scholarly journals Analysis of Gene Expression in Escherichia coli in Response to Changes of Growth-Limiting Nutrient in Chemostat Cultures

2004 ◽  
Vol 70 (4) ◽  
pp. 2354-2366 ◽  
Author(s):  
Qiang Hua ◽  
Chen Yang ◽  
Taku Oshima ◽  
Hirotada Mori ◽  
Kazuyuki Shimizu
Keyword(s):  
Gene Expression ◽  
Escherichia Coli ◽  
Growth Rate ◽  
Steady State ◽  
Specific Growth ◽  
Differentially Expressed ◽  
Transcriptional Responses ◽  
Chemostat Cultures ◽  
Limiting Nutrient ◽  
Slow Growing

ABSTRACT Studies of steady-state metabolic fluxes in Escherichia coli grown in nutrient-limited chemostat cultures suggest remarkable flux alterations in response to changes of growth-limiting nutrient in the medium (Hua et al., J. Bacteriol. 185:7053-7067, 2003). To elucidate the physiological adaptation of cells to the nutrient condition through the flux change and understand the molecular mechanisms underlying the change in the flux, information on gene expression is of great importance. DNA microarray analysis was performed to investigate the global transcriptional responses of steady-state cells grown in chemostat cultures with limited glucose or ammonia while other environmental conditions and the growth rate were kept constant. In slow-growing cells (specific growth rate of 0.10 h−1), 9.8% of a total of 4,071 genes investigated, especially those involved in amino acid metabolism, central carbon and energy metabolism, transport system and cell envelope, were observed to be differentially expressed between the two nutrient-limited cultures. One important characteristic of E. coli grown under nutrient limitation was its capacity to scavenge carbon or nitrogen from the medium through elevating the expression of the corresponding transport and assimilation genes. The number of differentially expressed genes in faster-growing cells (specific growth rate of 0.55 h−1), however, decreased to below half of that in slow-growing cells, which could be explained by diverse transcriptional responses to the growth rate under different nutrient limitations. Independent of the growth rate, 92 genes were identified as being differentially expressed. Genes tightly related to the culture conditions were highlighted, some of which may be used to characterize nutrient-limited growth.

scholarly journals Homeostatic Adjustment and Metabolic Remodeling in Glucose-limited Yeast Cultures

2005 ◽  
Vol 16 (5) ◽  
pp. 2503-2517 ◽  
Author(s):  
Matthew J. Brauer ◽  
Alok J. Saldanha ◽  
Kara Dolinski ◽  
David Botstein
Keyword(s):  
Gene Expression ◽  
Growth Rate ◽  
Steady State ◽  
Stress Response ◽  
The State ◽  
Second Phase ◽  
Diauxic Shift ◽  
Batch Cultures ◽  
Chemostat Cultures ◽  
Metabolic Remodeling

We studied the physiological response to glucose limitation in batch and steady-state (chemostat) cultures of Saccharomyces cerevisiae by following global patterns of gene expression. Glucose-limited batch cultures of yeast go through two sequential exponential growth phases, beginning with a largely fermentative phase, followed by an essentially completely aerobic use of residual glucose and evolved ethanol. Judging from the patterns of gene expression, the state of the cells growing at steady state in glucose-limited chemostats corresponds most closely with the state of cells in batch cultures just before they undergo this “diauxic shift.” Essentially the same pattern was found between chemostats having a fivefold difference in steady-state growth rate (the lower rate approximating that of the second phase respiratory growth rate in batch cultures). Although in both cases the cells in the chemostat consumed most of the glucose, in neither case did they seem to be metabolizing it primarily through respiration. Although there was some indication of a modest oxidative stress response, the chemostat cultures did not exhibit the massive environmental stress response associated with starvation that also is observed, at least in part, during the diauxic shift in batch cultures. We conclude that despite the theoretical possibility of a switch to fully aerobic metabolism of glucose in the chemostat under conditions of glucose scarcity, homeostatic mechanisms are able to carry out metabolic adjustment as if fermentation of the glucose is the preferred option until the glucose is entirely depleted. These results suggest that some aspect of actual starvation, possibly a component of the stress response, may be required for triggering the metabolic remodeling associated with the diauxic shift.

scholarly journals Nutritional Homeostasis in Batch and Steady-State Culture of Yeast

