scholarly journals Adaptation of Central Metabolite Pools to Variations in Growth Rate and Cultivation Conditions in Saccharomyces Cerevisiae

2020 ◽  
Author(s):  
Kanhaiya Kumar ◽  
Vishwesh Venkatraman ◽  
Per Bruheim
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Growth Rate ◽  
Amino Acid ◽  
Growth Rates ◽  
Building Blocks ◽  
Relative Reduction ◽  
Central Metabolism ◽  
Cultivation Conditions ◽  
Biological Studies ◽  
Metabolite Pool

Abstract Background: Saccharomyces cerevisiae is a well-known popular model system for basic biological studies and to serve as host organism for heterologous production of commercially interesting small molecules and proteins. The central metabolism is at the core to provide building blocks and energy to support growth and survival in normal situations as well as during exogeneous stresses and forced heterologous protein production. Here, we present a comprehensive study of intracellular central metabolite pool profiling when growing S. cerevisiae on different carbon sources in batch cultivations and at different growth rates in nutrient limited glucose chemostats. Latest versions of absolute quantitative mass spectrometry-based metabolite profiling methodology were applied to cover glycolytic and pentose phosphate pathway metabolites, TCA, complete amino acid and deoxy-/nucleoside phosphate pools. We have attempted to correlate the total metabolite pool composition with growth rates and nutrient limitation in both batch and chemostat cultivations. We have also tried to dissect the Crabtree-effect, i.e. ethanol-producing cultivation conditions, based on metabolite pool composition. Results: Glutamate, glutamine, alanine and citrate were the four most abundant metabolites for most conditions tested. Amino acid is the dominant metabolite class even though a marked relative reduction compared to the other metabolite classes was observed for nitrogen and phosphate limited chemostats. Interestingly, glycolytic and PPP metabolites display largest variation among the cultivation conditions while the nucleoside phosphate pools are more stable and vary within a closer concentration window. The overall trends for glucose and nitrogen limited chemostats were increased metabolite pools with increasing growth rate. Next, comparing the chosen chemostat reference growth rate (0.12 h -1 , approximate one-fourth of maximal unlimited growth rate) illuminates an interesting pattern: almost all pools are lower in nitrogen and phosphate limited conditions compared to glucose limitation, except for the TCA metabolites citrate, isocitrate and a-ketoglutarate. Conclusions: This study provides new knowledge how the central metabolism is adapting to various cultivations conditions and growth rates which is essential for expanding our understanding of cellular metabolism and development of improved phenotypes in metabolic engineering.

scholarly journals Adaptation of central metabolite pools to variations in growth rate and cultivation conditions in Saccharomyces cerevisiae

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Kanhaiya Kumar ◽  
Vishwesh Venkatraman ◽  
Per Bruheim
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Growth Rate ◽  
Amino Acid ◽  
Growth Rates ◽  
Pentose Phosphate Pathway ◽  
Pentose Phosphate ◽  
Relative Reduction ◽  
Central Metabolism ◽  
Cultivation Conditions ◽  
Biological Studies

Abstract Background Saccharomyces cerevisiae is a well-known popular model system for basic biological studies and serves as a host organism for the heterologous production of commercially interesting small molecules and proteins. The central metabolism is at the core to provide building blocks and energy to support growth and survival in normal situations as well as during exogenous stresses and forced heterologous protein production. Here, we present a comprehensive study of intracellular central metabolite pool profiling when growing S. cerevisiae on different carbon sources in batch cultivations and at different growth rates in nutrient-limited glucose chemostats. The latest versions of absolute quantitative mass spectrometry-based metabolite profiling methodology were applied to cover glycolytic and pentose phosphate pathway metabolites, tricarboxylic acid cycle (TCA), complete amino acid, and deoxy-/nucleoside phosphate pools. Results Glutamate, glutamine, alanine, and citrate were the four most abundant metabolites for most conditions tested. The amino acid is the dominant metabolite class even though a marked relative reduction compared to the other metabolite classes was observed for nitrogen and phosphate limited chemostats. Interestingly, glycolytic and pentose phosphate pathway (PPP) metabolites display the largest variation among the cultivation conditions while the nucleoside phosphate pools are more stable and vary within a closer concentration window. The overall trends for glucose and nitrogen-limited chemostats were increased metabolite pools with the increasing growth rate. Next, comparing the chosen chemostat reference growth rate (0.12 h−1, approximate one-fourth of maximal unlimited growth rate) illuminates an interesting pattern: almost all pools are lower in nitrogen and phosphate limited conditions compared to glucose limitation, except for the TCA metabolites citrate, isocitrate and α-ketoglutarate. Conclusions This study provides new knowledge-how the central metabolism is adapting to various cultivations conditions and growth rates which is essential for expanding our understanding of cellular metabolism and the development of improved phenotypes in metabolic engineering.

