scholarly journals Growth Phase- and Cell Division-Dependent Activation and Inactivation of the σ32 Regulon in Escherichia coli

2008 ◽  
Vol 191 (5) ◽  
pp. 1695-1702 ◽  
Author(s):  
Maria Anna Wagner ◽  
Doris Zahrl ◽  
Gernot Rieser ◽  
Günther Koraimann
Keyword(s):  
Escherichia Coli ◽  
Cell Division ◽  
Stationary Phase ◽  
Transcriptional Activation ◽  
Target Genes ◽  
Expression Patterns ◽  
Logarithmic Phase ◽  
Protein Levels ◽  
Late Logarithmic Phase ◽  
Functional Inactivation

ABSTRACT Alternative sigma factors allow bacteria to reprogram global transcription rapidly and to adapt to changes in the environment. Here we report on growth- and cell division-dependent σ32 regulon activity in Escherichia coli in batch culture. By analyzing σ32 expression in growing cells, an increase in σ32 protein levels is observed during the first round of cell division after exit from stationary phase. Increased σ32 protein levels result from transcriptional activation of the rpoH gene. After the first round of bulk cell division, rpoH transcript levels and σ32 protein levels decrease again. The late-logarithmic phase and the transition to stationary phase are accompanied by a second increase in σ32 levels and enhanced stability of σ32 protein but not by enhanced transcription of rpoH. Throughout growth, σ32 target genes show expression patterns consistent with oscillating σ32 protein levels. However, during the transition to early-stationary phase, despite high σ32 protein levels, the transcription of σ32 target genes is downregulated, suggesting functional inactivation of σ32. It is deduced from these data that there may be a link between σ32 regulon activity and cell division events. Further support for this hypothesis is provided by the observation that in cells in which FtsZ is depleted, σ32 regulon activation is suppressed.

scholarly journals Birdsong Decreases Protein Levels of FoxP2, a Molecule Required for Human Speech

2008 ◽  
Vol 100 (4) ◽  
pp. 2015-2025 ◽  
Author(s):  
Julie E. Miller ◽  
Elizabeth Spiteri ◽  
Michael C. Condro ◽  
Ryan T. Dosumu-Johnson ◽  
Daniel H. Geschwind ◽  
...  
Keyword(s):  
Mrna Expression ◽  
Target Genes ◽  
Expression Patterns ◽  
Vocal Learning ◽  
Brain Regions ◽  
Motor Deficits ◽  
Mrna Levels ◽  
Adult Males ◽  
Protein Levels ◽  
Area X

Cognitive and motor deficits associated with language and speech are seen in humans harboring FOXP2 mutations. The neural bases for FOXP2 mutation-related deficits are thought to reside in structural abnormalities distributed across systems important for language and motor learning including the cerebral cortex, basal ganglia, and cerebellum. In these brain regions, our prior research showed that FoxP2 mRNA expression patterns are strikingly similar between developing humans and songbirds. Within the songbird brain, this pattern persists throughout life and includes the striatal subregion, Area X, that is dedicated to song development and maintenance. The persistent mRNA expression suggests a role for FoxP2 that extends beyond the formation of vocal learning circuits to their ongoing use. Because FoxP2 is a transcription factor, a role in shaping circuits likely depends on FoxP2 protein levels which might not always parallel mRNA levels. Indeed our current study shows that FoxP2 protein, like its mRNA, is acutely downregulated in mature Area X when adult males sing with some differences. Total corticosterone levels associated with the different behavioral contexts did not vary, indicating that differences in FoxP2 levels are not likely attributable to stress. Our data, together with recent reports on FoxP2's target genes, suggest that lowered FoxP2 levels may allow for expression of genes important for circuit modification and thus vocal variability.

scholarly journals Key Regulatory Pathways, MicroRNAs, and Target Genes Participate in Adventitious Root Formation of Acer Rubrum L

