Genome-Wide Localization Study of Yeast Pex11 Identifies Peroxisome-Mitochondria Interactions through the ERMES Complex.

Pex11 is a peroxin that regulates the number of peroxisomes in eukaryotic cells. Recently, it was found that a mutation in one of the three mammalian paralogs, PEX11ß, results in a neurological disorder. The molecular function of Pex11, however, is not known. Saccharomyces cerevisiae Pex11 has been shown to recruit to peroxisomes the mitochondrial fission machinery, thus enabling proliferation of peroxisomes. This process is essential for efficient fatty acid ß-oxidation. In this study, we used high-content microscopy on a genome-wide scale to determine the subcellular localization pattern of yeast Pex11 in all non-essential gene deletion mutants, as well as in temperature-sensitive essential gene mutants. Pex11 localization and morphology of peroxisomes was profoundly affected by mutations in 104 different genes that were functionally classified. A group of genes encompassing MDM10, MDM12 and MDM34 that encode the mitochondrial and cytosolic components of the ERMES complex was analyzed in greater detail. Deletion of these genes caused a specifically altered Pex11 localization pattern, whereas deletion of MMM1, the gene encoding the fourth, endoplasmic-reticulum-associated component of the complex, did not result in an altered Pex11 localization or peroxisome morphology phenotype. Moreover, we found that Pex11 and Mdm34 physically interact and that Pex11 plays a role in establishing the contact sites between peroxisomes and mitochondria through the ERMES complex. Based on these results, we propose that the mitochondrial/cytosolic components of the ERMES complex establish a direct interaction between mitochondria and peroxisomes through Pex11.

Genetic interactions between a phospholipase A2 and the Rim101 pathway components in S. cerevisiae reveal a role for this pathway in response to changes in membrane composition and shape.

Modulating composition and shape of biological membranes is an emerging mode of regulation of cellular processes. We investigated the global effects that such perturbations have on a model eukaryotic cell. Phospholipases A(2) (PLA(2)s), enzymes that cleave one fatty acid molecule from membrane phospholipids, exert their biological activities through affecting both membrane composition and shape. We have conducted a genome-wide analysis of cellular effects of a PLA(2) in the yeast Saccharomyces cerevisiae as a model system. We demonstrate functional genetic and biochemical interactions between PLA(2) activity and the Rim101 signaling pathway in S. cerevisiae. Our results suggest that the composition and/or the shape of the endosomal membrane affect the Rim101 pathway. We describe a genetically and functionally related network, consisting of components of the Rim101 pathway and the prefoldin, retromer and SWR1 complexes, and predict its functional relation to PLA(2) activity in a model eukaryotic cell. This study provides a list of the players involved in the global response to changes in membrane composition and shape in a model eukaryotic cell, and further studies are needed to understand the precise molecular mechanisms connecting them.

Rule-based clustering for gene promoter structure discovery.

BACKGROUND: The genetic cellular response to internal and external changes is determined by the sequence and structure of gene-regulatory promoter regions. OBJECTIVES: Using data on gene-regulatory elements (i.e., either putative or known transcription factor binding sites) and data on gene expression profiles we can discover structural elements in promoter regions and infer the underlying programs of gene regulation. Such hypotheses obtained in silico can greatly assist us in experiment planning. The principal obstacle for such approaches is the combinatorial explosion in different combinations of promoter elements to be examined. METHODS: Stemming from several state-of-the-art machine learning approaches we here propose a heuristic, rule-based clustering method that uses gene expression similarity to guide the search for informative structures in promoters, thus exploring only the most promising parts of the vast and expressively rich rule-space. RESULTS: We present the utility of the method in the analysis of gene expression data on budding yeast S. cerevisiae where cells were induced to proliferate peroxisomes. CONCLUSIONS: We demonstrate that the proposed approach is able to infer informative relations uncovering relatively complex structures in gene promoter regions that regulate gene expression.

HMG-CoA reductase is regulated by environmental salinity and its activity is essential for halotolerance in halophilic fungi.

The activity and level of HMG-CoA reductase (HMGR) were addressed in halophilic fungi isolated from solar saltpans. Representative fungi belonging to the orders Dothideales, Eurotiales and Wallemiales have a specific pattern of HMGR regulation, which differs from salt-sensitive and moderately salt-tolerant yeasts. In all of the halophilic fungi studied, HMGR amounts and activities were the lowest at optimal growth salinity and increased under hyposaline and hypersaline conditions. This profile paralleled isoprenylation of cellular proteins in H. werneckii. Inhibition of HMGR in vivo by lovastatin impaired the halotolerant character. HMGR may thus serve as an important molecular marker of halotolerance.

Clustering gene expression data with temporal abstractions.

This paper describes a new technique for clustering short time series coming from gene expression data. The technique is based on the labelling of the time series through temporal trend abstractions and a consequent clustering of the series on the basis of their labels. Clustering is performed at three different levels of aggregation of the original time series, so that the results are organized and visualized as a three-levels hierarchical tree. Results on simulated and on yeast data are shown. The technique appears robust and efficient and the results obtained are easy to be interpreted.

Xerotolerant mycobiota from high altitude Anapurna soil, Nepal.

Xerophilic and xerotolerant microfungi were isolated from soil samples collected in Anapurna Mountains, Nepal, at altitudes from 3000 to 5400 m. The total numbers and proportions of xerotolerant and psychrophilic strains in comparison with mesophilic mycobiota were determined by using different enumeration, selective media and four isolation methods. The most extreme xerophilic fungi were taxonomically identified as belonging to the genera Eurotium and Aspergillus. The low water activity of the soil due to dry climate and frequent binding of water in ice crystals favors a high proportion of xerotolerant fungal species. The correlation between xerotolerant and psychrophilic fungi was observed.

Salt stress affects sterol biosynthesis in the halophilic black yeast Hortaea werneckii.

Hortaea werneckii is a black yeast recently isolated from salterns in Slovenia. Some of the adaptations of halophilic microorganisms to increased salinity and osmolarity of the environment are alterations in membrane properties. By modulating the fluidity, sterols play an important role as a component of eukaryotic biological membranes. We studied the regulation of sterol biosynthesis in H. werneckii through the activity and amount of 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMG R), a key regulatory enzyme in the biosynthesis of sterols. We found some differences in the characteristics of HMG R and in its regulation by different environmental salinities in H. werneckii when compared to the mesophilic baker's yeast, Saccharomyces cerevisiae. Our results suggest that halophilic black yeast regulates sterol biosynthesis through HMG R in a different way than mesophiles, which might be a consequence of the different ecophysiology of halophilic black yeasts. From this perspective, H. werneckii is an interesting novel model organism for studies on salt stress-responsive proteins as well as on sterol biosynthesis in eukaryotes.