LauraTerada Individual Journal Assignment Week 11

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Acclimation of Saccharomyces cerevisiae to Low Temperature: A Chemostat-Based Transcriptome Analysis

Term Definitions

  1. Trehalose: "a crystalline disaccharide C12H22O11 that is found in various organisms (as fungi and insects)" [[1]]
  2. Desaturase: "Any of several enzymes that putdouble bonds into the hydrocarbon areasof fatty acids." [[2]]
  3. Biogenesis: "The process in which life forms arise from similar life forms." [[3]]
  4. Mannoprotein: "yeast cell wall components that are proteins with large numbers of mannose groups attached; highly antigenic." [[4]]
  5. Transcriptome: "Transcriptome is the complement of mature messenger RNAs produced in a given cell in a given moment of its life." [[5]]
  6. Prototrophic: "Strain's that have the same nutritional requirements as the wild-type strain." [[6]]
  7. Interference: "opposition or hampering of an action or procedure." [[7]]
  8. Motif: "The smallest group of atoms in a polymer that, when under the influence of a rotation-translation operator, will assemble the rest of the atoms in the chain." [[8]]
  9. Assay: "The determination of the amount of a particular constituent of a mixture or of the biological or pharmacological potency of a drug." [[9]]
  10. Catabolite: "product of catabolism, the breakdown of complex molecules into simpler ones." [[10]]

Outline

  • Transcriptional responses to low temperatures were analyzed in this study
    • Adaptation is the stress-response to a rapid phenomena, while acclimation is the physiological response from a long-term phenomena
    • This study focuses on acclimation
    • There are known genes that have been seen in cold-shock studies (e.g. trehalose-synthesis genes, cell-wall mannoproteins, fatty-acid desaturase, ribosome biogenesis, etc.)
    • Chemostat cultures are better than batch cultures because it allows a controlled environment independent of other culture conditions
    • This study is significant because it shows a difference between chemostat-based and literature data in regards to low-temperature acclimation over long-term and short-term scales
    • Goal is to study stead-state, acclimatized growth of the yeast at cold temperatures through transcriptional regulation data
  • Steady-state chemostat conditions
    • Yeast strain used: haploid, S. cerevisiae strain CEN.PK113-7D (MATa)
    • Dilution rate fixed at 0.03 1/h
    • Chemostat at both 12C and 30C with a 1.0 L volume and pH of 5.0
    • Growth medium was limited by either carbon or nitrogen with all other factors controlled in excess
    • Trehalose (triplicate) and glycogen (duplicate) measurements were performed; trehalose n=3, glycogen n=2 under 4 growth conditions
    • Three independently cultured replicates for the 4 growth conditions
    • 4 growth conditions: glucose limiting 12C, glucose limiting 30C, ammonium limiting 12C, ammonium limiting 30C
  • Used microarray analysis, promoter analysis, and statistical assessment
    • Microarrays were performed for RNA quality and used microsoft Excel for significance analysis
    • Promoter analysis was used by a web-based software
    • Statistical assessment was performed for overrepresentation of transcription-factor binding sites
    • Used Fisher's exact text, with a Bonferroni correction and a p value threshold of 0.01
    • The datasets generated were compared with other datasets from previous studies
  • Growth efficiency was not affected by varying growth temperatures (Table 1)
    • Proven by similar biomass and fermentation yields at 12C and 30C in carbon and nitrogen limiting chemostats
  • In glucose limitation, 494 genes changed transcription levels between the two temperatures, while 806 genes did the same but in nitrogen limitation (Fig 1)
    • 16% of the yeast genes was temperature-responsive
  • The temperature-responsive genes were screened for functional categories (Fig 2)
  • Low temperatures result in changed kinetics for the limiting nutrient and enhanced catabolite repression
    • 12C, residual concentrations of growth-limiting nutrients were higher than at 30C
    • Changes in transport kinetics from changes in transcript levels of genes involved in growth-limiting nutrient uptake (Fig 2)
    • Ex: HXT2 and HXT3 hexose-transport genes increased transcription at 13C compared to 30C
    • Residual concentrations of the limiting nutrient is low to prevent catabolite repression
  • The induction of trelahose and glycogen formation genes are not needed for yeast acclimation to low temperatures
    • At 12C, trelahose and glycogen metabolism genes were not upregulated
    • In glucose limitation, gene transcription did not change, and im ammonia limitation it slightly decreased
  • When adapted to low temperatures, the yeast cells recede the up-regulation of storage carbohydrate synthesis (Table 3)
  • 16 genes in ribosome biogenesis in both conditions and 80 genes in protein synthesis in ammonia limited conditions showed higher transcription levels at 13C
    • Increased protein content compensates for impaired enzyme kinetics at 13C
  • In comparison to other studies, gene regulation differs
    • When comparing to 3 other studies, 259 (low-adaptation) genes also responded to decreasing temperature, but the responses were not consistent (Fig 3)
    • 29 of these genes were transcriptionally regulated at adaptation and acclimation to low temperature (Fig 4)
    • Only 4 of these showed consistent regulation patterns
  • Environmental stress response is not a response to low temperatures, but it is a response due to adaptation from rapid exposure to low temperatures
  • Conclusion
    • Growth-limiting nutrients were higher at 12C shown by gene expression for nutrient transporters
    • Transcription of environmental stress response genes decreased at 12C
    • Trehalose is not involved in steady-state low temperature adaptation
    • Acclimation does not only rely on transcriptional reprogramming, but on changing intracellular metabolite levels as well
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