2021 ◽  
Author(s):  
Wenpeng Zhu ◽  
Manyu Zhang ◽  
Jianyi Li ◽  
Hewen Zhao ◽  
Kezhong Zhang ◽  
...  
Keyword(s):  
Transcriptional Activation ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Seedling Survival ◽  
Expression Patterns ◽  
Economic Value ◽  
Acer Rubrum ◽  
Pcr Analysis ◽  
Asexual Propagation ◽  
Regulatory Pathways

Abstract BackgroundAcer rubrum L. is a colorful ornamental tree with great economic value. Because this tree is difficult to root under natural conditions and the seedling survival rate is low, vegetative propagation methods are often used. Because the formation of adventitious roots (ARs) is essential for the survival of asexual propagation of A. rubrum, it is necessary to investigate the molecular regulatory mechanisms in the formation of ARs of A. ruburm. To address this knowledge gap, we sequenced the transcriptome and sRNA of the A. rubrum variety ‘Autumn Fantasy’ using high-throughput sequencing and explored changes in gene and microRNA (miRNA) expression in response to exogenous auxin treatment. ResultsWe identified 82,468 differentially expressed genes between the treated and untreated ARs, as well as 48 known and 95 novel miRNAs. We also identified 172 target genes of the known miRNAs using degradome sequencing. Two regulatory pathways (ubiquitin mediated proteolysis and plant hormone signal transduction), Ar-miR160a and the target gene ArARF10 were shown to be involved in the auxin response. We further investigated the expression patterns and regulatory roles of ArARF10 through subcellular localization, transcriptional activation, plant transformation, qRT-PCR analysis, and GUS staining. ConclusionsDifferential expression patterns indicated the Ar-miR160a-ArARF10 interaction might play a significant role in the regulation of AR formation in A. rubrum. Our study provided new insights into mechanisms underlying the regulation of AR formation in A. rubrum.

scholarly journals Key Regulatory Pathways, microRNAs, and Target Genes Participate in Adventitious Root Formation of Acer Rubrum L.

2021 ◽  
Author(s):  
Wenpeng Zhu ◽  
Manyu Zhang ◽  
Jianyi Li ◽  
Hewen Zhao ◽  
Kezhong Zhang ◽  
...  
Keyword(s):  
Transcriptional Activation ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Seedling Survival ◽  
Expression Patterns ◽  
Economic Value ◽  
Acer Rubrum ◽  
Pcr Analysis ◽  
Asexual Propagation ◽  
Regulatory Pathways

Abstract BackgroundAcer rubrum L. is a colorful ornamental tree with great economic value. Because this tree is difficult to root under natural conditions and the seedling survival rate is low, vegetative propagation methods are often used. Because the formation of adventitious roots (ARs) is essential for the survival of asexual propagation of A. rubrum, it is necessary to investigate the molecular regulatory mechanisms in the formation of ARs of A. ruburm. To address this knowledge gap, we sequenced the transcriptome and sRNA of the A. rubrum variety ‘Autumn Fantasy’ using high-throughput sequencing and explored changes in gene and microRNA (miRNA) expression in response to exogenous auxin treatment. ResultsWe identified 82,468 differentially expressed genes between the treated and untreated ARs, as well as 48 known and 95 novel miRNAs. We also identified 172 target genes of the known miRNAs using degradome sequencing. Two regulatory pathways (ubiquitin mediated proteolysis and plant hormone signal transduction), Ar-miR160a and the target gene ArARF10 were shown to be involved in the auxin response. We further investigated the expression patterns and regulatory roles of ArARF10 through subcellular localization, transcriptional activation, plant transformation, qRT-PCR analysis, and GUS staining. ConclusionsDifferential expression patterns indicated the Ar-miR160a-ArARF10 interaction might play a significant role in the regulation of AR formation in A. rubrum. Our study provided new insights into mechanisms underlying the regulation of AR formation in A. rubrum.

scholarly journals Induction of the HIF pathway: Differential regulation by chemical hypoxia and oxygen glucose deprivation