scholarly journals Do Growing Rabbits with a High Growth Rate Require Diets with High Levels of Essential Amino Acids? A Choice-Feeding Trial

Animals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 824
Author(s):  
Pablo Jesús Marín-García ◽  
Mari Carmen López-Luján ◽  
Luís Ródenas ◽  
Eugenio Martínez-Paredes ◽  
María Cambra-López ◽  
...  
Keyword(s):  
Amino Acids ◽  
Growth Rate ◽  
Amino Acid ◽  
Growth Rates ◽  
Nutrient Retention ◽  
High Growth ◽  
Feeding Trial ◽  
Nutritional Recommendations ◽  
Sulphur Amino Acids ◽  
Choice Feeding

As a consequence of the genetic selection process in growing rabbits, there are currently fast-growing animals exhibiting an average daily gain that may exceed 45 g/d. The protein requirements of these animals, namely amino acid requirements, may differ from animals with low growth rates. The objective of this work was to evaluate growth performance, the coefficient of total tract apparent digestibility (CTTAD), the apparent ileal digestibility (AID) of amino acids and nutrient retention of fast-growing rabbits when they had access to a diet with high levels of amino acids and/or a diet formulated with current nutritional recommendations in a choice-feeding trial. To this end, two diets were formulated: the M diet following current nutritional recommendations for growing rabbits (including 8.1, 5.8 and 6.9 g/kg dry matter (DM) of total lysine, sulphur amino acids and threonine, respectively) and the H diet with higher levels of total lysine, sulphur amino acids and threonine (9.4, 6.6 and 7.8 g/kg DM, respectively). A total of 220 weaned rabbits, from a paternal line selected for the growth rate, had free access to the M diet, the H diet or both (MH) diets from 28 to 63 days of age. The CTTAD of DM, crude protein and gross energy from 49 to 53 days of age as well as the AID of amino acids of the diets at 63 days of age were determined. Protein, amino acids and energy retained in the empty body from 28 to 63 days of age were also registered. No significant differences in growth performance, CTTAD, AID and nutrient retention between dietary treatments were observed. However, animals fed the H diet showed a higher AID of cysteine (p < 0.05) and higher threonine retention (p < 0.05) compared to the M diet. As regards the choice-feeding trial, MH animals showed a higher feed intake of the M diet compared to the H diet (+8.61%; p < 0.001), and furthermore, more than 50% of the animals preferred the M diet throughout the experimental period (p < 0.05). Our results suggest that animals with high growth rates do not show significantly higher productive traits when fed the H diet compared to the M diet. As regards choice feeding, MH animals were capable of choosing their preferred diet, showing high intra-individual repeatability in preference for the M diet. It would be interesting to continue studying this behaviour of choice based on amino acid levels.

scholarly journals INHIBITION OF GROWTH BY AMBER SUPPRESSORS IN YEAST

Genetics ◽  
1976 ◽  
Vol 82 (2) ◽  
pp. 233-249
Author(s):  
Susan W Liebman ◽  
Fred Sherman
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Growth Rate ◽  
Growth Rates ◽  
Nutrient Medium ◽  
Normal Growth ◽  
Yeast Saccharomyces Cerevisiae ◽  
Highly Efficient ◽  
Critical Range ◽  
Inhibition Of Growth ◽  
Amber Suppressor

ABSTRACT Strains of the yeast Saccharomyces cerevisiae that contain highly efficient amber (UAG) suppressors grow poorly on nutrient medium, while normal or nearly normal growth rates are observed when these strains lose the suppressors or when the suppressors are mutated to lower efficiencies. The different growth rates account for the accumulation of mutants with lowered efficiencies in cultures of strains with highly efficient amber suppressors. Genetic analyses indicate that one of the mutations with a lowered efficiency of suppression is caused by an intragenic mutation of the amber suppressor. The inhibition of growth caused by excessive suppression is expected to be exacerbated when appropriate suppressors are combined together in haploid cells if two suppressors act with a greater efficiency than a single suppressor. Such retardation of growth is observed with combinations of two UAA (ochre) suppressors (Gilmore 1967) and with combinations of two UAG suppressors when the efficiencies of each of the suppressors are within a critical range. In contrast, combinations of a UAA suppressor and a UAG suppressor do not affect growth rate. Apparently while either excessive UAA or excessive UAG suppression is deleterious to yeast, a moderate level of simultaneous UAA and UAG suppression is not.

