scholarly journals Global Responses of Methanococcus maripaludis to Specific Nutrient Limitations and Growth Rate

2008 ◽  
Vol 190 (6) ◽  
pp. 2198-2205 ◽  
Author(s):  
Erik L. Hendrickson ◽  
Yuchen Liu ◽  
Guillermina Rosas-Sandoval ◽  
Iris Porat ◽  
Dieter Söll ◽  
...  
Keyword(s):  
Growth Rate ◽  
Amino Acid ◽  
Ribosomal Protein ◽  
Mrna Level ◽  
Mrna Abundance ◽  
Phosphate Limitation ◽  
Specific Response ◽  
Mrna Levels ◽  
Ribosomal Protein Genes ◽  
Methanococcus Maripaludis

ABSTRACT Continuous culture, transcriptome arrays, and measurements of cellular amino acid pools and tRNA charging levels were used to determine the response of Methanococcus maripaludis to leucine limitation. For comparison, the responses to phosphate and H2 limitations were measured as well. In addition, the effect of growth rate was determined. Leucine limitation resulted in a broad response. tRNALeu charging decreased, but only small increases in mRNA were seen for amino acid biosynthesis genes. However, the cellular levels of free isoleucine and valine showed significant increases, indicating a coordinate regulation of branched-chain amino acids at a post-mRNA level. Leucine limitation also resulted in increased mRNA abundance for ribosomal protein genes, increased rRNA abundance, and decreased mRNA abundance for genes of methanogenesis. In contrast, phosphate limitation induced a specific response, a marked increase in mRNA levels for a phosphate transporter. Some mRNA levels responded to more than one factor; for example, transcripts for flagellum synthesis genes decreased under conditions of leucine limitation and increased under H2 limitation. Increased growth rate resulted in increased mRNA levels for ribosomal protein genes, increased rRNA abundance, and increased mRNA for a gene encoding an S-layer protein.

scholarly journals Yeast NOP2 encodes an essential nucleolar protein with homology to a human proliferation marker.

1994 ◽  
Vol 127 (6) ◽  
pp. 1799-1813 ◽  
Author(s):  
E de Beus ◽  
J S Brockenbrough ◽  
B Hong ◽  
J P Aris
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Ribosomal Protein ◽  
Nucleolar Protein ◽  
Mrna Levels ◽  
Multicopy Plasmid ◽  
Yeast Saccharomyces Cerevisiae ◽  
Protein Levels ◽  
Significant Amino Acid Sequence ◽  
Ribosomal Protein L3

We have isolated a gene (NOP2) encoding a nucleolar protein during a search for previously unidentified nuclear proteins in the yeast Saccharomyces cerevisiae. The protein encoded by NOP2 (Nop2p) has a predicted molecular mass of 70 kD, migrates at 90 kD by SDS-PAGE, and is essential for cell viability. Nop2p shows significant amino acid sequence homology to a human proliferation-associated nucleolar protein, p120. Approximately half of Nop2p exhibits 67% amino acid sequence identity to p120. Analysis of subcellular fractions indicates that Nop2p is located primarily in the nucleus, and nuclear fractionation studies suggest that Nop2p is associated with the nucleolus. Indirect immunofluorescence localization of Nop2p shows a nucleolar-staining pattern, which is heterogeneous in appearance, and a faint staining of the cytoplasm. The expression of NOP2 during the transition from stationary phase growth arrest to rapid growth was measured, and compared to the expression of TCM1, which encodes the ribosomal protein L3. Nop2p protein levels are markedly upregulated during the onset of growth, compared to the levels of ribosomal protein L3, which remain relatively constant. NOP2 mRNA levels also increase during the onset of growth, accompanied by a similar increase in the levels of TCM1 mRNA. The consequences of overexpressing NOP2 from the GAL10 promoter on a multicopy plasmid were investigated. Although NOP2 overexpression produced no discernible growth phenotype and had no effect on ribosome subunit synthesis, overexpression was found to influence the morphology of the nucleolus, as judged by electron microscopy. Overexpression caused the nucleolus to become detached from the nuclear envelope and to become more rounded and/or fragmented in appearance. These findings suggest roles for NOP2 in nucleolar function during the onset of growth, and in the maintenance of nucleolar structure.