2019 ◽  
Author(s):  
Alicia E. Novak ◽  
Susan M. Jones ◽  
J. Paul Elliott
Keyword(s):  
Transcriptional Activation ◽  
Cellular Response ◽  
Target Genes ◽  
Expression Patterns ◽  
Hypoxia Inducible Factor ◽  
Glucose Deprivation ◽  
Oxygen Glucose Deprivation ◽  
Oxygen Levels ◽  
Chemical Hypoxia ◽  
Hif Pathway

AbstractThe Hypoxia Inducible Factor (HIF) proteins are the master regulators in the cellular response to varying oxygen levels, including hypoxia. The HIF complex is stabilized and accumulates when oxygen levels drop through inhibition of a degradative enzyme. An active HIF complex can act as a transcriptional regulator of hundreds of genes. In turn, these genes determine the response of the cell by inducing pathways which can promote survival, or result in cell death. However, little is known about the regulation of the transcriptional process. We were interested in learning more about the time dependence of transcriptional activation in order to target those pathways which could enhance cell survival after ischemia. Using mouse hippocampal organotypic cultures (HOTCs), we compared oxygen-glucose deprivation with the hypoxia mimetic cobalt, which inhibits the oxygen dependent prolyl hydroylase and blocks degradation of the HIF proteins. We demonstrated that two of the most studied HIF target genes (VEGF, EPO) as well as HIF structural genes show complex time and dose-dependent expression patterns in response to the two different insults. Understanding of these molecular responses is crucial for the development of future treatments to enhance recovery from hypoxia and stroke.

Expression patterns of vHNF1 and HNF1 homeoproteins in early postimplantation embryos suggest distinct and sequential developmental roles

Development ◽  
1992 ◽  
Vol 116 (3) ◽  
pp. 783-797 ◽  
Author(s):  
S. Cereghini ◽  
M.O. Ott ◽  
S. Power ◽  
M. Maury
Keyword(s):  
Transcriptional Activation ◽  
Target Genes ◽  
Fetal Liver ◽  
Expression Patterns ◽  
Yolk Sac ◽  
Control Element ◽  
Visceral Endoderm ◽  
Mouse Development ◽  
F9 Cells

The homeoproteins HNF1 (LFB1/HNF1-A) and vHNF1 (LFB3/HNF1 beta) interact with an essential control element of a group of liver-specific genes. During development, these putative target genes are initially expressed in the visceral endoderm of the yolk sac and subsequently in fetal liver. To assess the possible involvement of HNF1 and/or vHNF1 as transcriptional regulators in the early steps of visceral endoderm differentiation, we have analyzed the expression pattern of both factors both in vitro during differentiation of murine F9 embryonal carcinoma cells and in vivo during early postimplantation mouse development. We show here that differentiation of F9 cells into either visceral or parietal endoderm is accompanied by a sharp induction in vHNF1 mRNA and protein. By contrast, only low levels of aberrantly sized HNF1 transcripts, but not DNA-binding protein, are found in F9 cells and its differentiated derivatives. At 6–7.5 days of gestation, high levels of vHNF1 mRNA are present in the visceral extraembryonic endoderm, which co-localize with transcripts of the transthyretin gene. HNF1 transcripts are first detected in the yolk sac roughly two embryonic days later, after the developmental onset of transcription of target genes. As development proceeds, discrepancies are observed between the level of transcripts of both vHNF1 and HNF1 and their respective nuclear binding proteins, notably in the yolk sac and embryonic kidney. In addition, we show that two alternative spliced isoforms of vHNF1 mRNA, vHNF-A and vHNF1-B, are expressed in both embryonic and adult tissues. Taken together, these data suggest that vHNF1 participates as a regulatory factor in the initial transcriptional activation of the target genes in the visceral endoderm of the yolk sac, whereas the later appearance of HNF1 could be required for maintenance of their expression. Our results also provide evidence of a posttranscriptional level of control of vHNF1 and HNF1 gene expression during development, in addition to the spatial restriction in transcription.

scholarly journals Posttranscriptional Regulation of tnaA by Protein-RNA Interaction Mediated by Ribosomal Protein L4 in Escherichia coli

