Surveying <i>Saccharomyces</i> Genomes to Identify Functional Elements by Comparative DNA Sequence Analysis

Cliften, Paul; Hillier, La Deana W.; Fulton, Lucinda L.; Graves, Tina; Miner, Tracie L.; Gish, Warren; Waterston, Robert H.; Johnston, Mark

doi:10.1101/gr.182901

Cited by 231 publications

(192 citation statements)

References 42 publications

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“…Despite the ability to readily identify putative Erf2p homologs by sequence homology, we have been unable to identify apparent homologs of Erf4p except in fungal databases (56). This is surprising, since both Erf2p and Erf4p are required for Ras palmitoyltransferase activity (23).…”

Section: Discussionmentioning

confidence: 68%

Erf4p and Erf2p Form an Endoplasmic Reticulum-associated Complex Involved in the Plasma Membrane Localization of Yeast Ras Proteins

Zhao¹,

Lobo²,

Dong³

et al. 2002

Journal of Biological Chemistry

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Ras oncogene proteins are plasma membrane-associated signal transducers that are found in all eukaryotes. Posttranslational addition of lipid to a carboxyl-terminal CaaX box (where "C" represents a cysteine, "a" is generally an aliphatic residue, and X can be any amino acid) is required to target Ras proteins to the cytosolic surface of the plasma membrane. The pathway by which Ras translocates from the endoplasmic reticulum to the plasma membrane is currently not clear. We have performed a genetic screen to identify components of the Ras plasma membrane localization pathway. Mutations in two genes, ERF2 and ERF4/SHR5, have been shown to affect the palmitoylation and subcellular localization of Ras proteins. In this report, we show that Erf4p is localized on the endoplasmic reticulum as a peripheral membrane protein in a complex with Erf2p, an integral membrane protein that was identified from the same genetic screen. Erf2p has been shown to be required for the plasma membrane localization of GFP-Ras2p via a pathway distinct from the classical secretory pathway (X. Dong and R. J. Deschenes, manuscript in preparation). We show here that Erf4p, like Erf2p, is involved in the plasma membrane localization of Ras2p. Erf2p and Erf4p represent components of a previously uncharacterized subcellular transport pathway involved in the plasma membrane targeting of Ras proteins.Ras proteins are plasma membrane-bound small GTPases that regulate signal transduction pathways by cycling between GTP-and GDP-bound forms (1, 2). Ras proteins are initially synthesized as cytosolic precursors, but then undergo modifications at a carboxyl-terminal motif called the CaaX box (where "C" represents a cysteine, "a" is generally an aliphatic residue, and "X" can be any amino acid) (3). These modifications include farnesylation of the CaaX box cysteine, proteolysis of the -aaX, and carboxyl methylation (4 -8). The last two steps occur on the cytosolic surface of the ER. 1 Most Ras proteins, including yeast Ras1p and Ras2p and mammalian H-Ras and N-Ras, are further modified by palmitoylation on one or two additional cysteine residues often found adjacent to the CaaX box. Not all prenylated Ras proteins undergo palmitoylation. Mammalian K-Ras4B, for example, lacks a palmitoylation site but contains multiple basic residues near the C terminus that are required for plasma membrane targeting (4, 9 -11). These observations have led to a two-signal hypothesis for trafficking in which CaaX box processing plus at least one additional signal is required for plasma membrane localization of Ras (12).The mechanism by which Ras and other prenylated proteins are transported from the cytoplasmic surface of the ER to the plasma membrane is not clear. The classical secretory pathway, which has been explored extensively by genetic studies in S. cerevisiae and biochemical fractionation of mammalian cell lines, is an obvious candidate (13-15). Many proteins are transported via the classical secretory pathway by a process of vesicle budding and fusion (16,17). Li...

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Section: Discussionmentioning

confidence: 68%

Erf4p and Erf2p Form an Endoplasmic Reticulum-associated Complex Involved in the Plasma Membrane Localization of Yeast Ras Proteins

Zhao¹,

Lobo²,

Dong³

et al. 2002

Journal of Biological Chemistry

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“…Nucleotide-level multiple alignment of the GDH1, GDH3, ASN1 and ASN2 promoter regions was done using CLUSTALW2 (http://www.ebi.ac.uk/Tools/clustalw2). Promoter sequences were obtained from http://www.broad.mit.edu/annotation/fungi/comp_ yeasts/downloads.html for Saccharomyces paradoxus and Saccharomyces mikatae (Kellis et al, 2003), from http://www.genetics.wustl.edu/ saccharomycesgenomes/download.html for Saccharomyces kudriavzevii (Cliften et al, 2001), and from http://www.yeastgenome.org/ for S. cerevisiae (Saccharomyces Genome Database).…”