Protein kinase A mediates growth-regulated expression of yeast ribosomal protein genes by modulating RAP1 transcriptional activity

1994 ◽  
Vol 14 (3) ◽  
pp. 1920-1928
Author(s):  
C Klein ◽  
K Struhl
Keyword(s):  
Amino Acid ◽  
Protein Kinase ◽  
Carbon Source ◽  
Ribosomal Protein ◽  
Binding Sites ◽  
Transcriptional Activity ◽  
Amino Acid Starvation ◽  
Ribosomal Protein Genes ◽  
Regulated Expression ◽  
Kinase A

Yeast ribosomal protein genes are coordinately regulated as a function of cell growth; RNA levels decrease during amino acid starvation but increase following a carbon source upshift. Binding sites for RAP1, a multifunctional transcription factor, are present in nearly all ribosomal protein genes and are associated with growth rate regulation. We show that ribosomal protein mRNA levels are increased twofold in strains that have constitutively high levels of cyclic AMP-dependent protein kinase (protein kinase A [PKA]) activity. The PKA-dependent induction requires RAP1 binding sites, and it reflects increased transcriptional activation by RAP1. Growth-regulated transcription of ribosomal protein genes strongly depends on the ability to regulate PKA activity. Cells with constitutively high PKA levels do not show the transcriptional decrease in response to amino acid starvation. Conversely, in cells with constitutively low PKA activity, ribosomal protein mRNAs levels are lower and largely uninducible upon carbon source upshift. We suggest that modulation of RAP1 transcriptional activity by PKA accounts for growth-regulated expression of ribosomal protein genes.

scholarly journals The effect of calnexin deletion on the expression level of PDI in Saccharomyces cerevisiae under heat stress conditions

2008 ◽  
Vol 13 (1) ◽  
Author(s):  
Huili Zhang ◽  
Jianwei He ◽  
Yanyan Ji ◽  
Akio Kato ◽  
Youtao Song
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Growth Rate ◽  
Heat Stress ◽  
Protein Expression ◽  
Molecular Chaperone ◽  
Mrna Level ◽  
Stress Conditions ◽  
Mrna Levels ◽  
Wild Type ◽  
Wild Type Yeast

AbstractWe cultured calnexin-disrupted and wild-type Saccharomyces cerevisiae strains under conditions of heat stress. The growth rate of the calnexin-disrupted yeast was almost the same as that of the wild-type yeast under those conditions. However, the induced mRNA level of the molecular chaperone PDI in the ER was clearly higher in calnexin-disrupted S. cerevisiae relative to the wild type at 37°C, despite being almost the same in the two strains under normal conditions. The western blotting analysis for PDI protein expression in the ER yielded results that show a parallel in their mRNA levels in the two strains. We suggest that PDI may interact with calnexin under heat stress conditions, and that the induction of PDI in the ER can recover part of the function of calnexin in calnexin-disrupted yeast, and result in the same growth rate as in wild-type yeast.

Association of RAP1 binding sites with stringent control of ribosomal protein gene transcription in Saccharomyces cerevisiae

1991 ◽  
Vol 11 (5) ◽  
pp. 2723-2735 ◽  
Author(s):  
C M Moehle ◽  
A G Hinnebusch
Keyword(s):  
Gene Expression ◽  
Saccharomyces Cerevisiae ◽  
Amino Acid ◽  
Ribosomal Protein ◽  
Binding Sites ◽  
Protein Gene ◽  
Ribosomal Protein Gene ◽  
Ribosomal Protein Genes ◽  
Biosynthetic Genes ◽  
Stringent Control

An amino acid limitation in bacteria elicits a global response, called stringent control, that leads to reduced synthesis of rRNA and ribosomal proteins and increased expression of amino acid biosynthetic operons. We have used the antimetabolite 3-amino-1,2,4-triazole to cause histidine limitation as a means to elicit the stringent response in the yeast Saccharomyces cerevisiae. Fusions of the yeast ribosomal protein genes RPL16A, CRY1, RPS16A, and RPL25 with the Escherichia coli lacZ gene were used to show that the expression of these genes is reduced by a factor of 2 to 5 during histidine-limited exponential growth and that this regulation occurs at the level of transcription. Stringent regulation of the four yeast ribosomal protein genes was shown to be associated with a nucleotide sequence, known as the UASrpg (upstream activating sequence for ribosomal protein genes), that binds the transcriptional regulatory protein RAP1. The RAP1 binding sites also appeared to mediate the greater ribosomal protein gene expression observed in cells growing exponentially than in cells in stationary phase. Although expression of the ribosomal protein genes was reduced in response to histidine limitation, the level of RAP1 DNA-binding activity in cell extracts was unaffected. Yeast strains bearing a mutation in any one of the genes GCN1 to GCN4 are defective in derepression of amino acid biosynthetic genes in 10 different pathways under conditions of histidine limitation. These Gcn- mutants showed wild-type regulation of ribosomal protein gene expression, which suggests that separate regulatory pathways exist in S. cerevisiae for the derepression of amino acid biosynthetic genes and the repression of ribosomal protein genes in response to amino acid starvation.

scholarly journals Sex-specific alterations in mRNA level of key lipid metabolism enzymes in skeletal muscle of overweight and obese subjects following endurance exercise

