Whi2 or Whiskey 2 is a 55 kDa globular, [1] scaffold protein located to cell periphery [2] in Saccharomyces cerevisiae, which plays an essential role in regulating stress response pathways, apparently by passing input signals about nutrient availability on to stress responsive elements and autophagy/mitophagy mechanisms. It is encoded by a 1.46 kbp gene located on chromosome 15. [3] Whi2p shares a conserved BTB structure domain to the family of human potassium channel tetramerization domain proteins (KCTDs). [4] KCTD family members have been associated with several type of cancers and epilepsy disorders.
Upon complexing with plasma membrane associated phosphatase Psr1 and Psr2, Whi2 induces general stress response by dephosphorylating general stress response transcription factor Msn2. [5] Whi2 is essential for Msn2 activity, moreover activation by Whi2 is dominant and independent of the PKA and TOR activation pathways. [6] Additionally, experiments suggests Whi2 plays a role in Ras2 deactivation or degradation during nutrient depletion. [7] Whi2-Psr1/Psr2 complex is also required for inhibition of TORC1 activity under conditions of nutrient deprivation. [8] Furthermore, a striking characteristic of Whi2 is the repeated observation of spontaneous mutations in the WHI2 gene in the yeast library of knock-out strains and in genome evolutionary studies. [9] [4] Recently a novel function of Whi2-Psr1/Psr2 complex identified in balancing cell population and regulating expansion of cells with fitness advantage in dense yeast populations. [10]
Saccharomyces cerevisiae is a species of yeast. The species has been instrumental in winemaking, baking, and brewing since ancient times. It is believed to have been originally isolated from the skin of grapes. It is one of the most intensively studied eukaryotic model organisms in molecular and cell biology, much like Escherichia coli as the model bacterium. It is the microorganism behind the most common type of fermentation. S. cerevisiae cells are round to ovoid, 5–10 μm in diameter. It reproduces by budding.
Schizosaccharomyces pombe, also called "fission yeast", is a species of yeast used in traditional brewing and as a model organism in molecular and cell biology. It is a unicellular eukaryote, whose cells are rod-shaped. Cells typically measure 3 to 4 micrometres in diameter and 7 to 14 micrometres in length. Its genome, which is approximately 14.1 million base pairs, is estimated to contain 4,970 protein-coding genes and at least 450 non-coding RNAs.
The G0 phase describes a cellular state outside of the replicative cell cycle. Classically, cells were thought to enter G0 primarily due to environmental factors, like nutrient deprivation, that limited the resources necessary for proliferation. Thus it was thought of as a resting phase. G0 is now known to take different forms and occur for multiple reasons. For example, most adult neuronal cells, among the most metabolically active cells in the body, are fully differentiated and reside in a terminal G0 phase. Neurons reside in this state, not because of stochastic or limited nutrient supply, but as a part of their developmental program.
Autophagy is the natural, conserved degradation of the cell that removes unnecessary or dysfunctional components through a lysosome-dependent regulated mechanism. It allows the orderly degradation and recycling of cellular components. Although initially characterized as a primordial degradation pathway induced to protect against starvation, it has become increasingly clear that autophagy also plays a major role in the homeostasis of non-starved cells. Defects in autophagy have been linked to various human diseases, including neurodegeneration and cancer, and interest in modulating autophagy as a potential treatment for these diseases has grown rapidly.
Eisosomes are large, heterodimeric, immobile protein complexes at the plasma membrane which mark the site of endocytosis in some eukaryotes, and were discovered in the yeast Saccharomyces cerevisiae in 2006. Currently, seven genes: Pil1, Lsp1 and Sur7, Eis1, Seg1 and Ygr130C, Seg2, are annotated to the formation of the proteins identified in eisosomes. These organelle-like structures have put to rest the idea that sites of endocytosis in cells are chosen at random. Eisosomes have a profound role in regulating plasma membrane architecture and organization in yeast. Microscopic and genetic analyses link these stable, ultrastructural assemblies to the endocytosis of both lipid and protein cargoes in cells.
Adaptive mutation, also called directed mutation or directed mutagenesis is a controversial evolutionary theory. It posits that mutations, or genetic changes, are much less random and more purposeful than traditional evolution, implying that organisms can respond to environmental stresses by directing mutations to certain genes or areas of the genome. There have been a wide variety of experiments trying to support the idea of adaptive mutation, at least in microorganisms.
Cell division control protein 6 homolog is a protein that in humans is encoded by the CDC6 gene.
Dual specificity protein phosphatase CDC14A is an enzyme that in humans is encoded by the CDC14A gene.
Dual specificity protein phosphatase CDC14B is an enzyme that in humans is encoded by the CDC14B gene.
