by showing that Fli-1 facilitates GATA-1/FOG-1 dependent expression of the αIIb gene. However, studies by others with a targeted disruption of the Fli-1 gene in mice showed that while Fli-1 is essential for normal megakaryocyte maturation, αIIb mRNA levels were not significantly reduced in the resulting megakaryocytes, suggesting that a related Ets factor(s) might compensate for the loss of Fli-1. Here we show that the widely expressed pointed domain Ets protein GABPα specifically binds in vitro to Ets elements from two early megakaryocyte-specific genes, αIIb and c-mpl. Chromatin immunoprecipitation (ChIP) experiments using primary murine fetal liver-derived megakaryocytes reveal that GABPα associates with αIIb and c-mpl in vivo. Moreover, GABPα is capable of mediating GATA-1/FOG-1 synergy in the context of αIIb promoter constructs. These results suggest that GABPα contributes to megakaryocyte-restricted gene expression and is capable of at least partially compensating for the loss of Fli-1. However, loss of Fli-1 leads to a pronounced decrease in the expression of the late megakaryocyte-specific gene GPIX, indicating that compensation by GABPα is incomplete. Consistent with this observation, ChIP experiments fail to detect significant levels of GABPα at the regulatory region of GPIX while Fli-1 is readily detected there. Together, these results point to a model in which Fli-1 and GABPα serve overlapping, but distinct roles, during the development of megakaryocytes. GABPα may be important during early megakaryopoiesis, but Fli-1 exerting an essential role during late stages of maturation.

Genomic-based predictive biomarkers to anti-HER2 therapies: A combined analysis of CALGB 40601 (Alliance) and PAMELA clinical trials.

2019 ◽  
Vol 37 (15_suppl) ◽  
pp. 571-571 ◽  
Author(s):  
Aranzazu Fernandez-Martinez ◽  
Maki Tanioka ◽  
Cheng Fan ◽  
Joel S. Parker ◽  
Katherine A. Hoadley ◽  
...  
Keyword(s):  
Gene Expression ◽  
Clinical Trials ◽  
Predictive Biomarkers ◽  
Specific Gene ◽  
Mrna Levels ◽  
Clinical Implementation ◽  
Luminal A ◽  
Her2 Positive ◽  
Luminal B ◽  
Erbb2 Mrna

571 Background: In HER2-positive breast cancer, new biomarkers of response are needed in order to direct multi-agent anti-HER2 combinations towards patients in whom they are truly needed. CALGB 40601 and PAMELA trials tested neoadjuvant dual HER2 blockade and included gene expression analysis aimed to evaluate different genomic biomarkers of trastuzumab and/or lapatinib benefit. Methods: Gene expression by mRNA sequencing (RNAseq) was performed on 265 and 142 pre-treatment tumors of the CALGB 40601 and the PAMELA clinical trials respectively. Intrinsic subtypes were determined by nCounter PAM50-predictor on the PAMELA samples. A new HER2-positive specific gene-centering method was trained on the PAMELA RNAseq data, and showed a higher concordance with PAM50 predictions obtained from nCounter platform. This method was then applied to CALGB 40601 samples. Results: In the combined cohort, the subtype distribution was 10% Luminal A, 8% Luminal B, 62% HER2-enriched (HER2-E), 10% Basal and 10% Normal-like. The pCR rate was significantly higher in HER2-E vs. not HER2-E subtypes (48.6% vs. 20.7%; P < 0.001). HER2-E subtype correlation, ERBB2 amplicon and B-cell genomic signatures were associated with pCR, while luminal signatures were associated with non-responders. In multivariate analysis HER2-E subtype, ERBB2 mRNA and IgG signature expression were independent predictors of response to paclitaxel + trastuzumab +/-lapatinib (OR = 1.98, OR = 1.51, OR = 1.48, respectively, P <0.05). The event free survival analysis at 5 years in the CALGB 40601 cohort showed a benefit of dual vs single anti-HER2-blockade (HR 0.35, P <0.05). Within the HER2-E, ERBB2-high and IgG–high subpopulations, there were also a benefit of dual vs. single anti-HER2 treatment (HR = 0.32, HR = 0.15, HR =0.15, respectively, P <0.05). Conclusions: Intrinsic subtype, ERBB2 mRNA levels, and IgG genomic signature are independent predictive biomarkers of response in the combined cohort. The clinical implementation of these biomarkers could help to design future escalation/de-escalation clinical trials in the HER2-positive neoadjuvant setting. Support: U10CA180821, U10CA180882, U24CA196171, P50-CA58223, GSK, SPORE, BCRF and SEOM. https://acknowledgments.alliancefound.org .