2004 ◽  
Vol 15 (9) ◽  
pp. 4089-4104 ◽  
Author(s):  
Alok J. Saldanha ◽  
Matthew J. Brauer ◽  
David Botstein
Keyword(s):  
Gene Expression ◽  
Cell Cycle ◽  
Steady State ◽  
Stress Response ◽  
Stress Responses ◽  
Global Pattern ◽  
Batch Cultures ◽  
Cycle Arrest ◽  
Chemostat Cultures ◽  
Limiting Nutrient

We studied the physiological response to limitation by diverse nutrients in batch and steady-state (chemostat) cultures of S. cerevisiae. We found that the global pattern of transcription in steady-state cultures in limiting phosphate or sulfate is essentially identical to that of batch cultures growing in the same medium just before the limiting nutrient is completely exhausted. The massive stress response and complete arrest of the cell cycle that occurs when nutrients are fully exhausted in batch cultures is not observed in the chemostat, indicating that the cells in the chemostat are “poor, not starving.” Similar comparisons using leucine or uracil auxotrophs limited on leucine or uracil again showed patterns of gene expression in steady-state closely resembling those of corresponding batch cultures just before they exhaust the nutrient. Although there is also a strong stress response in the auxotrophic batch cultures, cell cycle arrest, if it occurs at all, is much less uniform. Many of the differences among the patterns of gene expression between the four nutrient limitations are interpretable in light of known involvement of the genes in stress responses or in the regulation or execution of particular metabolic pathways appropriate to the limiting nutrient. We conclude that cells adjust their growth rate to nutrient availability and maintain homeostasis in the same way in batch and steady state conditions; cells in steady-state cultures are in a physiological condition normally encountered in batch cultures.

Growth kinetics of Escherichia coli with galactose and several other sugars in carbon-limited chemostat culture

1999 ◽  
Vol 46 (1) ◽  
pp. 72-80 ◽  
Author(s):  
Urs Lendenmann ◽  
Mario Snozzi ◽  
Thomas Egli
Keyword(s):  
Escherichia Coli ◽  
Growth Rate ◽  
Steady State ◽  
Specific Growth Rate ◽  
Growth Kinetics ◽  
Specific Growth ◽  
Chemostat Culture ◽  
Monod Model ◽  
E Coli ◽  
Kinetics Of

Kinetic models for microbial growth describe the specific growth rate (μ) as a function of the concentration of the growth-limiting nutrient (s) and a set of parameters. A typical example is the model proposed by Monod, where μ is related to s using substrate affinity (Ks) and the maximum specific growth rate (μmax). The preferred method to determine such parameters is to grow microorganisms in continuous culture and to measure the concentration of the growth-limiting substrate as a function of the dilution rate. However, owing to the lack of analytical methods to quantify sugars in the microgram per litre range, it has not been possible to investigate the growth kinetics of Escherichia coli in chemostat culture. Using an HPLC method able to determine steady-state concentrations of reducing sugars, we previously have shown that the Monod model adequately describes glucose-limited growth of E. coli ML30. This has not been confirmed for any other sugar. Therefore, we carried out a similar study with galactose and found steady-state concentrations between 18 and 840 μg·L-1 for dilution rates between 0.2 and 0.8·h-1, respectively. With these data the parameters of several models giving the specific growth rate as a function of the substrate concentration were estimated by nonlinear parameter estimation, and subsequently, the models were evaluated statistically. From all equations tested, the Monod model described the data best. The parameters for galactose utilisation were μmax = 0.75·h-1 and Ks = 67 μg·L-1. The results indicated that accurate Ks values can be estimated from a limited set of steady-state data when employing μmax measured during balanced growth in batch culture. This simplified procedure was applied for maltose, ribose, and fructose. For growth of E. coli with these sugars, μmax and Ks were for maltose 0.87·h-1, 100 μg·L-1; for ribose 0.57·h-1, 132 μg·L-1, and for fructose 0.70·h-1, 125 μg·L-1. Key words: monod model, continuous culture, galactose, glucose, fructose, maltose, ribose.

scholarly journals Identity of the Growth-Limiting Nutrient Strongly Affects Storage Carbohydrate Accumulation in Anaerobic Chemostat Cultures of Saccharomyces cerevisiae

2009 ◽  
Vol 75 (21) ◽  
pp. 6876-6885 ◽  
Author(s):  
Lucie A. Hazelwood ◽  
Michael C. Walsh ◽  
Marijke A. H. Luttik ◽  
Pascale Daran-Lapujade ◽  
Jack T. Pronk ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Growth Rate ◽  
Glycogen Phosphorylase ◽  
Specific Growth ◽  
Glycogen Synthase ◽  
The Other ◽  
Carbohydrate Accumulation ◽  
Storage Carbohydrate ◽  
Chemostat Cultures ◽  
Limiting Nutrient

