The yeast MOT2 gene encodes a putative zinc finger protein that serves as a global negative regulator affecting expression of several categories of genes, including mating-pheromone-responsive genes

Deletion of the NOT4 gene impairs hyphal development and pathogenicity in Candida albicans

The Candida albicans NOT4 gene was disrupted in order to investigate the role of Not4p in growth, morphogenesis and pathogenicity. Heterozygote (NOT4/not4), null (not4/not4) and reconstructed heterozygote ([NOT4]/not4) strains of C. albicans, as well as CAF2-1, the parental strain, were grown under conditions that promote hyphal formation. When cultured in liquid medium 199 the heterozygote, reconstructed and wild-type strains began the yeast-to-hyphal transition within 3 h and continued hyphal growth for the duration of experiments. The null mutant also began hyphal growth within 3-5 h but hyphae tended to be shorter and distorted. Subsequently, hyphal growth was arrested and growth returned predominantly to the yeast form. Similar differences were observed when strains were grown on solid Spider medium and medium 199. The parental, heterozygote and reconstructed strains formed normal filamentous networks emanating from colonies. In contrast, the null mutant failed to form hyphae on all solid media tested. The ability of the NOT4 null strain to form biofilms was also investigated, and it was observed that biofilm development does not readily occur for this strain. Virulence of each strain was examined utilizing the mouse model of systemic candidiasis. Mice infected with CAF2-1 succumbed to infection within 3-7 days. All mice infected with the null strain survived for the duration of experiments, while the heterozygote and reconstructed heterozygote strains showed an intermediate level of virulence. These findings suggest that NOT4 may play a role in affecting strain pathogenicity, possibly by regulating expression of certain genes that effect cellular morphogenesis and virulence.

The CCR4-NOT complex plays diverse roles in mRNA metabolism

It is increasingly clear that the synthesis of eukaryotic mRNA involves an integrated series of events involving large multisubunit protein complexes. The evolutionarily conserved CCR4-NOT complex of proteins has been found to be involved in several aspects of mRNA formation, including repression and activation of mRNA initiation, control of mRNA elongation, and the deadenylation and subsequent degradation of mRNA. Its roles in such diverse processes make the CCR4-NOT complex central to the regulation of mRNA metabolism. In this review we describe the CCR4-NOT complex, its constituents, and its organization, discussing both the well characterized yeast proteins and their higher eukaryotic orthologs. The known biochemical roles of the individual components and of the complex are described with particular emphasis on the two known functions of the complex, repression of TFIID action and deadenylation of mRNA. Finally, the functional diversity of the CCR4-NOT complex is related to its mediating responses from a number of cellular signaling pathways.

Global control of gene expression in yeast by the Ccr4-Not complex

The Ccr4-Not complex is a global regulator of gene expression that is conserved from yeast to human. It is a large complex that in the yeast Saccharmyces cerevisiae exists in two prominent forms of 0.9-1.2 and 1.9-2 MDa, and consists of at least nine core subunits: the five Not proteins (Not1p to Not5p), Caf1p, Caf40p, Caf130p and Ccr4p. It was initially described to be a global regulator of transcription, based upon the observation that the levels of many transcripts were increased or decreased in mutants. However, the recent finding that Caf1p and Ccr4p encode the major yeast deadenylase has suggested that this complex may additionally play a role in RNA degradation. In this review, the events that led to the identification of the Ccr4-Not complex are described and the elements that clearly demonstrate that the Ccr4-Not complex regulates many different cellular functions are discussed, including RNA degradation and transcription initiation. The evidence points to a role for the Ccr4-Not complex as a regulatory platform that senses nutrient levels and stress.

Characterization of mutations in NOT2 indicates that it plays an important role in maintaining the integrity of the CCR4-NOT complex

The NOT2 protein is a component of the CCR4-NOT complex that plays multiple roles in the regulation of mRNA production in the yeast Saccharomyces cerevisiae. We have identified four novel not2 mutations and have characterized these and two previously described alleles as to the means by which they affect CCR4-NOT function. While two of the not2 alleles, not2-4 (carrying a G31R alteration) and not2::L9P, resulted in severe growth defects and caused a not phenotype at the HIS3 locus, these phenotypes appear to arise from partially different effects. The not2::L9P mutation resulted in complete loss of the 1.9x10(6)Da (1.9MDa) CCR4-NOT complex, and the not2::L9P protein displayed increased ability to associate with the NOT5 protein. In contrast, the not2-4 allele destabilized the CCR4-NOT complex to a lesser extent and had no effect on NOT5 association with NOT2. Instead, as previously reported, it displayed defective interactions with ADA2, a component of the SAGA complex. The not2::R165G also abrogated NOT2 ability to interact with ADA2 but had little effect on the integrity of the CCR4-NOT complex. Alterations in NOT2 contacts to ADA2, therefore, do not necessarily result in effects on the CCR4-NOT complex nor result in severe growth defects. We also observed that the four NOT2 N-terminal mutations affected NOT5 association with the CCR4-NOT complexes, suggesting that it is the N terminus of NOT2 that contacts and stabilizes NOT5 interactions. These results indicate that it is the loss of the integrity of the CCR4-NOT complex which leads to severe not2 phenotypes and that the NOT2 contacts to ADA2 play a lesser role in NOT2 function.