Section: Methodsmentioning

confidence: 99%

Hap2-3-5-Gln3 determine transcriptional activation of GDH1 and ASN1 under repressive nitrogen conditions in the yeast Saccharomyces cerevisiae

et al. 2011

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The transcriptional activation response relies on a repertoire of transcriptional activators, which decipher regulatory information through their specific binding to cognate sequences, and their capacity to selectively recruit the components that constitute a given transcriptional complex. We have addressed the possibility of achieving novel transcriptional responses by the construction of a new transcriptional regulator -the Hap2-3-5-Gln3 hybrid modulator -harbouring the HAP complex polypeptides that constitute the DNA-binding domain (Hap2-3-5) and the Gln3 activation domain, which usually act in an uncombined fashion. The results presented in this paper show that transcriptional activation of GDH1 and ASN1 under repressive nitrogen conditions is achieved through the action of the novel Hap2-3-5-Gln3 transcriptional regulator. We propose that the combination of the Hap DNA-binding and Gln3 activation domains results in a hybrid modulator that elicits a novel transcriptional response not evoked when these modulators act independently. INTRODUCTIONThe response of Saccharomyces cerevisiae to nutrient limitation is a model whose study has amply contributed to our knowledge of the mechanisms determining transcriptional activation (Zaman et al., 2008). Nutrient limitation results in a complex adaptation of the physiology of yeast cells, which allows them to redefine their transcription programme. This leads to the activation of particular sets of genes, whose products are needed to evoke an appropriate physiological response. Transcriptional activators are composed of a DNA-binding domain, which targets these proteins to specialized binding sites, and an activation domain that mediates transcription initiation; these two domains can be contained in single or different polypeptides (Zaman et al., 2008).When yeast cells are provided with poor nitrogen sources, such as proline, genes coding for enzymes involved in the catabolism of these compounds are highly expressed. Conversely, in the presence of high-quality nitrogen sources such as glutamine, a decrease in the levels of catabolic enzymes is observed. The reduced expression of the genes coding for enzymes involved in the utilization of poor nitrogen sources is brought about through the action of a regulatory system known as nitrogen catabolite repression (NCR) (Blinder & Magasanik, 1995;Coffman et al., 1995Coffman et al., , 1996Courchesne & Magasanik, 1988;Minehart & Magasanik, 1991) NCR operates through the action of two transcriptional activators, Gln3 and Nil1/ Gat1, and two repressors, Dal80 and Gzf3/Deh1/Nil2 (Minehart & Magasanik, 1991;Stanbrough et al., 1995;Svetlov & Cooper, 1998;Magasanik & Kaiser, 2002), whose expression is regulated by nitrogen levels. In the presence of repressive nitrogen sources, the TOR signalling pathway promotes the association of the GATA transcription factors Gln3 and Gat1 with the cytoplasmic protein Ure2, thus retaining Gln3 and Gat1 in the cytoplasm (Beck & Hall, 1999;Cardenas et al., 1999;Hardwick et al., 1999). Dissociation o...

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“…Branch distances were estimated using the Jukes and Cantor's (1969) one-parameter model based on data from Cliften et al (2001). We analyzed all aligned octamers in each of Figure 2 Functional enrichment of genes associated with motif families.…”

Section: Methods Estimating Substitution Ratesmentioning

confidence: 99%

“…According to the predominant paradigm, a collection of genomes is used to annotate sequence regions as "conserved" or "not conserved." Conservation based methods were used to identify regulatory loci in yeast promoters and to organize them around consensus motifs (Cliften et al 2001(Cliften et al , 2003Kellis et al 2003;Moses et al 2003). The dynamics of evolutionary changes, however, carries much richer information on the functional role of sequence elements.…”

mentioning

confidence: 99%

A Global View of the Selection Forces in the Evolution of Yeast Cis-Regulation

Tanay

Gat‐Viks²,

Shamir³

2004

Genome Res.

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The interaction between transcription factors and their DNA binding sites is key to understanding gene regulation. By performing a genome-wide study of the evolutionary dynamics in yeast promoters, we provide a first global view of the network of selection forces in the evolution of transcription factor binding sites. This analysis gives rise to new models for binding site activity, identifies families of related binding sites, and characterizes the functional similarities among them. We discovered rich and highly optimized selective pressures operating inside and around these families. In several cases, this organization reveals that a single transcription factor has multiple functional modes. We demonstrate how such functional heterogeneity is related to the binding site's affinity and how it is exploited in transcription programs.

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Surveying Saccharomyces Genomes to Identify Functional Elements by Comparative DNA Sequence Analysis

Cited by 231 publications

References 42 publications

Erf4p and Erf2p Form an Endoplasmic Reticulum-associated Complex Involved in the Plasma Membrane Localization of Yeast Ras Proteins

Erf4p and Erf2p Form an Endoplasmic Reticulum-associated Complex Involved in the Plasma Membrane Localization of Yeast Ras Proteins

Hap2-3-5-Gln3 determine transcriptional activation of GDH1 and ASN1 under repressive nitrogen conditions in the yeast Saccharomyces cerevisiae

A Global View of the Selection Forces in the Evolution of Yeast Cis-Regulation

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