Production of ligand-specific mutants using a yeast two-hybrid mating assay

Acquiring functional knowledge from protein-protein interaction studies often necessitates the production of binding-impaired mutants and the study of their effects in biological systems. In many cases, multiple ligands compete for binding to the same protein domain and it becomes useful to produce specific mutations that prevent binding to one ligand but not to the others. We have combined PCR mutagenesis and a two hybrid mating assay to produce a screening strategy that has already proven useful in isolating ligand-specific mutants of the Grb10 and Raf-1 signaling proteins.NRC publication: Ye

Review : The long hard road to a completed Candida albicans genome

After almost a decade of work, the sequencing, assembly, and annotation of the genome of the fungal pathogen Candida albicans is finally close at hand. This review covers the early history of the C. albicans genome project, from the release of early assemblies that provided the impetus for an explosion in functional genomics research, to a community-based annotation and a preview of the work that was necessary for the production of a final genome assembly.NRC publication: Ye

Morphogenetic signaling in Candida albicans.

NRC publication: Ye

Rapid detection of aneuploidy following the generation of mutants in Candida albicans

Techniques used to generate mutants in Candida albicans commonly result in additional and undesired genetic rearrangements. Detection of aneuploidy is, therefore, an important step forward in the quality control of mutant phenotypes. In this chapter, we describe how to extract genomic DNA and perform a quantitative multiplex PCR to compare the karyotype of any mutant strain to that of its parent and allow the detection of any unwanted aneuploidy.Peer reviewed: YesNRC publication: N

Localization of endogenous Grb10 to the mitochondria and its interaction with the mitochondrial-associated Raf-1 pool

Grb10 belongs to a small family of adapter proteins that are known to interact with a number of receptor tyrosine kinases and signaling molecules. We have recently demonstrated that the Grb10 SH2 domain interacts with both the Raf-1 and MEK1 kinases. Overexpression of Grb10 genes with mutations in their SH2 domains promotes apoptosis in cultured cells, a phenotype that is reversed by concomitant overexpression of the wild type gene. Using immunofluorescence microscopy and subcellular fractionation we now show that most of the Grb10 molecules are peripherally associated with mitochondria. Following insulin-like growth factor I or serum treatment, small pools of Grb10 can also be found at the plasma membrane and in actin-rich membrane ruffles, whereas overexpression of Grb10 leads to its mislocalization to the cytosol. Two-hybrid analysis shows that the Grb10-binding site on Raf-1 co-localizes with its Ras-binding domain. Finally, we show that the endogenous Grb10 and Raf-1 proteins can be co-immunoprecipitated from a partially purified mitochondrial extract, an interaction that is enhanced following the activation of Raf-1 by ultraviolet radiation. Thus, we infer that Grb10 may regulate signaling between plasma membrane receptors and the apoptosis-inducing machinery on the mitochondrial outer membrane by modulating the anti-apoptotic activity of mitochondrial Raf-1.UI - 20054454NRC publication: Ye

The serine/threonine protein phosphatase SIT4 modulates yeast-to-hypha morphogenesis and virulence in Candida albicans

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Transcription factor substitution during the evolution of fungal ribosome regulation

Coordinated ribosomal protein (RP) gene expression is crucial for cellular viability, but the transcriptional network controlling this regulon has only been well characterized in the yeast Saccharomyces cerevisiae. We have used whole-genome transcriptional and location profiling to establish that, in Candida albicans, the RP regulon is controlled by the Myb domain protein Tbf1 working in conjunction with Cbf1. These two factors bind both the promoters of RP genes and the rDNA locus; Tbf1 activates transcription at these loci and is essential. Orthologs of Tbf1 bind TTAGGG telomeric repeats in most eukaryotes, and TTAGGG cis-elements are present upstream of RP genes in plants and fungi, suggesting that Tbf1 was involved in both functions in ancestral eukaryotes. In all Hemiascomycetes, Rap1 substituted Tbf1 at telomeres and, in the S. cerevisiae lineage, this substitution also occurred independently at RP genes, illustrating the extreme adaptability and flexibility of transcriptional regulatory networks.Peer reviewed: YesNRC publication: Ye

Pyruvate kinase deficiency in mice protects against malaria

English2003510001873635-0020See Contents-PageJournalNRC publication: Ye

Modeling the transcriptional regulatory network that controls the early hypoxic response in Candida albicans

We determined the changes in transcriptional profiles that occur in the first hour following the transfer of Candida albicans to hypoxic growth conditions. The impressive speed of this response is not compatible with current models of fungal adaptation to hypoxia that depend on the depletion of sterol and heme. Functional analysis using Gene Set Enrichment Analysis (GSEA) identified the Sit4 phosphatase, Ccr4 mRNA deacetylase, and Sko1 transcription factor (TF) as potential regulators of the early hypoxic response. Cells mutated in these and other regulators exhibit a delay in their transcriptional responses to hypoxia. Promoter occupancy data for 29 TFs were combined with the transcriptional profiles of 3,111 in vivo target genes in a Network Component Analysis (NCA) to produce a model of the dynamic and highly interconnected TF network that controls this process. With data from the TF network obtained from a variety of sources, we generated an edge and node model that was capable of separating many of the hypoxia-upregulated and -downregulated genes. Upregulated genes are centered on Tye7, Upc2, and Mrr1, which are associated with many of the gene promoters that exhibit the strongest activations. The connectivity of the model illustrates the high redundancy of this response system and the challenges that lie in determining the individual contributions of specific TFs. Finally, treating cells with an inhibitor of the oxidative phosphorylation chain mimics most of the early hypoxic profile, which suggests that this response may be initiated by a drop in ATP production.Peer reviewed: YesNRC publication: Ye

Pyruvate kinase deficiency is associated with protection against malaria

NRC publication: Ye