2020 ◽  
Vol 202 (10) ◽  
Author(s):  
Dharam Singh ◽  
Oleg N. Murashko ◽  
Sue Lin-Chao
Keyword(s):  
Escherichia Coli ◽  
Cell Growth ◽  
Stationary Phase ◽  
Ribosomal Protein ◽  
Fine Tuning ◽  
Mrna Levels ◽  
Rnase E ◽  
Early Stationary Phase ◽  
Protein Levels ◽  
Rna Interaction

ABSTRACT Escherichia coli ribosomal protein (r-protein) L4 has extraribosomal biological functions. Previously, we described L4 as inhibiting RNase E activity through protein-protein interactions. Here, we report that from stabilized transcripts regulated by L4-RNase E, mRNA levels of tnaA (encoding tryptophanase from the tnaCAB operon) increased upon ectopic L4 expression, whereas TnaA protein levels decreased. However, at nonpermissive temperatures (to inactivate RNase E), tnaA mRNA and protein levels both increased in an rne temperature-sensitive [rne(Ts)] mutant strain. Thus, L4 protein fine-tunes TnaA protein levels independently of its inhibition of RNase E. We demonstrate that ectopically expressed L4 binds with transcribed spacer RNA between tnaC and tnaA and downregulates TnaA translation. We found that deletion of the 5′ or 3′ half of the spacer compared to the wild type resulted in a similar reduction in TnaA translation in the presence of L4. In vitro binding of L4 to the tnaC-tnaA transcribed spacer RNA results in changes to its secondary structure. We reveal that during early stationary-phase bacterial growth, steady-state levels of tnaA mRNA increased but TnaA protein levels decreased. We further confirm that endogenous L4 binds to tnaC-tnaA transcribed spacer RNA in cells at early stationary phase. Our results reveal the novel function of L4 in fine-tuning TnaA protein levels during cell growth and demonstrate that r-protein L4 acts as a translation regulator outside the ribosome and its own operon. IMPORTANCE Some ribosomal proteins have extraribosomal functions in addition to ribosome translation function. The extraribosomal functions of several r-proteins control operon expression by binding to own-operon transcripts. Previously, we discovered a posttranscriptional, RNase E-dependent regulatory role for r-protein L4 in the stabilization of stress-responsive transcripts. Here, we found an additional extraribosomal function for L4 in regulating the tna operon by L4-intergenic spacer mRNA interactions. L4 binds to the transcribed spacer RNA between tnaC and tnaA and alters the structural conformation of the spacer RNA, thereby reducing the translation of TnaA. Our study establishes a previously unknown L4-mediated mechanism for regulating gene expression, suggesting that bacterial cells have multiple strategies for controlling levels of tryptophanase in response to varied cell growth conditions.

scholarly journals Cation Transport in Escherichia coli

1962 ◽  
Vol 46 (1) ◽  
pp. 159-166 ◽  
Author(s):  
Stanley G. Schultz ◽  
Norman L. Wilson ◽  
Wolfgang Epstein
Keyword(s):  
Escherichia Coli ◽  
Stationary Phase ◽  
Growth Medium ◽  
Bacterial Culture ◽  
Cation Transport ◽  
Logarithmic Phase ◽  
E Coli

The intracellular Cl concentration in E. coli has been studied as a function of the Cl concentration in the growth medium and the age of the bacterial culture. The ratio of extracellular to intracellular Cl concentration is shown to be 3.0 in the logarithmic phase and 1.13 in the stationary phase, both ratios being independent of the extracellular Cl concentration. If it may be assumed that Cl is passively distributed in this organism, these results are consistent with a transmembrane P.D. of 29 mv, interior negative, during the logarithmic phase, and 3 mv, interior negative, in the stationary phase.