scholarly journals Novel Strategy for the Calorimetry-Based Control of Fed-Batch Cultivations of Saccharomyces cerevisiae

Processes ◽  
2021 ◽  
Vol 9 (4) ◽  
pp. 723
Author(s):  
Jérémy Kottelat ◽  
Brian Freeland ◽  
Michal Dabros
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Growth Rate ◽  
Specific Growth Rate ◽  
Growth Rates ◽  
Specific Growth ◽  
Fed Batch ◽  
Estimation And Control ◽  
Novel Strategy ◽  
Specific Growth Rates ◽  
Mean Square Errors

Typical controllers for fed-batch cultivations are based on the estimation and control of the specific growth rate in real time. Biocalorimetry allows one to measure a heat signal proportional to the substrate consumed by cells. The derivative of this heat signal is usually used to evaluate the specific growth rate, introducing noise to the resulting estimate. To avoid this, this study investigated a novel controller based directly on the heat signal. Time trajectories of the heat signal setpoint were modelled for different specific growth rates, and the controller was set to follow this dynamic setpoint. The developed controller successfully followed the setpoint during aerobic cultivations of Saccharomyces cerevisiae, preventing the Crabtree effect by maintaining low glucose concentrations. With this new method, fed-batch cultivations of S. cerevisiae could be reliably controlled at specific growth rates between 0.075 h−1 and 0.20 h−1, with average root mean square errors of 15 ± 3%.

Growth inhibition of Neisseria gonorrhoeae isolates by L-phenylalanine and its analogues in defined media

1984 ◽  
Vol 30 (11) ◽  
pp. 1319-1325 ◽  
Author(s):  
A. T. Hendry ◽  
J. R. Dillon
Keyword(s):  
Growth Rate ◽  
Amino Acid ◽  
Neisseria Gonorrhoeae ◽  
Growth Inhibition ◽  
Growth Rates ◽  
Acid Synthesis ◽  
The Other ◽  
Amino Acid Synthesis ◽  
Defined Media ◽  
Agar Media

Growth inhibition by phenylalanine (0.25 mmol/L in defined agar media) was present in about 1% of over 1000 clinical isolates of Neisseria gonorrhoeae isolates tested. Turbidometry of several phenylalanine-sensitive isolates showed that their growth rates decreased in proportion to phenylalanine concentrations up to about 1 mmol/L. The growth rate was unaffected if 0.04 mmol/L tyrosine was also present. The phenylalanine analogue DL-3-fluorophenylalanine inhibited the growth of all 23 isolates further tested on agar. This inhibition was derepressed by phenylalanine in all 17 phenylalanine-resistant isolates. Phenylalanine plus tyrosine were required to derepress the analogue inhibition in the other six phenylalanine-sensitive isolates. Phenylalanine-sensitive isolates may have a defect in aromatic amino acid synthesis, not involving auxotrophy, but manifested through regulation of the pathways. Phenylalanine effectively repressed tyrosine and phenylalanine synthesis. In 125 isolates including 85 β-lactamase producers (PPNG) and 32 phenylalanine-sensitive isolates, phenylalanine inhibited 63.2% of 38 PPNG isolates carrying the 3.2 megadalton (Md) plasmid, but only one of 47 PPNG isolates carrying the 4.5 Md plasmid. PPNG isolates are most often of the proline, ornithine, or nonrequiring auxotypes. Phenylalanine sensitivity did not appear to be auxotype dependent.

scholarly journals Impaired Growth Rates in Milk of Lactobacillus helveticus Peptidase Mutants Can Be Overcome by Use of Amino Acid Supplements

2003 ◽  
Vol 185 (11) ◽  
pp. 3297-3306 ◽  
Author(s):  
Jeffrey E. Christensen ◽  
James L. Steele
Keyword(s):  
Growth Rate ◽  
Amino Acid ◽  
Growth Rates ◽  
Gene Replacement ◽  
Defined Medium ◽  
Lactobacillus Helveticus ◽  
Amino Acid Requirements ◽  
Dipeptidyl Aminopeptidase ◽  
Specific Growth Rates ◽  
Broad Specificity

