Quantifying absolute gene expression profiles reveals distinct regulation of central carbon metabolism genes in yeast

In addition to controlled expression of genes by specific regulatory circuits, the abundance of proteins and transcripts can also be influenced by physiological states of the cell such as growth rate and metabolism. Here we examine the control of gene expression by growth rate and metabolism, by analyzing a multi-omics dataset consisting of absolute-quantitative abundances of the transcriptome, proteome, and amino acids in 22 steady-state yeast cultures. We find that transcription and translation are coordinately controlled by the cell growth rate via RNA polymerase II and ribosome abundance, but they are independently controlled by nitrogen metabolism via amino acid and nucleotide availabilities. Genes in central carbon metabolism, however, are distinctly regulated and do not respond to the cell growth rate or nitrogen metabolism as all other genes. Understanding these effects allows the confounding factors of growth rate and metabolism to be accounted for in gene expression profiling studies.

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Quantifying absolute gene expression profiles reveals distinct regulation of central carbon metabolism genes in yeast

10.1101/2020.12.22.423946 ◽

2020 ◽

Author(s):

Rosemary Yu ◽

Egor Vorontsov ◽

Carina Sihlbom ◽

Jens Nielsen

Keyword(s):

Gene Expression ◽

Growth Rate ◽

Cell Growth ◽

Carbon Metabolism ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Central Carbon Metabolism ◽

Metabolic Parameters ◽

Cell Growth Rate ◽

Central Carbon

AbstractIn addition to specific regulatory circuits, gene expression is also regulated by global physiological cues such as the cell growth rate and metabolic parameters. Here we examine these global control mechanisms by analyzing an orthogonal multi-omics dataset consisting of absolute-quantitative abundances of the transcriptome, proteome, and intracellular amino acids in 22 steady-state yeast cultures. Our model indicates that transcript and protein abundance are coordinately controlled by the cell growth rate via RNA polymerase II and ribosome abundance, but are independently controlled by metabolic parameters relating to amino acid and nucleotide availability. Genes in central carbon metabolism, however, are regulated independently of these global physiological cues. Our findings can be used to augment gene expression profiling analyses in the distantly related yeast Schizosaccharomyces pombe and a human cancer cell model. Our results provide a framework to analyze gene expression profiles to gain novel biological insights, a key goal of systems biology.

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Faculty Opinions recommendation of Comprehensive analysis of central carbon metabolism illuminates connections between nutrient availability, growth rate, and cell morphology in Escherichia coli.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.732647498.793544523 ◽

2018 ◽

Author(s):

Kevin D Young ◽

Matthew Jorgenson

Keyword(s):

Escherichia Coli ◽

Growth Rate ◽

Nutrient Availability ◽

Cell Morphology ◽

Carbon Metabolism ◽

Central Carbon Metabolism ◽

Comprehensive Analysis ◽

Central Carbon

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Airpnp: Auto- and Integrated Regulation of Polynucleotide Phosphorylase

Journal of Bacteriology ◽

10.1128/jb.00794-15 ◽

2015 ◽

Vol 197 (24) ◽

pp. 3748-3750 ◽

Cited By ~ 1

Author(s):

Ciarán Condon

Keyword(s):

Gene Expression ◽

Carbon Metabolism ◽

Rna Degradation ◽

Central Carbon Metabolism ◽

Polynucleotide Phosphorylase ◽

Link Type ◽

Central Carbon ◽

Integrated Regulation ◽

Complex Regulation ◽

Posttranscriptional Level

The properties and expression of polynucleotide phosphorylase (PNPase), capable of both RNA degradation and polymerization, have been studied for 60 years. In this issue of theJournal of Bacteriology,Park et al.(H. Park, H. Yakhnin, M. Connolly, T. Romeo, and P. Babitzke, J Bacteriol 197:3751–3759, 2015,http://dx.doi.org/10.1128/JB.00721-15) write the latest chapter on the complex regulation ofpnpgene expression involving CsrA. I describe how this new piece of the puzzle fits into the global scheme of PNPase autoregulation and how this is influenced by central carbon metabolism at both the posttranscriptional level and that of enzyme activity.

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Transcriptomic Analysis of the Influence of Methanol Assimilation on the Gene Expression in the Recombinant Pichia pastoris Producing Hirudin Variant 3

Genes ◽

10.3390/genes10080606 ◽

2019 ◽

Vol 10 (8) ◽

pp. 606 ◽

Cited By ~ 3

Author(s):

Li ◽

Ma ◽

Xu ◽

Wang ◽

...