Genetic basis of mitochondrial function and morphology in Saccharomyces cerevisiae

The understanding of the processes underlying organellar function and inheritance requires the identification and characterization of the molecular components involved. We pursued a genomic approach to define the complements of genes required for respiratory growth and inheritance of mitochondria with normal morphology in yeast. With the systematic screening of a deletion mutant library covering the nonessential genes of Saccharomyces cerevisiae the numbers of genes known to be required for respiratory function and establishment of wild-type-like mitochondrial structure have been more than doubled. In addition to the identification of novel components, the systematic screen revealed unprecedented mitochondrial phenotypes that have never been observed by conventional screens. These data provide a comprehensive picture of the cellular processes and molecular components required for mitochondrial function and structure in a simple eukaryotic cell.

Isolation and characterization of the Candida albicans MOT2 gene

A putative Candida albicans homologue of Saccharomyces cerevisiae MOT2 (modulator of transcription) has been cloned and analyzed. A cDNA fragment corresponding to a portion of S. cerevisiae MOT2 was used to isolate a similar C. albicans gene (CaMOT2). CaMOT2 is comprised of two exons of 50 bp and 1,714 bp, respectively, with a single 82 bp intron located near the 5' end of the gene. The gene encodes a protein (CaMot2p) with an estimated mass of 67 kDa. The 5' region of the gene shows sequence homology with S. cerevisiae MOT2, whereas no significant similarity was observed in the 3' region. Similarly, the N-terminal portion of C. albicans Mot2p exhibits approximately 80% homology with S. cerevisiae Mot2p, while no significant homology to any known protein was observed in the carboxy-terminal half of the C. albicans protein. The N-terminal portion of CaMot2p contains a cysteine-rich domain (amino acids 18-62). The distribution of the cysteine residues identifies CaMot2p as a zinc-finger protein. The data suggest two potential Zn-binding sites, similar to the arrangement found in S. cerevisiae. Reverse-transcriptase polymerase chain reaction was used to compare the level of CaMOT2 expression between C. albicans grown in vitro and growth during in vivo infection in the rat model of oral candidiasis. The results showed CaMOT2 is down-regulated during growth in the rat oral cavity compared to in vitro culture. Although the function of C. albicans MOT2 has not been determined, comparison to S. cerevisiae MOT2 suggests the gene product may act as a general negative regulator.

Functional interaction of CCR4-NOT proteins with TATAA-binding protein (TBP) and its associated factors in yeast

The CCR4-NOT transcriptional regulatory complex affects expression of a number of genes both positively and negatively. We report here that components of the CCR4-NOT complex functionally and physically interact with TBP and TBP-associated factors. First, mutations in CCR4-NOT components suppressed the his4-912delta insertion in a manner similar to that observed for the defective TBP allele spt15-122. Second, using modified HIS3 promoter derivatives containing specific mutations within the TATA sequence, we found that the NOT proteins were general repressors that disrupt TBP function irrespective of the DNA sequence. Third, increasing the dosage of NOT1 specifically inhibited the ability of spt15-122 to suppress the his4-912delta insertion but did not affect the Spt- phenotype of spt3 or spt10 at this locus. Fourth, spt3, spt8, and spt15-21 alleles (all involved in affecting interaction of SPT3 with TBP) suppressed ccr4 and caf1 defects. Finally, we show that NOT2 and NOT5 can be immunoprecipitated by TBP. NOT5 was subsequently shown to associate with TBP and TAFs and this association was dependent on the integrity of TFIID. These genetic and physical interactions indicate that one role of the CCR4-NOT proteins is to inhibit functional TBP-DNA interactions, perhaps by interacting with and modulating the function of TFIID.

Identification of yeast meiosis-specific genes by differential display

Meiosis, a specialized cell division process, occurs in all sexually reproducing organisms. During this process a diploid cell undergoes a single round of DNA replication followed by two rounds of nuclear division to produce four haploid gametes. In yeast, the meiotic products are packaged into four spores that are enclosed in a sac known as an ascus. To enhance our understanding of the meiotic developmental pathway and spore formation, we followed differential expression of genes in meiotic versus vegetatively growing cells in the yeast Saccharomyces cerevisiae. Such comparative analyses have identified five different classes of genes that are expressed at different stages of the sporulation program. We identified several meiosis-specific genes including some already known to be induced during meiosis. Here we describe one of these previously uncharacterized genes, SSP1, which plays an essential role in meiosis and spore formation. SSP1 is induced midway through meiosis, and the homozygous mutant-diploid cells fail to sporulate. In ssp1 cells, meiosis is delayed, nuclei fragment after meiosis II, and viability declines rapidly. The ssp1 defect is not related to a microtubule-cytoskeletal-dependent event and is independent of two rounds of meiotic divisions. Our results suggest that Ssp1 is likely to function in a pathway that controls meiotic nuclear divisions and coordinates meiosis and spore formation. Functional analysis of other uncharacterized genes is underway.