ABSTRACT Accumulation of glycogen and trehalose in nutrient-limited cultures of Saccharomyces cerevisiae is negatively correlated with the specific growth rate. Additionally, glucose-excess conditions (i.e., growth limitation by nutrients other than glucose) are often implicated in high-level accumulation of these storage carbohydrates. The present study investigates how the identity of the growth-limiting nutrient affects accumulation of storage carbohydrates in cultures grown at a fixed specific growth rate. In anaerobic chemostat cultures (dilution rate, 0.10 h−1) of S. cerevisiae, the identity of the growth-limiting nutrient (glucose, ammonia, sulfate, phosphate, or zinc) strongly affected storage carbohydrate accumulation. The glycogen contents of the biomass from glucose- and ammonia-limited cultures were 10- to 14-fold higher than those of the biomass from cultures grown under the other three glucose-excess regimens. Trehalose levels were specifically higher under nitrogen-limited conditions. These results demonstrate that storage carbohydrate accumulation in nutrient-limited cultures of S. cerevisiae is not a generic response to excess glucose but instead is strongly dependent on the identity of the growth-limiting nutrient. While transcriptome analysis of wild-type and msn2Δ msn4Δ strains confirmed that transcriptional upregulation of glycogen and trehalose biosynthesis genes is mediated by Msn2p/Msn4p, transcriptional regulation could not quantitatively account for the drastic changes in storage carbohydrate accumulation. The results of assays of glycogen synthase and glycogen phosphorylase activities supported involvement of posttranscriptional regulation. Consistent with the high glycogen levels in ammonia-limited cultures, the ratio of glycogen synthase to glycogen phosphorylase in these cultures was up to eightfold higher than the ratio in the other glucose-excess cultures.

scholarly journals Specific Growth Rate Determines the Sensitivity of Escherichia coli to Thermal, UVA, and Solar Disinfection

2006 ◽  
Vol 72 (4) ◽  
pp. 2586-2593 ◽  
Author(s):  
Michael Berney ◽  
Hans-Ulrich Weilenmann ◽  
Julian Ihssen ◽  
Claudio Bassin ◽  
Thomas Egli
Keyword(s):  
Escherichia Coli ◽  
Growth Rate ◽  
Specific Growth Rate ◽  
Growth Rates ◽  
Specific Growth ◽  
E Coli ◽  
Mild Heat ◽  
Uva Light ◽  
Specific Growth Rates ◽  
Slow Growing

ABSTRACT Knowledge about the sensitivity of the test organism is essential for the evaluation of any disinfection method. In this work we show that sensitivity of Escherichia coli MG1655 to three physical stresses (mild heat, UVA light, and sunlight) that are relevant in the disinfection of drinking water with solar radiation is determined by the specific growth rate of the culture. Batch- and chemostat-cultivated cells from cultures with similar specific growth rates showed similar stress sensitivities. Generally, fast-growing cells were more sensitive to the stresses than slow-growing cells. For example, slow-growing chemostat-cultivated cells (D = 0.08 h−1) and stationary-phase bacteria from batch culture that were exposed to mild heat had very similar T 90 (time until 90% of the population is inactivated) values (T 90, chemostat = 2.66 h; T 90, batch = 2.62 h), whereas T 90 for cells growing at a μ of 0.9 h−1 was 0.2 h. We present evidence that the stress sensitivity of E. coli is correlated with the intracellular level of the alternative sigma factor RpoS. This is also supported by the fact that E. coli rpoS mutant cells were more stress sensitive than the parent strain by factors of 4.9 (mild heat), 5.3 (UVA light), and 4.1 (sunlight). Furthermore, modeling of inactivation curves with GInaFiT revealed that the shape of inactivation curves changed depending on the specific growth rate. Inactivation curves of cells from fast-growing cultures (μ = 1.0 h−1) that were irradiated with UVA light showed a tailing effect, while for slow-growing cultures (μ = 0.3 h−1), inactivation curves with shoulders were obtained. Our findings emphasize the need for accurate reporting of specific growth rates and detailed culture conditions in disinfection studies to allow comparison of data from different studies and laboratories and sound interpretation of the data obtained.

scholarly journals Transcriptional profiling of the murine airway response to acute ozone exposure