HIF-1α-targeted pathways are activated by heat acclimation and contribute to acclimation-ischemic cross-tolerance in the heart

2005 ◽  
Vol 23 (1) ◽  
pp. 79-88 ◽  
Author(s):  
Alina Maloyan ◽  
Luba Eli-Berchoer ◽  
Gregg L. Semenza ◽  
Gary Gerstenblith ◽  
Michael D. Stern ◽  
...  
Keyword(s):  
Transcriptional Activation ◽  
Target Genes ◽  
Hypoxia Inducible Factor ◽  
Heat Acclimation ◽  
Heme Oxygenase 1 ◽  
Mrna Levels ◽  
Rt Pcr ◽  
Cross Tolerance ◽  
Protein Levels ◽  
Rat Hearts

Hypoxia-inducible factor-1 (HIF-1) is a key regulator of the cellular hypoxic response. We previously showed that HIF-1 activation is essential for heat acclimation (AC) in Caenorhabditis elegans. Metabolic changes in AC rat hearts indicate HIF-1α activation in mammals as well. Here we characterize the HIF-1α profile and the transcriptional activation of its target genes following AC and following heat stress (HS) in hearts from nonacclimated (C; 24°C) and AC (34°C, 1 mo) rats. We used Western blot and immunohistochemistry to measure HIF-1α levels and EMSA and RT-PCR/quantitative RT-PCR to detect expression of the HIF-1α-targeted genes, including vascular endothelial growth factor ( Vegf), heme oxygenase-1 ( HO1), erythropoietin ( Epo), and Epo receptor ( EpoR). EpoR and Epo mRNA levels were measured to determine systemic effects in the kidneys and cross-tolerance effects in C and AC ischemic hearts (Langendorff, 75% ischemia, 40 min). The results demonstrated that 1) after AC, HIF-1α protein levels were increased, 2) HS alone induced transient HIF-1α upregulation, and 3) VEGF and HO1 mRNA levels increased after HS, with greater magnitude in the AC hearts. Epo mRNA in AC kidneys and EpoR mRNA in AC hearts were also elevated. In AC hearts, EpoR expression was markedly higher after HS or ischemia. Hearts from AC rats were dramatically protected against infarction after ischemia-perfusion. We conclude that HIF-1 contributes to the acclimation-ischemia cross-tolerance mechanism in the heart by induction of both chronic and inducible adaptive components.

scholarly journals Secretion of Amylase by the Marine Bacterium, Alteromonas rubra

1982 ◽  
Vol 35 (1) ◽  
pp. 111 ◽  
Author(s):  
Lilian Gavrilovic ◽  
RW O'Brien ◽  
RL Sanders
Keyword(s):  
Carbon Source ◽  
Stationary Phase ◽  
Marine Bacterium ◽  
Control Level ◽  
Logarithmic Phase ◽  
Amylase Secretion ◽  
Late Logarithmic Phase

A. rubra possesses a constitutive IX-amylase which is secreted during the stationary phase of growth when glucose (at concentrations below 5 mM) is the carbon source. The activity of the enzyme was increased about eightfold over the control level when the organism was grown on O� 2 % (wjv) starch or maltose, with secretion starting in the late logarithmic phase of growth and continuing into the stationary phase. IX-Amylase secretion was repressed by the addition of glucose, at concentrations in excess of 5 mM, when the organism was grown on a medium containing starch or maltose as carbon source.

scholarly journals Random Insertion of a TetR-Inducing Peptide Tag into Escherichia coli Proteins Allows Analysis of Protein Levels by Induction of Reporter Gene Expression

2006 ◽  
Vol 72 (8) ◽  
pp. 5637-5642 ◽  
Author(s):  
Maximilian Schlicht ◽  
Christian Berens ◽  
Janko Daam ◽  
Wolfgang Hillen
Keyword(s):  
Gene Expression ◽  
Escherichia Coli ◽  
Protein Expression ◽  
Reporter Gene ◽  
Expression Patterns ◽  
Reporter Gene Expression ◽  
Published Data ◽  
Insertion Element ◽  
Protein Levels ◽  
Fusion Protein Expression

ABSTRACT The insertion element InsTipα was constructed to generate protein expression data. It randomly fuses the TetR-inducing peptide Tip to the affected reading frame. Fusion protein expression is quantified by Tet-regulated reporter gene expression. The expression patterns of tagged Escherichia coli genes fully agree with published data from transcriptional fusions or microarrays, validating the Tip tag approach.

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