Alterations in the Interaction Between GAL4 and GAL80 Effect Regulation of the Yeast GAL Regulon Mediated by the F box Protein Dsg1

How the ubiquitin proteasome system regulates the regulators of transcription

The ubiquitin proteasome system plays an important role in transcription. Monoubiquitination of activators is believed to aid their function, while the 26S proteasomal degradation of repressors is believed to restrict their function. What remains controversial is the question of whether the degradation of activators aids or restricts their function.

Mechanistic perspective of mitochondrial fusion: tubulation vs. fragmentation

Mitochondrial fusion is a fundamental process driven by dynamin related GTPase proteins (DRPs), in contrast to the general SNARE-dependence of most cellular fusion events. The DRPs Mfn1/Mfn2/Fzo1 and OPA1/Mgm1 are the key effectors for fusion of the mitochondrial outer and inner membranes, respectively. In order to promote fusion, these two DRPs require post-translational modifications and proteolysis. OPA1/Mgm1 undergoes partial proteolytic processing, which results in a combination between short and long isoforms. In turn, ubiquitylation of mitofusins, after oligomerization and GTP hydrolysis, promotes and positively regulates mitochondrial fusion. In contrast, under conditions of mitochondrial dysfunction, negative regulation by proteolysis on these DRPs results in mitochondrial fragmentation. This occurs by complete processing of OPA1 and via ubiquitylation and degradation of mitofusins. Mitochondrial fragmentation contributes to the elimination of damaged mitochondria by mitophagy, and may play a protective role against Parkinson's disease. Moreover, a link of Mfn2 to Alzheimer's disease is emerging and mutations in Mfn2 or OPA1 cause Charcot-Marie-Tooth type 2A neuropathy or autosomal-dominant optic atrophy. Here, we summarize our current understanding on the molecular mechanisms promoting or inhibiting fusion of mitochondrial membranes, which is essential for cellular survival and disease control. This article is part of a Special Issue entitled: Mitochondrial dynamics and physiology.

Mediator acts upstream of the transcriptional activator Gal4

We show that Mediator, a protein originally isolated on the basis of its ability to respond to transcriptional activators, and thought to be regulated by an activator, can also be the master that controls the activator.

The proteasome inhibitor MG132 had been shown to prevent galactose induction of the S. cerevisiae GAL1 gene, demonstrating that ubiquitin proteasome-dependent degradation of transcription factors plays an important role in the regulation of gene expression. The deletion of the gene encoding the F-box protein Mdm30 had been reported to stabilize the transcriptional activator Gal4 under inducing conditions and to lead to defects in galactose utilization, suggesting that recycling of Gal4 is required for its function. Subsequently, however, it was argued that Gal4 remains stably bound to the enhancer under inducing conditions, suggesting that proteolytic turnover of Gal4 might not be required for its function. We have performed an alanine-scanning mutagenesis of ubiquitin and isolated a galactose utilization-defective ubiquitin mutant. We have used it for an unbiased suppressor screen and identified the inhibitor Gal80 as a suppressor of the transcriptional defects of the ubiquitin mutant, indicating that the protein degradation of the inhibitor Gal80, and not of the activator Gal4, is required for galactose induction of the GAL genes. We also show that in the absence of Gal80, Mdm30 is not required for Gal4 function, strongly supporting this hypothesis. Furthermore, we have found that Mediator controls the galactose-induced protein degradation of Gal80, which places Mediator genetically upstream of the activator Gal4. Mediator had originally been isolated by its ability to respond to transcriptional activators, and here we have discovered a leading role for Mediator in the process of transcription. The protein kinase Snf1 senses the inducing conditions and transduces the signal to Mediator, which initiates the degradation of the inhibitor Gal80 with the help of the E3 ubiquitin ligase SCF^Mdm30. The ability of Mediator to control the protein degradation of transcriptional inhibitors indicates that Mediator is actually able to direct its own recruitment to gene promoters.

The expression levels of proteins are tightly regulated, not only via their production but also via their degradation. Genes are transcribed only if their encoded proteins are required by the environmental or developmental conditions of a cell, and once a certain protein is no longer needed, it is rapidly degraded by the ubiquitin proteasome system (UPS). Transcriptional activators appeared to contradict this simple economic principle, as it had been claimed that they had to be degraded in order to function. The claim was based upon a correlation: if the degradation of an activator was prevented by drugs or mutations in the UPS, the activator became stable but also nonfunctional. We have now shown that it is not the activator itself but its inhibitor that is the functionally relevant target of the UPS. Furthermore, we have found that the degradation of the inhibitor is controlled by a protein complex called Mediator. The activator is known to recruit Mediator to gene promoters, where Mediator assists RNA polymerase in initiating transcription. Mediator was always considered to be completely under the control of the activator; however, we observe that by regulating the degradation of the inhibitor, Mediator is also able to control the activator and thereby to orchestrate its own recruitment to gene promoters.

