Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcriptome analysis of Beijerinckiaceae bacterium RH AL1 grown with pyruvate as the carbon source in response to lanthanum supplementation

ABSTRACT: The increased fitness when grown with pyruvate as carbon source in response to lanthanum supplementation was used as starting point to study genes induced in Beijerinckiaceae bacterium RH AL1 upon exposure to lanthanum.

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): Beijerinckiaceae bacterium RH AL1

SUBMITTER: Carl-Eric Wegner

PROVIDER: E-MTAB-9481 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Cultivation methods used to investigate microbial calorie restriction often result in carbon and energy starvation. This study aims to dissect cellular responses to calorie restriction and starvation in Saccharomyces cerevisiae by using retentostat cultivation. In retentostats, cells are continuously supplied with a small, constant carbon and energy supply, sufficient for maintenance of cellular viability and integrity but insufficient for growth. When glucose-limited retentostats cultivated under extreme calorie restriction were subjected to glucose starvation, calorie-restricted and glucose-starved cells were found to share characteristics such as increased heat-shock tolerance and expression of quiescence-related genes. However, they also displayed strikingly different features. While calorie-restricted yeast cultures remained metabolically active and viable for prolonged periods of time, glucose starvation resulted in rapid consumption of reserve carbohydrates, population heterogeneity due to appearance of senescent cells and, ultimately, loss of viability. Moreover, during starvation, calculated rates of ATP synthesis from storage carbohydrates were 2-3 orders of magnitude lower than steady-state ATP-turnover rates calculated under extreme calorie restriction in retentostats. Stringent reduction of ATP turnover during glucose starvation was accompanied by a strong down-regulation of genes involved in protein synthesis. These results demonstrate that extreme calorie restriction and carbon starvation represent different physiological states in S. cerevisiae. The yeast was first grown for 14 days under extreme calorie restriction in anaerobic, glucose-limited retentostats (Boender et al., 2009, Appl.Environ.Microbiol., 75: 5607-5614.). Subsequently, starvation was started by terminating the glucose feed. Yeast transcriptional reprogramming in response to calorie restriction and starvation was monitored by microarray analysis. Independent duplicate retentostat cultures, and subsequently starvation, were sampled for transcriptome analysis using Affymetrix microarrays. One time-point was sampled during calorie restriction (T0) and four time points were sampled during the starvation phase 10, 30, 60 and 120 minutes after switching of the feed, resulting in a dataset of 10 arrays.

Dataset Information

Transcriptome analysis of Beijerinckiaceae bacterium RH AL1 grown with pyruvate as the carbon source in response to lanthanum supplementation

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