Transcriptional regulation in the yeast
            <i>GAL</i>
            gene family: a complex genetic network

Lohr, D.; Venkov, Pencho; Zlatanova, Jordanka

doi:10.1096/fasebj.9.9.7601342

Cited by 399 publications

(438 citation statements)

References 58 publications

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“…GAL4, a third regulator, was not found to be up-regulated. These results are in close agreement with previous reports (Johnston 1987;Lohr et al 1995). Among the most up-regulated genes in S. cerevisiae grown YPD medium were two genes coding for high affinity glucose transporters, HXT4 and HXT2, whose expression increased 34.3-and 21.6-fold, respectively, and two NAD-dependent formate dehydrogenase genes, FDH2…”

Section: Benchmarkingfermentationssupporting

confidence: 93%

“…The core genes that allow S. cerevisiae to utilize galactose as the carbon source include GAL2, which encodes a permease for galactose transport into the cell, and GAL 1, GAL 7, GAL 10 and GALS, the structural genes for galactokinase, uridylyltransferase, epimerase and phosphoglucomutase, respectively. The transcriptional regulation of the GAL operon is not fully understood, but three of the main regulators are encoded by GAL3, GAL80 and GAL4 (Johnston, 1987;Lohr et al, 1995;Ideker et al, 2001). Comparative gene expression analysis studies of S. cerevisiae in large scales have been published (Ideker et al, 2001;Hittinger et al, 2004) and are used here as benchmarks.…”

Section: Department Of Biology Mit) We Use the Analysis Of Global Gmentioning

confidence: 99%

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Microbioreactors for Bioprocess Development

Zhang

Perozziello

Boccazzi

et al. 2007

JALA: Journal of the Association for Laboratory Automation

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As a step toward high-throughput bioprocess development, we present design, fabrication, and characterization of polymer based microbioreactors integrated with automated sensors and actuators. The devices are realized, in increasing levels of complexity, in poly(dimethylsiloxane) and poly(methyl methacrylate) by micromachining and multilayer thermal compression bonding procedures. Online optical measurements for optical density, pH, and dissolved oxygen are integrated. Active mixing is made possible by a miniature magnetic stir bar. Plug-in-and-flow microfluidic connectors and fabricated polymer micro-optical lenses/connectors are integrated in the microbioreactors for fast set up and easy operation. Application examples demonstrate the feasibility of culturing microbial cells, specifically Escherichia coli, in 150 μL-volume bioreactors in batch, continuous, and fed-batch operations. (JALA 2007;12:143–51)

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Section: Benchmarkingfermentationssupporting

confidence: 93%

Section: Department Of Biology Mit) We Use the Analysis Of Global Gmentioning

confidence: 99%

Microbioreactors for Bioprocess Development

Zhang

Perozziello

Boccazzi

et al. 2007

JALA: Journal of the Association for Laboratory Automation

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“…3A). Once the galactose is replaced with glucose, transcription is immediately repressed (20,30); the mRNA derived both from GAL1-RPL30 ( Fig. 2) and from the GAL1 and GAL10 genes themselves declines rapidly (Fig.…”

Section: Resultsmentioning

confidence: 99%

Transcriptional Elements Involved in the Repression of Ribosomal Protein Synthesis

