Alternative Mechanisms of Transcriptional Activation by Rap1p

Idrissi, Fátima-Zahra; García-Reyero, Natàlia; Fernández-Larrea, Juan; Piña, Benjamı́n

doi:10.1074/jbc.m101746200

Cited by 16 publications

(26 citation statements)

References 68 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The approximately twofold increase in GFP down-regulation observed with GFP2XRAP suggests that the Rap1p site can be modular for down-regulation within a TU. These results are less consistent with models based on internal transcriptional activation from the introduced Rap1p site or effects on histone repression as mechanisms for Rap1p-mediated down-regulation, as we did not see a synergistic effect from the addition of extra Rap1p sites, an effect that has been observed for both transcriptional activation and release from histone repression at the promoter of Rap1p bound genes (Woudt et al 1987;Idrissi and Pina 1999;Idrissi et al 2001).…”

Section: Down-regulation Depends On Orientation and Number Of Sitescontrasting

confidence: 53%

“…Furthermore, mutation of the core at positions 1, 3, and 5 individually to G prevented down-regulation of GFP ( Figure 4E). Interestingly, changes to the Rap1p ACCCA consensus at position 2 to T and/or position 5 to G are present in some ribosomal protein promoter Rap1p binding sites (Idrissi et al 2001;Lieb et al 2001). These specific changes in our system prevented down-regulation of GFP, thus not all Rap1p binding sites are equally capable of TU-specific downregulation.…”

Section: Mutation Of Accca Core Binding Site Of Rap1p Rescues Expressionmentioning

confidence: 95%

See 1 more Smart Citation

Novel Transcript Truncating Function of Rap1p Revealed by Synthetic Codon-Optimized Ty1 Retrotransposon

et al. 2012

View full text Add to dashboard Cite

Extensive mutagenesis via massive recoding of retrotransposon Ty1 produced a synthetic codon-optimized retrotransposon (CO-Ty1). CO-Ty1 is defective for retrotransposition, suggesting a sequence capable of down-regulating retrotransposition. We mapped this sequence to a critical 20-bp region within CO-Ty1 reverse transcriptase (RT) and confirmed that it reduced Ty1 transposition, protein, and RNA levels. Repression was not Ty1 specific; when introduced immediately downstream of the green fluorescent protein (GFP) stop codon, GFP expression was similarly reduced. Rap1p mediated this down-regulation, as shown by mutagenesis and chromatin immunoprecipitation. A regular threefold drop is observed in different contexts, suggesting utility for synthetic circuits. A large reduction of RNAP II occupancy on the CO-Ty1 construct was observed 39 to the identified Rap1p site and a novel 39 truncated RNA species was observed. We propose a novel mechanism of transcriptional regulation by Rap1p whereby it serves as a transcriptional roadblock when bound to transcription unit sequences. SACCHAROMYCES cerevisiae Ty1 is the best-characterized and most abundant of five retrotransposon families present in the genome. Ty1 shares many similarities with retroviruses, such as HIV-1 and makes similar use of an RNA intermediate in its propagation. Unsurprisingly, this Ty1 RNA intermediate is essential for Ty1 retrotransposition. Not only does this "mRNA" code for the GAG and POL proteins required for retrotransposition, but it also serves a critical function as the genetic material for replication. Both Ty1 mRNA and its cDNA product contain cis-acting nucleotide determinants required for retrotransposition.Mutagenesis of Ty1 and screening for cis-acting nucleotide determinants has been previously performed with various strategies, including in-frame linker insertion mutagenesis Devine and Boeke 1994;Monokian et al. 1994), analysis of synthetic Ty1 DNA fragments to determine minimal requirements for the integration reaction (Eichinger and Boeke 1990;Braiterman et al. 1994;Devine and Boeke 1994;Sharon et al. 1994), deletion analysis and PCR-mediated mutagenesis of mini-Ty1 elements (Xu and Boeke 1990;Bolton et al. 2005), and comparative sequence analysis followed by targeted mutagenesis and/or generation of complementary mutations in RNA stem regions (Chapman et al. 1992;Heyman et al. 1995;Lauermann et al. 1995;Friant et al. 1998;Cristofari et al. 2002;Bolton et al. 2005). These studies provided insights into mechanisms underlying Ty1 retrotransposition and revealed several cis-acting sequences, including the Met i -tRNA:primer binding site (PBS) interaction (Chapman et al. 1992; Friant et al. 1998), LTRs (Eichinger andBraiterman et al. 1994;Devine and Boeke 1994;Sharon et al. 1994), polypurine tracts (PPTs) (Heyman et al. 1995;Lauermann et al. 1995), the GAG-POL frameshift region (Belcourt and Farabaugh 1990; Lawler et al. 2001), CYC5 and CYC3 (Cristofari et al. 2002), and an extensive 59 RNA structure required for efficient ini...