Application of structure equation modeling for inferring a serial transcriptional regulation in yeast

Revealing the gene regulatory systems among DNA and proteins in living cells is one of the central aims of systems biology. In this study, I used Structural Equation Modeling (SEM) in combination with stepwise factor analysis to infer the protein-DNA interactions for gene expression control from only gene expression profiles, in the absence of protein information. I applied my approach to infer the causalities within the well-studied serial transcriptional regulation composed of GAL-related genes in yeast. This allowed me to reveal the hierarchy of serial transcriptional regulation, including previously unclear protein-DNA interactions. The validity of the constructed model was demonstrated by comparing the results with previous reports describing the regulation of the transcription factors. Furthermore, the model revealed combinatory regulation by Gal4p and Gal80p. In this study, the target genes were divided into three types: those regulated by one factor and those controlled by a combination of two factors.

Galactose induction of the GAL1 gene requires conditional degradation of the Mig2 repressor

Skp1 an essential component of the SCF (Skp1/cullin/F-box) E3 ubiquitin ligases, which target proteins for degradation by the 26S proteasome. We generated a skp1dM mutant strain that is defective for galactose induction of the GAL1 gene and we have found that galactose-induced protein degradation of the repressor Mig2 is defective in this strain. Mig2 degradation was also abolished in cells lacking the protein kinase Snf1 and the F-box protein Das1, suggesting that Snf1 triggers galactose-induced protein degradation of Mig2 by SCFDas1. Chromatin immunoprecipitation showed that Mig2 associates with the GAL1 promoter upon the galactose-induced exit of Mig1 in skp1dM cells, but not in wild-type cells, suggesting that the conditional degradation of Mig2 is required to prevent it from binding to the GAL1 promoter under inducing conditions. A galactose-stable deletion derivative of Mig2 caused a strong Mig (multi-copy inhibition of GAL gene expression) phenotype, confirming that galactose induction of the GAL1 gene requires the degradation of the repressor Mig2. Our results shed new light on the conflicting reports about the functional role of the degradation of transcriptional activators and indicate that gene expression studies interfering with proteasome degradation should take the stabilization of potential repressors into account.

Ugo1 and Mdm30 act sequentially during Fzo1-mediated mitochondrial outer membrane fusion

Dynamin-related GTPase proteins (DRPs) are main players in membrane remodelling. Conserved DRPs called mitofusins (Mfn1/Mfn2/Fzo1) mediate the fusion of mitochondrial outer membranes (OM). OM fusion depends on self-assembly and GTPase activity of mitofusins as well as on two other proteins, Ugo1 and Mdm30. Here, we define distinct steps of the OM fusion cycle using in vitro and in vivo approaches. We demonstrate that yeast Fzo1 assembles into homo-dimers, depending on Ugo1 and on GTP binding to Fzo1. Fzo1 homo-dimers further associate upon formation of mitochondrial contacts, allowing membrane tethering. Subsequent GTP hydrolysis is required for Fzo1 ubiquitylation by the F-box protein Mdm30. Finally, Mdm30-dependent degradation of Fzo1 completes Fzo1 function in OM fusion. Our results thus unravel functions of Ugo1 and Mdm30 at distinct steps during OM fusion and suggest that protein clearance confers a non-cycling mechanism to mitofusins, which is distinct from other cellular membrane fusion events.

Multiple metabolic signals influence GAL gene activation by modulating the interaction of Gal80p with the transcriptional activator Gal4p

Transcriptional status of the genes needed for galactose utilization in Saccharomyces cerevisiae is controlled by the interplay between the prototypical transcriptional activator Gal4p and the inhibitor protein Gal80p. Relief of the inhibition from Gal4p requires the interaction between Gal80p and the galactokinase paralog, Gal3p. Here, we present evidence that decrease in the intracellular levels of ATP or NADP(H) impairs the GAL gene expression. All these induction defects are rescued by overproducing Gal3p or producing Gal4p mutants with reduced interaction with Gal80p. We further demonstrate that removal of Gal80p from the GAL gene promoter is impaired in these mutants, and that NADP(H) cooperates with Gal3p in causing the dissociation of Gal80p from the in vitro preformed DNA-bound Gal80p-Gal4p complex. We also show that Gal80p is only partially removed from the GAL gene promoter in a mitochondria fusion-deficient mutant where the cotranscriptional mRNA processing is crippled. The efficient dissociation is restored by Gal4p mutants with altered interaction with Gal80p and is correlated with the recovered GAL gene expression. These results indicate that multiple metabolic signals exist to facilitate the efficient and appropriate dissociation of Gal80p from Gal4p by Gal3p to achieve the fully active state of Gal4p in the nucleus.