Characterization of NOT5 that encodes a new component of the Not protein complex

The yeast HIS3 gene has two core promoters: TC, a TATA-less element and TR, a canonical TATA element. Four genes encode global negative regulators of transcription that preferentially repress TC-dependent transcription: NOT1 (CDC39), NOT2 (CDC36), NOT3 and NOT4 (SIG1, MOT2). Genetic and biochemical experiments suggest that the products of these genes are associated in a complex and regulate TFIID function. In this paper, we describe a new gene, NOT5, that also represses transcription of the HIS3 TATA-less promoter preferentially and encodes a protein whose N-terminal region is 44% identical to that of Not3p. Our results indicate that NOT5 is involved in Not function and encodes a product that is physically associated with the other Not proteins. First, overexpression of NOT3 or NOT4 suppresses mutations in NOT5. Secondly, mutations in NOT4 are synthetically lethal with mutations in NOT5. Thirdly, NOT5 interacts with NOT1 and NOT3 in the two-hybrid assay. Finally, Not1p, Not3p and Not4p co-immunoprecipitate with Not5p.

Regena (Rga), a Drosophila homolog of the global negative transcriptional regulator CDC36 (NOT2) from yeast, modifies gene expression and suppresses position effect variegation

A mutation in Regena (Rga) was isolated in screens for modifiers of white eye color gene expression. The reduction in the level of the Rga product results in a complex modulation of white mRNA both positively and negatively, depending on the developmental stage. In addition to white, Rga also affects the expression of several other tested genes, with one of them, Vinculin, being regulated in a strong sex-specific manner. Rga was cloned by transposon tagging. Its predicted product lacks any recognized nucleic acid-binding motif but is homologous to a global negative transcriptional regulator, CDC36 (NOT2), from yeast. Rga also acts as a suppressor of position effect variegation, suggesting that a possible function of Rga could be mediation of an interaction between chromatin proteins and the transcriptional complex.

Regulation of the mating pheromone and invasive growth responses in yeast by two MAP kinase substrates

BACKGROUND

In the budding yeast Saccharomyces cerevisiae, components of a single mitogen-activated protein (MAP) kinase pathway transduce two distinct signals, each of which activates an independent developmental programme: peptide mating pheromones initiate the mating response, whereas nutrient limitation initiates filamentous growth. One of the MAP kinases in this pathway, Fus3, triggers mating but antagonizes filamentous growth, while the other, Kss 1, preferentially triggers filamentous growth. Both kinases activate the same transcription factor, Ste 12, which can stimulate gene expression specific to each of the developmental programmes. The precise mechanism by which these MAP kinases activate Ste 12, however, is not clear.

RESULTS

Two newly identified proteins, Rst 1 and Rst 2 (also known as Dig1 and Dig2), were found to associate physically with Fus3 and Ste12. Rst1 and Rst2 were prominent substrates in kinase reactions of Fus3 immune complexes from pheromone-treated cells. Association of Fus3 with Ste12 required Rst1 and Rst2, and activation of Fus3 by pheromone caused release of Ste12 from the Fus3 complex. Although rst1 and rst2 single mutants had no obvious phenotype, both filamentous growth and mating-specific gene expression were constitutive in rst1 rst2 double mutants. The phenotype of rst1 rst2 cells required Ste12 function, but did not require the function of upstream kinases. Consistent with Rst1 and Rst2 having a role in Ste12 regulation, both proteins were localized to the nucleus.

CONCLUSIONS

Rst1 and Rst2 repress the mating and filamentous growth responses of S. cerevisiae by directly inhibiting Ste12. Activation of Fus3 or Kss1 may cause phosphorylation-dependent release of Ste12 from Rst1/Rst2 and thereby activate Ste12-dependent transcription.

Functional analysis of the genes of yeast chromosome V by genetic footprinting

Genetic footprinting was used to assess the phenotypic effects of Ty1 transposon insertions in 268 predicted genes of chromosome V of Saccharomyces cerevisiae. When seven selection protocols were used, Ty1 insertions in more than half the genes tested (157 of 268) were found to result in a detectable reduction in fitness. Results could not be obtained for fewer than 3 percent of the genes tested (7 of 268). Previously known mutant phenotypes were confirmed, and, for about 30 percent of the genes, new mutant phenotypes were identified.