2009 ◽  
Vol 36 (3) ◽  
pp. 149-157 ◽  
Author(s):  
Ira J. Smith ◽  
Kim M. Huffman ◽  
Michael T. Durheim ◽  
Brian D. Duscha ◽  
William E. Kraus
Keyword(s):  
Skeletal Muscle ◽  
Lipid Metabolism ◽  
Endurance Exercise ◽  
Regulatory Element ◽  
Mrna Level ◽  
Mrna Abundance ◽  
Peroxisome Proliferator ◽  
Mrna Levels ◽  
Middle Aged ◽  
Metabolism Enzymes

Endurance exercise (EE) leads to beneficial alterations in skeletal muscle lipid metabolism in overweight and obese individuals; however, the mechanisms of these improvements are poorly understood. The primary goal of the current investigation was to test the hypothesis that long-term EE training (6 mo) leads to alterations in the mRNA abundance of key lipid metabolism enzymes in skeletal muscle of overweight and obese middle-aged women and men. A secondary aim of this study was to investigate the hypothesis that exercise-mediated adaptations in mRNA levels differ between women and men. The mRNA abundance of representative lipogenic and lipolytic genes from major lipid metabolism pathways, as well as representative lipogenic and lipolytic transcription factors, were determined by real-time PCR from skeletal muscle biopsies collected before and ∼24 h after the final bout of 6 mo of EE. Six months of EE led to increases in muscle lipoprotein lipase, peroxisome proliferator-activated receptor-γ coactivator-1α, carnitine palmitoyltransferase-1 β, diacylglycerol acyltransferase-1, and acid ceramidase mRNA in women, but not men. In contrast, in men, EE led to reductions in the mRNA content of the lipogenic factors sterol regulatory element binding protein-1c and serine palmitoyl transferase. These data suggest that EE-mediated alterations in the abundance of the lipid metabolism genes studied here are fundamentally different between overweight and obese middle-aged women and men. Future studies should determine whether these adaptations in mRNA levels translate into changes in protein function.

Functional analysis of a duplicated linked pair of ribosomal protein genes in Saccharomyces cerevisiae

1990 ◽  
Vol 10 (11) ◽  
pp. 6097-6100
Author(s):  
D M Donovan ◽  
M P Remington ◽  
D A Stewart ◽  
J C Crouse ◽  
D J Miles ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Functional Analysis ◽  
Growth Rate ◽  
Ribosomal Protein ◽  
Vegetative Growth ◽  
Maximum Growth ◽  
Gene Replacement ◽  
Maximum Growth Rate ◽  
Ribosomal Protein Genes ◽  
Genome Copy

Ribosomal protein genes RP28 and S16A (RP55) are closely linked. Another set of this pair of genes exists in the genome (copy 2), genetically unlinked to copy 1. By using gene replacement techniques, we have shown that RP28 from copy 1 is required for vegetative growth and that the cells need S16A from copy 2 to achieve maximum growth rate.

Differential regulation of Na-K-ATPase isoform gene expression by T3 during rat brain development

1991 ◽  
Vol 261 (1) ◽  
pp. C124-C131 ◽  
Author(s):  
I. Corthesy-Theulaz ◽  
A. M. Merillat ◽  
P. Honegger ◽  
B. C. Rossier
Keyword(s):  
Gene Expression ◽  
Brain Development ◽  
Culture System ◽  
Mrna Level ◽  
Mrna Abundance ◽  
Mrna Levels ◽  
Basal Transcription ◽  
Mrna Accumulation ◽  
Atpase Gene ◽  
Beta 2

A fetal rat telencephalon organotypic cell culture system was found to reproduce the developmental pattern of Na-K-adenosinetriphosphatase (ATPase) gene expression observed in vivo [Am. J. Physiol. 258 (Cell Physiol. 27): C1062-C1069, 1990]. We have used this culture system to study the effects of triiodothyronine (T3; 0.003-30 nM) on mRNA abundance and basal transcription rates of Na-K-ATPase isoforms. Steady-state mRNA levels were low at culture day 6 (corresponding to the day of birth) but distinct for each isoform alpha 3 much greater than beta 1 = beta 2 greater than alpha 2 greater than alpha 1. At culture day 6, T3 did not modify mRNA abundance of any isoform. At culture day 12 (corresponding to day 7 postnatal), T3 increased the mRNA level of alpha 2 (4- to 7-fold), beta 2 (4- to 5-fold), alpha 1 (3- to 6-fold), and beta 1 (1.5-fold), whereas alpha 3 mRNA levels remained unchanged. Interestingly, the basal transcription rate for each isoform differed strikingly (alpha 2 greater than alpha 1 much greater than beta 1 = beta 2 greater than alpha 3) but remained stable throughout 12 days of culture and was not regulated by T3. Thus we observed an inverse relationship between rate of transcription and rate of mRNA accumulation for each alpha-isoform, suggesting that alpha 1- and alpha 2-mRNA are turning over rapidly whereas alpha 3-mRNA is turning over slowly. Our data indicate that one of the mechanisms by which T3 selectively controls Na-K-ATPase gene expression during brain development in vitro occurs at the posttranscriptional level.

