Glucose triggers different global responses in yeast, depending on the strength of the signal, and transiently stabilizes ribosomal protein mRNAs

Yin, Zhikang; Wilson, Sean B.; Hauser, Nicole; Tournu, Hélène; Hoheisel, Jörg D.; Brown, Alistair J. P.

doi:10.1046/j.1365-2958.2003.03478.x

Cited by 78 publications

(123 citation statements)

References 59 publications

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“…It is important to note that the ribosomal protein synthesis genes were downregulated in the aerial tissue at 12 hr. Transcription of ribosomal protein genes declines during carbon starvation in fungi (Klein and Struhl 1994;Yin et al 2003). This is consistent with our findings for carbon metabolism genes discussed above, suggesting that aerial hyphae of N. crassa are subject to carbon starvation.…”

Section: Resultssupporting

confidence: 90%

Temporal and Spatial Regulation of Gene Expression During Asexual Development ofNeurospora crassa

et al. 2010

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In this study we profiled spatial and temporal transcriptional changes during asexual sporulation in the filamentous fungus Neurospora crassa. Aerial tissue was separated from the mycelium to allow detection of genes specific to each tissue. We identified 2641 genes that were differentially expressed during development, which represents 25% of the predicted genes in the genome of this model fungus. On the basis of the distribution of functional annotations of 1102 of these genes, we identified gene expression patterns that define key physiological events during conidial development. Not surprisingly, genes encoding transcription factors, cell wall remodeling proteins, and proteins involved in signal transduction were differentially regulated during asexual development. Among the genes differentially expressed in aerial tissues the majority were unclassified and tended to be unique to ascomycete genomes. This finding is consistent with the view that these genes evolved for asexual development in the Pezizomycotina. Strains containing deletions of several differentially expressed genes encoding transcription factors exhibited asexual development-associated phenotypes. Gene expression patterns during asexual development suggested that cAMP signaling plays a critical role in the transition from aerial growth to proconidial chain formation. This observation prompted us to characterize a deletion of the gene encoding a highaffinity cAMP phosphodiesterase (NCU00478). NCU00478 was determined to be allelic to aconidiate-2, a previously identified genetic locus controlling conidiation.

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Section: Resultssupporting

confidence: 90%

Temporal and Spatial Regulation of Gene Expression During Asexual Development ofNeurospora crassa

et al. 2010

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“…This study revealed that RP mRNAs are among the least stable messages in the cell (20), consistent with the existence of cis-acting determinants within yeast RP mRNAs. Our data and work by others (20,27,63) strongly suggest that yeast RP mRNAs are posttranscriptionally regulated at the levels of translation and stability. We were unable to identify potential cis-acting elements that are significantly conserved among the 5Ј or 3Ј untranslated regions of S. pombe 40S RP genes by using a variety of computational analyses.…”

Section: Discussionsupporting

confidence: 78%

Autoregulation of Ribosome Biosynthesis by a Translational Response in Fission Yeast