Nierras

Warner

1999

Molecular and Cellular Biology

103

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The ribosomal proteins (RPs) of Saccharomyces cerevisiae are encoded by 137 genes that are among the most transcriptionally active in the genome. These genes are coordinately regulated: a shift up in temperature leads to a rapid, but temporary, decline in RP mRNA levels. A defect in any part of the secretory pathway leads to greatly reduced ribosome synthesis, including the rapid loss of RP mRNA. Here we demonstrate that the loss of RP mRNA is due to the rapid transcriptional silencing of the RP genes, coupled to the naturally short lifetime of their transcripts. The data suggest further that a global inhibition of polymerase II transcription leads to overestimates of the stability of individual mRNAs. The transcription of most RP genes is activated by two Rap1p binding sites, 250 to 400 bp upstream from the initiation of transcription. Rap1p is both an activator and a silencer of transcription. The swapping of promoters between RPL30 and ACT1 or GAL1 demonstrated that the Rap1p binding sites of RPL30 are sufficient to silence the transcription of ACT1 in response to a defect in the secretory pathway. Sir3p and Sir4p, implicated in the Rap1p-mediated repression of silent mating type genes and of telomere-proximal genes, do not influence such silencing of RP genes. Sir2p, implicated in the silencing both of the silent mating type genes and of genes within the ribosomal DNA locus, does not influence the repression of either RP or rRNA genes. Surprisingly, the 180-bp sequence of RPL30 that lies between the Rap1p sites and the transcription initiation site is also sufficient to silence the Gal4p-driven transcription in response to a defect in the secretory pathway, by a mechanism that requires the silencing region of Rap1p. We conclude that for Rap1p to activate the transcription of an RP gene it must bind to upstream sequences; yet for Rap1p to repress the transcription of an RP gene it need not bind to the gene directly. Thus, the cell has evolved a two-pronged approach to effect the rapid extinction of RP synthesis in response to the stress imposed by a heat shock or by a failure of the secretory pathway. Calculations based on recent transcriptome data and on the half-life of the RP mRNAs suggest that in a rapidly growing cell the transcription of RP mRNAs accounts for nearly 50% of the total transcriptional events initiated by RNA polymerase II. Thus, the sudden silencing of the RP genes must have a dramatic effect on the overall transcriptional economy of the cell.The Saccharomyces cerevisiae cell invests enormous resources in the synthesis of ribosomes. In a rapidly growing cell, the 100 or more rRNA genes are responsible for at least 60% of total transcription (59). The 137 ribosomal protein (RP) genes are among the most active in the genome (57). As a result, the cell has evolved mechanisms that tightly control the synthesis of the components of the ribosome. The 78 RPs are synthesized in nearly equimolar amounts that are matched to the synthesis of rRNA. Furthermore, the synthesis of these components is coo...

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“…Besides these molecules which may be considered as mediators of an epigenetic control of gene expression, repressors acting directly either on enhancer-bound proteins or on the basal transcription machinery have been identi®ed and fall into two broad classes: (i) passive repressors which compete for the target of DNAbinding transcriptional activators or alter their binding activity (MyoD/Id, c-Jun/JunB) (Dias et al, 1994;Langlands et al, 1997;Mechta et al, 1997) or their activating properties (Gal4/Gal80) (Lohr et al, 1995); (ii) active repressors which operate through proteinprotein interactions with components of the basal or activated transcription apparatus, thereby preventing the assembly of functional pre-initiation complexes or mediating the formation of frozen complexes.…”

Section: Introductionmentioning

confidence: 99%

A murine ATFa-associated factor with transcriptional repressing activity

et al. 2000

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The ATFa proteins, which are members of the CREB/ ATF family of transcription factors, have previously been shown to interact with the adenovirus E1a oncoprotein and to mediate its transcriptional activity; they heterodimerize with Jun, Fos or related transcription factors, possibly altering their DNA-binding speci®city; they also stably bind JNK2, a stress-induced protein kinase. Here we report the identi®cation and characterization of a novel protein isolated in a yeast two-hybrid screen using the N-terminal half of ATFa as a bait. This 1306-residue protein (mAM, for mouse ATFa-associated Modulator) is rather acidic (pHi 4.5) and contains high proportions of Ser/Thr (21%) and Pro (11%) residues. It colocalizes and interacts with ATFa in mammalian cells, contains a bipartite nuclear localization signal and possesses an ATPase activity. Transfection experiments show that mAM is able to downregulate transcriptional activity, in an ATPase-independent manner. Our results indicate that mAM interacts with several components of the basal transcription machinery (TFIIE and TFIIH), including RNAPII itself. Together, these ®ndings suggest that mAM may be involved in the ®ne-tuning of ATFaregulated gene expression, by interfering with the assembly or stability of speci®c preinitiation transcription complexes.

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Transcriptional regulation in the yeast GAL gene family: a complex genetic network

Cited by 399 publications

References 58 publications

Microbioreactors for Bioprocess Development

Microbioreactors for Bioprocess Development

Transcriptional Elements Involved in the Repression of Ribosomal Protein Synthesis

A murine ATFa-associated factor with transcriptional repressing activity

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