show abstract

Section: Down-regulation Depends On Orientation and Number Of Sitescontrasting

confidence: 53%

Section: Mutation Of Accca Core Binding Site Of Rap1p Rescues Expressionmentioning

confidence: 95%

Novel Transcript Truncating Function of Rap1p Revealed by Synthetic Codon-Optimized Ty1 Retrotransposon

et al. 2012

View full text Add to dashboard Cite

show abstract

“…inserted into the KpnI and XhoI restriction sites of the pSLF⌬-178K plasmid (34). The plasmids pCDRE2 mut and pCDRE3 were constructed exactly as pCDRE2 except that the pairs of oligonucleotides 5Ј_CDRE2 mut _HXT2 and 3Ј_CDRE2 mut _ HXT2, and 5Ј_CDRE3_HXT2 and 3Ј_CDRE3_HXT2 were employed, respectively.…”

Section: Methodsmentioning

confidence: 99%

Direct Regulation of Genes Involved in Glucose Utilization by the Calcium/Calcineurin Pathway

Ruiz

Serrano

Ariño

2008

Journal of Biological Chemistry

View full text Add to dashboard Cite

Failure to use glucose as carbon source results in transcriptional activation of numerous genes whose expression is otherwise repressed. HXT2 encodes a yeast high affinity glucose transporter that is only expressed under conditions of glucose limitation. We show that HXT2 is rapidly and potently induced by environmental alkalinization, and this requires both the Snf1 and the calcineurin pathways. Regulation by calcineurin is mediated by the transcription factor Crz1, which rapidly translocates to the nucleus upon high pH stress, and acts through a previously unnoticed Crz1-binding element (calcineurindependent response element) in the HXT2 promoter (؊507 GGGGCTG ؊501). We demonstrate that, in addition to HXT2, many other genes required for adaptation to glucose shortage, such as HXT7, MDH2, or ALD4, transcriptionally respond to calcium and high pH signaling through binding of Crz1 to their promoters. Therefore, calcineurin-dependent transcriptional regulation appears to be a common feature for many genes encoding carbohydrate-metabolizing enzymes. Remarkably, extracellular calcium allows growth of a snf1 mutant on low glucose in a calcineurin/Crz1-dependent manner, indicating that activation of calcineurin is sufficient to override a major deficiency in the glucose-repression pathway. We propose that alkalinization of the medium results in impaired glucose utilization and that activation of certain glucose-metabolizing genes by calcineurin contributes to yeast survival under this stress situation.Glucose is the major carbon and energy source for most cells, and it is by far the preferred carbon source for the budding yeast Saccharomyces cerevisiae. In this organism glucose uptake is the limiting step in the utilization of this sugar, and the relevance of glucose to yeast metabolism is highlighted by the unusually large number of hexose transporter genes present in its genome (see Refs. 1 and 2 for reviews). These proteins transport their substrates by passive, gradient-dependent, energyindependent diffusion. At least six of them (Hxt1-7) have been shown to act as glucose transporters, whereas others are considered to transport galactose (Gal2) or other hexoses (Hxt5 and Hxt8 -17) (1, 3).These diverse glucose transporters exhibit different kinetic characteristics, and each of them appears particularly suited for a specific circumstance. For instance, Hxt1 is a low affinity, high capacity transporter, whereas Hxt2, Hxt6, and Hxt7 are examples of high affinity glucose transporters. Experimental evidence indicates that a strain lacking Hxt1-7 (often denominated as hxt null mutant) is unable to grow on glucose or other hexoses such as fructose or mannose (4, 5). Expression of HXT2, HXT6, and HXT7 allows growth of the hxt strain on low (0.1%) glucose, whereas other transporters are unable to do so (6). This confirms the role of these genes as high affinity glucose transporters, even though the major physiological role for glucose uptake under glucose shortage conditions can be attributed to Hxt2 (2).The expression pat...

show abstract

“…The C-terminal silencing domain represses mating-type, telomere-proximal, and RP genes under certain circumstances (31,32). Finally, a 34-amino acid (aa) Tox domain inhibits cell growth when overexpressed fused to the DBD (17,(33)(34)(35).…”

mentioning

confidence: 99%

“…Second, Rap1p functionally interacts with other DNA binding factors (i.e. Gcr1p-Gcr2p, Abf1p, Reb1p, Fhl1p-Ifh1p, Sfp1p, and Hmo1p) (45)(46)(47)(48)(49)(50)(51)(52), and with multisubunit transcriptional coregulators such as NuA4/Esa1p, SWI/SNF, and TFIID (34,53,54). We have recently shown that Rap1p directly binds several TAF subunits of TFIID (55).…”

mentioning

confidence: 99%

The Transcriptional Repressor Activator Protein Rap1p Is a Direct Regulator of TATA-binding Protein

Bendjennat

Weil

2008

Journal of Biological Chemistry

View full text Add to dashboard Cite

Alternative Mechanisms of Transcriptional Activation by Rap1p

Cited by 16 publications

References 68 publications

Novel Transcript Truncating Function of Rap1p Revealed by Synthetic Codon-Optimized Ty1 Retrotransposon

Novel Transcript Truncating Function of Rap1p Revealed by Synthetic Codon-Optimized Ty1 Retrotransposon

Direct Regulation of Genes Involved in Glucose Utilization by the Calcium/Calcineurin Pathway

The Transcriptional Repressor Activator Protein Rap1p Is a Direct Regulator of TATA-binding Protein

Contact Info

Product

Resources

About