ABSTRACT To evaluate the contribution of intracellular peptidases to the growth of the 14-amino-acid (aa) auxotroph Lactobacillus helveticus CNRZ32, single- and multiple-peptidase-deletion mutants were constructed. Two broad-specificity aminopeptidases (PepC and PepN) and X-prolyl dipeptidyl aminopeptidase (PepX) were inactivated through successive cycles of chromosomal gene replacement mutagenesis. The inactivation of all three peptidases in JLS247 (ΔpepC ΔpepN ΔpepX) did not affect the growth rate in amino acid-defined medium. However, the peptidase mutants generally had decreased specific growth rates when acquisition of amino acids required hydrolysis of the proteins in milk, the most significant result being a 73% increase in generation time for JLS247. The growth rate deficiencies in milk were overcome by amino acid supplements with some specificity to each of the peptidase mutants. For example, milk supplementation with Pro resulted in the most significant growth rate increase for ΔpepX strains and a 7-aa supplement (Asn, Cys, Ile, Pro, Ser, Thr, and Val) resulted in a JLS247 growth rate indistinguishable from that of the wild type. Our results show that characterization of the activities of the broad-specificity aminopeptidases had little predictive value regarding the amino acid supplements found to enhance the milk growth rates of the peptidase mutant strains. These results represent the first determination of the physiological roles with respect to specific amino acid requirements for peptidase mutants grown in milk.

scholarly journals Proteome allocations change linearly with specific growth rate of Saccharomyces cerevisiae under glucose-limitation

2021 ◽  
Author(s):  
Jianye Xia ◽  
Benjamin Sánchez ◽  
Yu Chen ◽  
Kate Campbell ◽  
Sergo Kasvandik ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Growth Rate ◽  
Specific Growth Rate ◽  
Growth Rates ◽  
Specific Growth ◽  
Cell Factory ◽  
Functional Protein ◽  
Wide Range ◽  
The Absolute ◽  
Specific Growth Rates

Abstract Saccharomyces cerevisiae is widely used as a cell factory and it is therefore important to understand how it organizes key functional parts when cultured under different conditions. Here we performed a multi-omics analysis of S. cerevisiae by culturing the strain under a wide range of specific growth rates using glucose as the sole limited nutrient. At these different conditions we measured the absolute transcriptome, the absolute proteome, the phosphproteome, and the metabolome. Most functional protein groups showed linear dependence on the cell specific growth rate. Proteins engaged with translation showed a perfect linear increase with the specific growth rate, while glycolysis and chaperone proteins showed a linear decrease at respiratory conditions. Glycolytic enzymes and chaperones, however, show decreased phosphorylation with increasing specific growth rates, resulting in an overall increased activity that is associated with increased flux through these pathways. Further analysis showed that proteome allocation was primarily determined at the transcriptome level. Finally, using enzyme constraint genome scale modeling we found that enzyme usage play an important role for controlling flux in amino acid biosynthesis.

Taxonomic characterization and identification of Saccharomyces cerevisiae D8 for brandy production from pineapple

2018 ◽  
Vol 39 (4) ◽  
pp. 474-482
Author(s):  
Hoang Thi Le Thuong ◽  
Nguyen Quang Hao ◽  
Tran Thi Thuy
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Low Ph ◽  
Yeast Strains ◽  
Biological Studies ◽  
Taxonomic Characterization

Eight yeast strains (denoted as D1 to D8) were isolated from samples of natural fermented pineapple. Strain D8 showed highest alcoholic production at low pH and special aroma of pineapple has been chosen for further study. Taxonomic characterization of strain D8 using morphological, biochemical and molecular biological studies confirmed that strain D8  belong to Saccharomycetaceae family, Saccharomycetales order and Saccharomyces cerevisiae species. Therefore, we named this strain as Saccharomyces cerevisiae D8 for further study on Brandy production from pineapple. Citation: Hoang Thi Le Thuong, Nguyen Quang Hao, Tran Thi Thuy, 2017. Taxonomic characterization and identification of Saccharomyces cerevisiae D8 for brandy production from pineapple. Tap chi Sinh hoc, 39(4): 474- 482. DOI: 10.15625/0866-7160/v39n4.10864.*Corresponding author: [email protected] Received 5 December 2016, accepted 12 August 2017

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