Pho4 is a protein with a basic helix-loop-helix (bHLH) transcription factor. It is found in S. cerevisiae and other yeasts. It functions as a transcription factor to regulate phosphate responsive genes located in yeast cells. The Pho4 protein homodimer is able to do this by binding to DNA sequences containing the bHLH binding site 5'-CACGTG-3'. This sequence is found in the promoters of genes up-regulated in response to phosphate availability such as the PHO5 gene.
Mitophagy is the selective degradation of mitochondria by autophagy. It often occurs to defective mitochondria following damage or stress. The process of mitophagy was first described over a hundred years ago by Margaret Reed Lewis and Warren Harmon Lewis. Ashford and Porter used electron microscopy to observe mitochondrial fragments in liver lysosomes by 1962, and a 1977 report suggested that "mitochondria develop functional alterations which would activate autophagy." The term "mitophagy" was in use by 1998.
Autophagy-related protein 8 (Atg8) is a ubiquitin-like protein required for the formation of autophagosomal membranes. The transient conjugation of Atg8 to the autophagosomal membrane through a ubiquitin-like conjugation system is essential for autophagy in eukaryotes. Even though there are homologues in animals, this article mainly focuses on its role in lower eukaryotes such as Saccharomyces cerevisiae.
Cdc14 and Cdc14 are a gene and its protein product respectively. Cdc14 is found in most of the eukaryotes. Cdc14 was defined by Hartwell in his famous screen for loci that control the cell cycle of Saccharomyces cerevisiae. Cdc14 was later shown to encode a protein phosphatase. Cdc14 is dual-specificity, which means it has serine/threonine and tyrosine-directed activity. A preference for serines next to proline is reported. Many early studies, especially in the budding yeast Saccharomyces cerevisiae, demonstrated that the protein plays a key role in regulating late mitotic processes. However, more recent work in a range of systems suggests that its cellular function is more complex.
The bZIP intron RNA motif is an RNA structure guiding splicing of a non-canonical intron from bZIP-containing genes called HAC1 in yeast, XBP1 in Metazoa, Hxl1 or Cib1 in Basidiomycota and bZIP60 in plants. Splicing is performed independently of the spliceosome by Ire1, a kinase with endoribonuclease activity. Exons are joined by a tRNA ligase. Recognition of the intron splice sites is mediated by a base-paired secondary structure of the mRNA that forms at the exon/intron boundaries. Splicing of the bZIP intron is a key regulatory step in the unfolded protein response (UPR). The Ire-mediated unconventional splicing was first described for HAC1 in S. cerevisiae.
Polyphosphoinositide phosphatase also known as phosphatidylinositol 3,5-bisphosphate 5-phosphatase or SAC domain-containing protein 3 (Sac3) is an enzyme that in humans is encoded by the FIG4 gene. Fig4 is an abbreviation for Factor-Induced Gene.
Ras2 is a Saccharomyces cerevisiae guanine nucleotide-binding protein which becomes activated by binding GTP when glucose is present in the environment. It affects growth regulation and starvation response.
SilentInformationRegulator (SIR) proteins are involved in regulating gene expression. SIR proteins organize heterochromatin near telomeres, ribosomal DNA (rDNA), and at silent loci including hidden mating type loci in yeast. The SIR family of genes encodes catalytic and non-catalytic proteins that are involved in de-acetylation of histone tails and the subsequent condensation of chromatin around a SIR protein scaffold. Some SIR family members are conserved from yeast to humans.
RRM3 is a gene that encodes a 5′-to-3′ DNA helicase known affect multiple cellular replication and repair processes and is most commonly studied in Saccharomyces cerevisiae. RRM3 formally stands for Ribosomal DNArecombination mutation 3. The gene codes for nuclear protein Rrm3p, which is 723 amino acids in length, and is part of a Pif1p DNA helicase sub-family that is conserved from yeasts to humans. RRM3 and its encoded protein have been shown to be vital for cellular replication, specifically associating with replication forks genome-wide. RRM3 is located on chromosome 8 in yeast cells and codes for 723 amino acids producing a protein that weighs 81,581 Da.
Pdr1p is a transcription factor found in yeast and is a key regulator of genes involved in general drug response. It induces the expression of ATP-binding cassette transporter, which can export toxic substances out of the cell, allowing cells to survive under general toxic chemicals. It binds to DNA sequences that contain certain motifs called pleiotropic drug response element (PDRE). Pdr1p is encoded by a gene called PDR1 on chromosome VII.
BCK2, also named CTR7, is an early cell cycle regulator expressed by the yeast Saccharomyces cerevisiae. It was first discovered in a screen for genes whose overexpression would suppress the phenotypes of PKC1 pathway mutations. Though its mechanism is currently unknown, it is believed to interact with Swi4 and Mcm1, both important transcriptional regulators of early cell cycle.