scholarly journals cDNA and predicted amino acid sequences of the human ribosomal protein genes rpSl2 and rpLl7

1991 ◽  
Vol 19 (14) ◽  
pp. 4001-4001 ◽  
Author(s):  
Yann Hérault ◽  
Denis Michel ◽  
Gilles Chatelain ◽  
Gilbert Brun
Keyword(s):  
Amino Acid ◽  
Ribosomal Protein ◽  
Amino Acid Sequences ◽  
Ribosomal Protein Genes ◽  
Human Ribosomal Protein

scholarly journals Quantitating Translational Control: mRNA Abundance-Dependent and Independent Contributions and the mRNA Sequences That Specify Them

2017 ◽  
Author(s):  
Jingyi Jessica Li ◽  
Guo-Liang Chew ◽  
Mark D. Biggin
Keyword(s):  
Translational Control ◽  
Mrna Level ◽  
Open Reading Frame ◽  
Mrna Abundance ◽  
Mrna Levels ◽  
Mrna Sequence ◽  
Translation Rate ◽  
Reading Frame ◽  
Protein Levels ◽  
Selective Pressures

AbstractTranslation rate per mRNA molecule correlates positively with mRNA abundance. As a result, protein levels do not scale linearly with mRNA levels, but instead scale with the abundance of mRNA raised to the power of an “amplification exponent”. Here we show that to quantitate translational control, the translation rate must be decomposed into two components. One, TRmD, depends on the mRNA level and defines the amplification exponent. The other, TRmIND, is independent of mRNA amount and impacts the correlation coefficient between protein and mRNA levels. We show that in S. cerevisiae TRmD represents ∼20% of the variance in translation and directs an amplification exponent of 1.20 with a 95% confidence interval [1.14, 1.26]. TRmIND constitutes the remaining ∼80% of the variance in translation and explains ∼5% of the variance in protein expression. We also find that TRmD and TRmIND are preferentially determined by different mRNA sequence features: TRmIND by the length of the open reading frame and TRmD both by a ∼60 nucleotide element that spans the initiating AUG and by codon and amino acid frequency. Our work provides more appropriate estimates of translational control and implies that TRmIND is under different evolutionary selective pressures than TRmD.

scholarly journals SSB, Encoding a Ribosome-Associated Chaperone, Is Coordinately Regulated with Ribosomal Protein Genes

1999 ◽  
Vol 181 (10) ◽  
pp. 3136-3143 ◽  
Author(s):  
Nelson Lopez ◽  
John Halladay ◽  
William Walter ◽  
Elizabeth A. Craig
Keyword(s):  
Heat Shock ◽  
Ribosomal Protein ◽  
Ribosomal Proteins ◽  
Chain Complex ◽  
Mrna Levels ◽  
Ribosomal Protein Genes ◽  
Genes Encoding ◽  
Synthetic Capacity ◽  
Translational Apparatus ◽  
Temperature Upshift

ABSTRACT Genes encoding ribosomal proteins and other components of the translational apparatus are coregulated to efficiently adjust the protein synthetic capacity of the cell. Ssb, a Saccharomyces cerevisiae Hsp70 cytosolic molecular chaperone, is associated with the ribosome-nascent chain complex. To determine whether this chaperone is coregulated with ribosomal proteins, we studied the mRNA regulation of SSB under several environmental conditions. Ssb and the ribosomal protein rpL5 mRNAs were up-regulated upon carbon upshift and down-regulated upon amino acid limitation, unlike the mRNA of another cytosolic Hsp70, Ssa. Ribosomal protein and Ssb mRNAs, like many mRNAs, are down-regulated upon a rapid temperature upshift. The mRNA reduction of several ribosomal protein genes and Ssb was delayed by the presence of an allele, EXA3-1, of the gene encoding the heat shock factor (HSF). However, upon a heat shock theEXA3-1 mutation did not significantly alter the reduction in the mRNA levels of two genes encoding proteins unrelated to the translational apparatus. Analysis of gene fusions indicated that the transcribed region, but not the promoter of SSB, is sufficient for this HSF-dependent regulation. Our studies suggest that Ssb is regulated like a core component of the ribosome and that HSF is required for proper regulation of SSB and ribosomal mRNA after a temperature upshift.

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