Bachand

Lackner

Bähler

et al. 2006

Molecular and Cellular Biology

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Maintaining the appropriate balance between the small and large ribosomal subunits is critical for translation and cell growth. We previously identified the 40S ribosomal protein S2 (rpS2) as a substrate of the protein arginine methyltransferase 3 (RMT3) and reported a misregulation of the 40S/60S ratio in rmt3 deletion mutants of Schizosaccharomyces pombe. For this study, using DNA microarrays, we have investigated the genome-wide biological response of rmt3-null cells to this ribosomal subunit imbalance. Whereas little change was observed at the transcriptional level, a number of genes showed significant alterations in their polysomal-to-monosomal ratios in rmt3⌬ mutants. Importantly, nearly all of the 40S ribosomal proteinencoding mRNAs showed increased ribosome density in rmt3 disruptants. Sucrose gradient analysis also revealed that the ribosomal subunit imbalance detected in rmt3-null cells is due to a deficit in small-subunit levels and can be rescued by rpS2 overexpression. Our results indicate that rmt3-null fission yeast compensate for the reduced levels of small ribosomal subunits by increasing the ribosome density, and likely the translation efficiency, of 40S ribosomal protein-encoding mRNAs. Our findings support the existence of autoregulatory mechanisms that control ribosome biosynthesis and translation as an important layer of gene regulation.The posttranslational modification of proteins is one way that cells extend the chemical diversity of polypeptides beyond the constraints of the encoded amino acids. Protein methylation has emerged as a covalent modification important for the regulation of cell growth and differentiation. Protein arginine methyltransferases (PRMT) use S-adenosylmethionine as a methyl donor to catalytically modify proteins by the addition of monomethyl groups onto the guanido nitrogen atom of the arginine side chain (5). PRMTs are divided into two classes depending on the type of dimethylarginine they generate (asymmetric [type I] or symmetric [type II]) (5). Cellular proteins harboring asymmetric and/or symmetric dimethylarginines have been identified through a variety of genetic and biochemical approaches (9,21,38). Many of the proteins modified by arginine methylation are involved in binding nucleic acids (17). Interestingly, a proteomic survey of Golgi-associated proteins identified several arginine-methylated polypeptides (61), suggesting a broad spectrum of cellular functions for substrates of arginine methylation.PRMTs are specific to eukaryotes and are evolutionarily conserved. This protein family presently includes eight vertebrate members, several of which show strong homology to gene products from other eukaryotic species, such as yeast, flies, and worms (8). Although the biological roles of PRMTs remain unclear, they have been associated with a variety of cellular functions, such as transcriptional response (12, 28), mRNA biogenesis and export (48, 65), DNA repair (10), and ribosome biosynthesis (4). The importance of PRMTs during the development of multicellular ...

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“…For these conditions, M. vaginatus has a conservative metabolism, accumulating much more biopolymer in a day than is necessary for the following night. We can speculate that biopolymer reserves may be accumulated such that sufficient quantities may drive physiological responses such as cell division, making it akin to the yeast metabolic cycling observed for low glucose conditions (Yin et al, 2003). Since this photoautotroph is limited by nutrients other than carbon, they are likely routing flux from intracellular biopolymers into EPS formation, consistent with our earlier results showing export of a 205 diversity of oligosaccharides (Baran et al, 2013).…”

Section: Experimentally Determined Fluxes During Photosynthesis and Rsupporting

confidence: 81%

Flux balance modelling to predict bacterial survival during pulsed activity events

Jose¹,

Lau²,

Swenson³

et al. 2017

Preprint

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10Desert biological soil crusts (BSCs) are cyanobacteria-dominated, surface soil microbial communities common to plant interspaces in arid environments. The capability to significantly dampen their metabolism allows them to exist for extended periods in a desiccated dormant state that is highly robust to environmental stresses. However, within minutes of wetting, metabolic functions reboot, maximizing activity during infrequent permissive periods. Microcoleus vaginatus, a primary producer within the crust ecosystem and an early colonizer, initiates crust formation by binding particles in the upper layer of 15 soil via exopolysaccharides, making microbial dominated biological soil crusts highly dependent on the viability of this organism. Previous studies have suggested that biopolymers play a central role in the survival of this organism by powering resuscitation, rapidly forming compatible solutes and fuelling metabolic activity in dark, hydrated conditions. To elucidate the mechanism of this phenomenon and provide a basis for future modelling of BSCs, we developed a manually-curated, genome-scale metabolic model of Microcoleus vaginatus (iNJ1153). To validate this model, GC/MS and LC/MS were used 20to characterize the rate of biopolymer accumulation and depletion in in hydrated Microcoleus vaginatus under light and dark conditions. Constraint-based flux balance analysis showed agreement between model predictions and experimental reaction fluxes. A significant amount of consumed carbon and light energy is invested into storage molecules glycogen and polyphosphate, while β-polyhydroxybutyrate may function as a secondary resource. Pseudo-steady state modelling suggests that glycogen, the primary carbon source with the fastest depletion rate, will be exhausted if M. vaginatus experiences dark 25 wetting events four times longer than light wetting events.

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Glucose triggers different global responses in yeast, depending on the strength of the signal, and transiently stabilizes ribosomal protein mRNAs

Cited by 78 publications

References 59 publications

Temporal and Spatial Regulation of Gene Expression During Asexual Development ofNeurospora crassa

Temporal and Spatial Regulation of Gene Expression During Asexual Development ofNeurospora crassa

Autoregulation of Ribosome Biosynthesis by a Translational Response in Fission Yeast

Flux balance modelling to predict bacterial survival during pulsed activity events

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