Loss of the B-lineage–specific gene expression program in Hodgkin and Reed-Sternberg cells of Hodgkin lymphoma

Blood ◽  
2003 ◽  
Vol 101 (4) ◽  
pp. 1505-1512 ◽  
Author(s):  
Ines Schwering ◽  
Andreas Bräuninger ◽  
Ulf Klein ◽  
Berit Jungnickel ◽  
Marianne Tinguely ◽  
...  
Keyword(s):  
Gene Expression ◽  
B Cells ◽  
B Cell ◽  
Hodgkin Lymphoma ◽  
Cell Lines ◽  
Expression Profiles ◽  
Specific Gene ◽  
Mrna Levels ◽  
Study Gene Expression ◽  
B Lineage

Hodgkin and Reed-Sternberg (HRS) cells represent the malignant cells in classical Hodgkin lymphoma (HL). Because their immunophenotype cannot be attributed to any normal cell of the hematopoietic lineage, the origin of HRS cells has been controversially discussed, but molecular studies established their derivation from germinal center B cells. In this study, gene expression profiles generated by serial analysis of gene expression (SAGE) and DNA chip microarrays from HL cell lines were compared with those of normal B-cell subsets, focusing here on the expression of B-lineage markers. This analysis revealed decreased mRNA levels for nearly all established B-lineage–specific genes. For 9 of these genes, lack of protein expression was histochemically confirmed. Down-regulation of genes affected multiple components of signaling pathways active in B cells, including B-cell receptor (BCR) signaling. Because several genes down-regulated in HRS cells are positively regulated by the transcriptional activator Pax-5, which is expressed in most HRS cells, we studied HL cell lines for mutations in the Pax-5gene. However, no mutations were found. We propose that the lost B-lineage identity in HRS cells may explain their survival without BCR expression and reflect a fundamental defect in maintaining the B-cell differentiation state in HRS cells, which is likely caused by a novel, yet unknown, pathogenic mechanism.

scholarly journals SpoT-Triggered Stringent Response Controls usp Gene Expression in Pseudomonas aeruginosa

2008 ◽  
Vol 190 (21) ◽  
pp. 7189-7199 ◽  
Author(s):  
Nelli Boes ◽  
Kerstin Schreiber ◽  
Max Schobert
Keyword(s):  
Gene Expression ◽  
Pseudomonas Aeruginosa ◽  
Stationary Phase ◽  
Stress Proteins ◽  
Stringent Response ◽  
Triple Mutant ◽  
Pyruvate Fermentation ◽  
Anaerobic Energy ◽  
In The Wild ◽  
Layer Chromatography

ABSTRACT The universal stress proteins (Usps) UspK (PA3309) and UspN (PA4352) of Pseudomonas aeruginosa are essential for surviving specific anaerobic energy stress conditions such as pyruvate fermentation and anaerobic stationary phase. Expression of the respective genes is under the control of the oxygen-sensing regulator Anr. In this study we investigated the regulation of uspN and three additional P. aeruginosa usp genes: uspL (PA1789), uspM (PA4328), and uspO (PA5027). Anr induces expression of these genes in response to anaerobic conditions. Using promoter-lacZ fusions, we showed that P uspL -lacZ, P uspM -lacZ, and P uspO -lacZ were also induced in stationary phase as described for P uspN -lacZ. However, stationary phase gene expression was abolished in the P. aeruginosa triple mutant Δanr ΔrelA ΔspoT. The relA and spoT genes encode the regulatory components of the stringent response. We determined pppGpp and ppGpp levels using a thin-layer chromatography approach and detected the accumulation of ppGpp in the wild type and the ΔrelA mutant in stationary phase, indicating a SpoT-derived control of ppGpp accumulation. Additional investigation of stationary phase in LB medium revealed that alkaline pH values are involved in the regulatory process of ppGpp accumulation.

Altered gene expression in human cells treated with the insecticide diazinon: correlation with decreased DNA excision repair capacity

2006 ◽  
Vol 25 (2) ◽  
pp. 57-65 ◽  
Author(s):  
T Mankame ◽  
R Hokanson ◽  
R Fudge ◽  
R Chowdhary ◽  
D Busbee
Keyword(s):  
Gene Expression ◽  
Excision Repair ◽  
Steroid Hormone ◽  
Human Cells ◽  
Specific Gene ◽  
Mrna Levels ◽  
Repair Capacity ◽  
Dna Excision Repair ◽  
Regulated Gene Expression ◽  
Mcf 7

Many industrial and agricultural chemicals have steroid hormone agonist or antagonist activities and disrupt hormone-regulated gene expression. The widely-used agricultural insecticide, diazinon, was evaluated using MCF-7 cells a breast cancer-derived, estrogen-dependent, human cell line-to examine the capacity of this chemical to alter steroid hormone-regulated gene expression. MCF-7 cells were treated with 30, 50, or 67 ppm of diazinon, and gene expression in treated cells was measured as mRNA levels in the cells compared to mRNA levels in untreated or estrogen-treated cells. DNA microarray analysis showed significant up-or down-regulation of a number of genes in treated cells compared to untreated cells. Of the 600 human genes on the chip utilized, specific genes with related functions were selected for additional consideration. Real time quantitative PCR (qrtPCR) completed to corroborate mRNA levels as a measure of specific gene expression, confirmed results obtained from analysis of the micro-array data. The data show that ERCC5, encoding Xeroderma pigmentosum protein G (XPG), essential for DNA excision repair, and ribonucleotide reductase subunit M1 (RNRM1), encoding a gene necessary for providing the nucleotides needed for DNA repair, were down-regulated in cells treated with diazinon. These studies were designed to provide base-line data on the gene expression-altering capacity of a specific agricultural chemical, diazinon, and allow assessment of some of the potentially deleterious effects associated with exposure of human cells to diazinon.

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