Keyword(s):

Gene Expression ◽

Amino Acid ◽

Pichia Pastoris ◽

Carbon Metabolism ◽

Fermentation Broth ◽

Alcohol Oxidase ◽

Central Carbon Metabolism ◽

Recombinant Pichia Pastoris ◽

Central Carbon ◽

Almost All

Hirudin and its variants, as strong inhibitors against thrombin, are present in the saliva of leeches and are recognized as potent anticoagulants. However, their yield is far from the clinical requirement up to now. In this study, the production of hirudin variant 3 (HV3) was successfully realized by cultivating the recombinant Pichia pastoris GS115/pPIC9K-hv3 under the regulation of the promoter of AOX1 encoding alcohol oxidase (AOX). The antithrombin activity in the fermentation broth reached the maximum value of 5000 ATU/mL. To explore an effective strategy for improving HV3 production in the future, we investigated the influence of methanol assimilation on the general gene expression in this recombinant by transcriptomic study. The results showed that methanol was partially oxidized into CO2, and the rest was converted into glycerone-P which subsequently entered into central carbon metabolism, energy metabolism, and amino acid biosynthesis. However, the later metabolic processes were almost all down-regulated. Therefore, we propose that the up-regulated central carbon metabolism, energy, and amino acid metabolism should be beneficial for methanol assimilation, which would accordingly improve the production of HV3.

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Fluxomic Analysis Reveals Central Carbon Metabolism Adaptation for Diazotroph Azotobacter vinelandii Ammonium Excretion

Scientific Reports ◽

10.1038/s41598-019-49717-6 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 2

Author(s):

Chao Wu ◽

Ryan A. Herold ◽

Eric P. Knoshaug ◽

Bo Wang ◽

Wei Xiong ◽

...

Keyword(s):

Growth Rate ◽

Carbon Metabolism ◽

Metabolic Flux ◽

Azotobacter Vinelandii ◽

Nitrogenase Activity ◽

Central Carbon Metabolism ◽

Nitrogen Fertilizers ◽

Ammonium Excretion ◽

Diazotrophic Bacteria ◽

Central Carbon

Abstract Diazotrophic bacteria are an attractive biological alternative to synthetic nitrogen fertilizers due to their remarkable capacity to fix atmospheric nitrogen gas to ammonium via nitrogenase enzymes. However, how diazotrophic bacteria tailor central carbon catabolism to accommodate the energy requirement for nitrogenase activity is largely unknown. In this study, we used Azotobacter vinelandii DJ and an ammonium excreting mutant, AV3 (ΔNifL), to investigate central carbon metabolism fluxes and central cell bioenergetics in response to ammonium availability and nitrogenase activity. Enabled by the powerful and reliable methodology of 13C-metabolic flux analysis, we show that the respiratory TCA cycle is upregulated in association with increased nitrogenase activity and causes a monotonic decrease in specific growth rate. Whereas the activity of the glycolytic Entner–Doudoroff pathway is positively correlated with the cell growth rate. These new observations are formulated into a 13C-metabolic flux model which further improves the understanding and interpretation of intracellular bioenergetics. This analysis leads to the conclusion that, under aerobic conditions, respiratory TCA metabolism is responsible for the supply of additional ATP and reducing equivalents required for elevated nitrogenase activity. This study provides a quantitative relationship between central carbon and nitrogen metabolism in an aerobic diazotroph for the first time.

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Steady-state and dynamic gene expression programs inSaccharomyces cerevisiaein response to variation in environmental nitrogen

Molecular Biology of the Cell ◽

10.1091/mbc.e14-05-1013 ◽

2016 ◽

Vol 27 (8) ◽

pp. 1383-1396 ◽

Cited By ~ 19

Author(s):

Edoardo M. Airoldi ◽

Darach Miller ◽

Rodoniki Athanasiadou ◽

Nathan Brandt ◽

Farah Abdul-Rahman ◽

...