2019 ◽  
Author(s):  
Adelaide Tovar ◽  
Gregory J. Smith ◽  
Joseph M. Thomas ◽  
Jack R. Harkema ◽  
Samir N. P. Kelada
Keyword(s):  
Gene Expression ◽  
Airway Inflammation ◽  
Cellular Proliferation ◽  
Expression Patterns ◽  
Differentially Expressed ◽  
Ozone Exposure ◽  
Matrix Remodeling ◽  
Transcriptional Responses ◽  
Morphological Alterations ◽  
Cell Counts

AbstractExposure to ambient ozone (O3) pollution causes airway inflammation, epithelial injury, and decreased lung function. Long-term exposure is associated with increased mortality and exacerbations of respiratory conditions. While the adverse health effects of O3 exposure have been thoroughly described, less is known about the molecular processes that drive these outcomes. The aim of this study was to describe the cellular and molecular alterations observed in murine airways after exposure to either 1 or 2 ppm O3. After exposing adult, female C57BL/6J mice to filtered air, 1 or 2 ppm O3 for 3 hours, we assessed hallmark responses including airway inflammatory cell counts, epithelial permeability, cytokine secretion, and morphological alterations of the large airways. Further, we performed RNA-seq to profile gene expression in two critical tissues involved in O3 responses: conducting airways (CA) and airway macrophages (AM). We observed a concentration-dependent increase in airway inflammation and injury, and a large number of genes were differentially expressed in both target tissues at both concentrations of O3. Genes that were differentially expressed in CA were generally associated with barrier function, detoxification processes, and cellular proliferation. The differentially expressed genes in AM were associated with innate immune signaling, cytokine production, and extracellular matrix remodeling. Overall, our study has described transcriptional responses to acute O3 exposure, revealing both shared and unique gene expression patterns across multiple concentrations of O3 and in two important O3-responsive tissues. These profiles provide broad mechanistic insight into pulmonary O3 toxicity, and reveal a variety of targets for refined follow-up studies.

scholarly journals Differential Gene Expression of Three Mastitis-Causing Escherichia coli Strains Grown under Planktonic, Swimming, and Swarming Culture Conditions

mSystems ◽  
2016 ◽  
Vol 1 (4) ◽  
Author(s):  
John D. Lippolis ◽  
Brian W. Brunelle ◽  
Timothy A. Reinhardt ◽  
Randy E. Sacco ◽  
Tyler C. Thacker ◽  
...  
Keyword(s):  
Gene Expression ◽  
Escherichia Coli ◽  
Bacterial Motility ◽  
Differentially Expressed ◽  
Iron Regulation ◽  
Content Type ◽  
E Coli ◽  
Different Types ◽  
Compare Gene Expression ◽  
Gene Expression Levels

ABSTRACT Bacteria can exhibit various types of motility. It is known that different types of motilities can be associated with virulence. In this work, we compare gene expression levels in bacteria that were grown under conditions that promoted three different types of E. coli motility. Better understanding of the mechanisms of how bacteria can cause an infection is an important first step to better diagnostics and therapeutics. Bacterial motility is thought to play an important role in virulence. We have previously shown that proficient bacterial swimming and swarming in vitro is correlated with the persistent intramammary infection phenotype observed in cattle. However, little is known about the gene regulation differences important for different motility phenotypes in Escherichia coli. In this work, three E. coli strains that cause persistent bovine mastitis infections were grown in three media that promote different types of motility (planktonic, swimming, and swarming). Using whole-transcriptome RNA sequencing, we identified a total of 935 genes (~21% of the total genome) that were differentially expressed in comparisons of the various motility-promoting conditions. We found that approximately 7% of the differentially expressed genes were associated with iron regulation. We show that motility assays using iron or iron chelators confirmed the importance of iron regulation to the observed motility phenotypes. Because of the observation that E. coli strains that cause persistent infections are more motile, we contend that better understanding of the genes that are differentially expressed due to the type of motility will yield important information about how bacteria can become established within a host. Elucidating the mechanisms that regulate bacterial motility may provide new approaches in the development of intervention strategies as well as facilitate the discovery of novel diagnostics and therapeutics. IMPORTANCE Bacteria can exhibit various types of motility. It is known that different types of motilities can be associated with virulence. In this work, we compare gene expression levels in bacteria that were grown under conditions that promoted three different types of E. coli motility. Better understanding of the mechanisms of how bacteria can cause an infection is an important first step to better diagnostics and therapeutics.