Keyword(s):

Gene Expression ◽

Growth Rate ◽

Steady State ◽

Cell Growth ◽

Nitrogen Source ◽

Transcriptional Control ◽

Molecular Form ◽

Protein Translation ◽

Cell Growth Rate ◽

Regulated Gene Expression

Cell growth rate is regulated in response to the abundance and molecular form of essential nutrients. In Saccharomyces cerevisiae (budding yeast), the molecular form of environmental nitrogen is a major determinant of cell growth rate, supporting growth rates that vary at least threefold. Transcriptional control of nitrogen use is mediated in large part by nitrogen catabolite repression (NCR), which results in the repression of specific transcripts in the presence of a preferred nitrogen source that supports a fast growth rate, such as glutamine, that are otherwise expressed in the presence of a nonpreferred nitrogen source, such as proline, which supports a slower growth rate. Differential expression of the NCR regulon and additional nitrogen-responsive genes results in >500 transcripts that are differentially expressed in cells growing in the presence of different nitrogen sources in batch cultures. Here we find that in growth rate–controlled cultures using nitrogen-limited chemostats, gene expression programs are strikingly similar regardless of nitrogen source. NCR expression is derepressed in all nitrogen-limiting chemostat conditions regardless of nitrogen source, and in these conditions, only 34 transcripts exhibit nitrogen source–specific differential gene expression. Addition of either the preferred nitrogen source, glutamine, or the nonpreferred nitrogen source, proline, to cells growing in nitrogen-limited chemostats results in rapid, dose-dependent repression of the NCR regulon. Using a novel means of computational normalization to compare global gene expression programs in steady-state and dynamic conditions, we find evidence that the addition of nitrogen to nitrogen-limited cells results in the transient overproduction of transcripts required for protein translation. Simultaneously, we find that that accelerated mRNA degradation underlies the rapid clearing of a subset of transcripts, which is most pronounced for the highly expressed NCR-regulated permease genes GAP1, MEP2, DAL5, PUT4, and DIP5. Our results reveal novel aspects of nitrogen-regulated gene expression and highlight the need for a quantitative approach to study how the cell coordinates protein translation and nitrogen assimilation to optimize cell growth in different environments.

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NM23 gene expression correlates with cell growth rate and S-phase

International Journal of Cancer ◽

10.1002/ijc.2910600619 ◽

1995 ◽

Vol 60 (6) ◽

pp. 837-842 ◽

Cited By ~ 44

Author(s):

Maria A. Caligo ◽

Giovanna Cipollini ◽

Lisa Fiore ◽

Simonetta Calvo ◽

Fulvio Basolo ◽

...

Keyword(s):

Gene Expression ◽

Growth Rate ◽

Cell Growth ◽

S Phase ◽

Cell Growth Rate ◽

Nm23 Gene

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Network Identification and Flux Quantification in the Central Metabolism of Saccharomyces cerevisiae under Different Conditions of Glucose Repression

Journal of Bacteriology ◽

10.1128/jb.183.4.1441-1451.2001 ◽

2001 ◽

Vol 183 (4) ◽

pp. 1441-1451 ◽

Cited By ~ 243

Author(s):

Andreas Karoly Gombert ◽

Margarida Moreira dos Santos ◽

Bjarke Christensen ◽

Jens Nielsen

Keyword(s):

Saccharomyces Cerevisiae ◽

Growth Rate ◽

Specific Growth Rate ◽

Batch Culture ◽

Network Structure ◽

Carbon Metabolism ◽

Specific Growth ◽

Central Carbon Metabolism ◽

Published Data ◽

Central Carbon

ABSTRACT The network structure and the metabolic fluxes in central carbon metabolism were characterized in aerobically grown cells ofSaccharomyces cerevisiae. The cells were grown under both high and low glucose concentrations, i.e., either in a chemostat at steady state with a specific growth rate of 0.1 h−1 or in a batch culture with a specific growth rate of 0.37 h−1. Experiments were carried out using [1-13C]glucose as the limiting substrate, and the resulting summed fractional labelings of intracellular metabolites were measured by gas chromatography coupled to mass spectrometry. The data were used as inputs to a flux estimation routine that involved appropriate mathematical modelling of the central carbon metabolism ofS. cerevisiae. The results showed that the analysis is very robust, and it was possible to quantify the fluxes in the central carbon metabolism under both growth conditions. In the batch culture, 16.2 of every 100 molecules of glucose consumed by the cells entered the pentose-phosphate pathway, whereas the same relative flux was 44.2 per 100 molecules in the chemostat. The tricarboxylic acid cycle does not operate as a cycle in batch-growing cells, in contrast to the chemostat condition. Quantitative evidence was also found for threonine aldolase and malic enzyme activities, in accordance with published data. Disruption of the MIG1 gene did not cause changes in the metabolic network structure or in the flux pattern.

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