Effect of specific growth rate on the production of a recombinant nuclease by Escherichia coli

2003 ◽  
Vol 14 (2) ◽  
pp. 101-107 ◽  
Author(s):  
Li-Chun Cheng ◽  
Lien-I Hor ◽  
Jau-Yann Wu ◽  
Teh-Liang Chen
Keyword(s):  
Escherichia Coli ◽  
Growth Rate ◽  
Specific Growth Rate ◽  
Specific Growth

Influence of specific growth rate over the secretory expression of recombinant potato carboxypeptidase inhibitor in fed-batch cultures of Escherichia coli

2010 ◽  
Vol 45 (8) ◽  
pp. 1334-1341 ◽  
Author(s):  
Juan-Miguel Puertas ◽  
Jordi Ruiz ◽  
Mónica Rodríguez de la Vega ◽  
Julia Lorenzo ◽  
Glòria Caminal ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Growth Rate ◽  
Specific Growth Rate ◽  
Specific Growth ◽  
Fed Batch ◽  
Secretory Expression ◽  
Batch Cultures ◽  
Carboxypeptidase Inhibitor

Sebatian Metoksiaromatik Sebagai Substrat Pertumbuhan dan Pengaruh Enzim Demetilase dalam Acetobacterium Woodii DSM 1030

2012 ◽  
Author(s):  
Mohd. Sahaid Hj. Kalil ◽  
Muhammad Zaki ◽  
Wan Mohtar Wan Yusoff ◽  
Mohammad Ramlan Mohd. Salleh
Keyword(s):  
Growth Rate ◽  
Steady State ◽  
Sole Carbon Source ◽  
Specific Growth ◽  
Chemostat Culture ◽  
Carbon Sources ◽  
Syringic Acid ◽  
Organic Substrate ◽  
Acetobacterium Woodii ◽  
Vanilic Acid

Penyelidikan ini bertujuan untuk menyaring substrat organik bagi untuk penghasilan sel–sel A. woodii teraruh demetilase. Pertumbuhan A. woodii dilakukan dalam medium “Balch” yang mengandungi sumber karbon berbeza dalam keadaan anaerobik. Sebanyak sebelas substrat telah diuji iaitu anisol, 2– dan 3–metoksifenol, asid vanilik, asid siringik, asid 2,3,4–, 2,4,5– dan 3,4,5–trimetoksi benzoik, 2,3,4–, 2,4,5– dan 3,4,5–trimetoksi benzil alkohol. 2–metoksifenol merupakan substrat terbaik untuk pertumbuhan A. woodii pada kadar pertumbuhan spesifik 0.14 j–1. Penghasilan sel–sel teraruh demetilase dilakukan dalam kultur kemostat pada kadar pencairan (D) 0.0j–1. Sel-sel pada keadaan mantap dituai dalam keadaan anaerobik dan dipekatkan sebelum digunakan. Pertumbuhan A. woodii didapati maksimum dengan menggunakan kepekatan 0.62 g/L 2–metoksifenol sebagai sumber karbon tunggal. Tindak balas penyahmetilan oleh sel–sel A. woodii meningkat sebanyak 78% apabila 2–metoksifenol sebanyak 0.31 g/L ditambah dalam medium yang mengandungi fruktosa (1% w/v) semasa kultur kemostat. Kata kunci: tindak balas penyahmetilan; demetilase; sel-sel tertuai; metosiaromatik, Acetobacteriumwoodii The objective of this project was to screen organic substrate suitable for the growth of A. woodii, and as for the production of demethylase. A. woodii was grown in “Balch” medium containing different carbon sources. Eleven substrates were tested including anisole, 2– and 3–methoxyphenol, vanilic acid, syringic acid, 2,3,4–, 2,4,5– and 3,4,5–trimethoxy benzoic acid and 2,3,4–, 2,4,5– and 3,4,5–trimethoxy benzyl alcohol. It was found that 2–methoxyphenol was the best substrate with a specific growth rate of 0.14 h–1. The production of demethylase induced cells was carried out in a chemostat culture at a dilution rate (D) of 0.08 h–1. Cells were harvested at steady state of growth and concentrated before use. Optimal concentration of 2–methoxvphenol as the sole carbon source was 0.62 g/L. Demethylation reaction of 0.31 g/L 2–methoxyphenol by induced culture increases 78% relative to the chemostat culture containing only fructose. Key words: Demethylation reaction; demethylase; harvested cells; methoxyaromatic; Acetobacteriumwoodii

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