High coding density on the largest Paramecium tetraurelia somatic chromosome.

Paramecium, like other ciliates, remodels its entire germline genome at each sexual generation to produce a somatic genome stripped of transposons and other multicopy elements. The germline chromosomes are fragmented by a DNA elimination process that targets heterochromatin to give a reproducible set of some 200 linear molecules 50 kb to 1 Mb in size. These chromosomes are maintained at a ploidy of 800n in the somatic macronucleus and assure all gene expression. We isolated and sequenced the largest megabase somatic chromosome in order to explore its organization and gene content. The AT-rich (72%) chromosome is compact, with very small introns (average size 25 nt), short intergenic regions (median size 202 nt), and a coding density of at least 74%, higher than that reported for budding yeast (70%) or any other free-living eukaryote. Similarity to known proteins could be detected for 57% of the 460 potential protein coding genes. Thirty-two of the proteins are shared with vertebrates but absent from yeast, consistent with the morphogenetic complexity of Paramecium, a long-standing model for differentiated functions shared with metazoans but often absent from simpler eukaryotes. Extrapolation to the whole genome suggests that Paramecium has at least 30,000 genes.

Complete genome sequence of Gluconacetobacter xylinus E25 strain--valuable and effective producer of bacterial nanocellulose.

This study reports the release of complete genome sequence of the producer of bacterial nanocellulose (BNC) - Gluconacetobacter xylinus E25, a vinegar-isolated strain. Preliminary sequence analysis revealed complexity of the genome structure and familiarized genetic basis of productive properties of E25 strain. The genome consists of one chromosome and five plasmids. Whole genome sequencing has opened up new perspectives for further bioinformatics and experimental studies allowing the elucidation of molecular mechanisms responsible for regulation of production of BNC - a valuable biomaterial.

Multiple functions of the vacuolar sorting protein Ccz1p in Saccharomyces cerevisiae.

The CCZ1 (YBR131w) gene encodes a protein required for fusion of various transport intermediates with the vacuole. Ccz1p, in a complex with Mon1p, is a close partner of Ypt7p in the processes of fusion of endosomes to vacuoles and homotypic vacuole fusion. In this work, we exploited the Ca(2+)-sensitivity of the ccz1Delta mutant to identify genes specifically interacting with CCZ1, basing on functional multicopy suppression of calcium toxicity. The presented results indicate that Ccz1p functions in the cell either in association with Mon1p and Ypt7p in fusion at the vacuolar membrane, or--separately--with Arl1p at early steps of vacuolar transport. We also show that suppression of calcium toxicity by the calcium pumps Pmr1p and Pmc1p is restricted only to the subset of mutants defective in vacuole morphology. The mechanisms of Ca(2+)-pump-mediated suppression also differ from each other, since the action of Pmr1p, but not Pmc1p, appears to require Arl1p function.

Alpha-Ketoglutarate dehydrogenase and lipoic acid synthase are important for the functioning of peroxisomes of Saccharomyces cerevisiae.

A method was devised to search for yeast mutants impaired in peroxisome functioning, indicating cross-talk between metabolic pathways. Two mutants were isolated; they are impaired in oleate utilisation and carry mutations in the KGD1 and LIP5 genes encoding the E1 component of the mitochondrial alpha-ketoglutarate dehydrogenase complex and lipoic acid synthase, respectively. The results presented indicate that the Kgd1 and Lip5 proteins are important for the expression of genes encoding peroxisomal matrix proteins, although they are not necessary for the biogenesis of this cellular compartment.

cDNA encoding protein O-mannosyltransferase from the filamentous fungus Trichoderma reesei; functional equivalence to Saccharomyces cerevisiae PMT2.

O-Mannosylation is suggested to be essential for protein secretion in Trichoderma reesei. In protein O-glycosylation, the first mannosyl residue is transferred to a serine or threonine hydroxyl group of the protein from dolichyl phosphate mannose by protein O-mannosyltransferase. In Saccharomyces cerevisiae, seven PMT genes have been cloned coding for these enzymes. In the present work, the characterisation of the pmt1 cDNA from T. reesei is reported. Sequence analysis of the predicted protein revealed the highest similarity to Schizosaccharomyces pombe Pmt and to Pmt4p of Saccharomyces cerevisiae. In contrast, expression of the T. reesei cDNA in various S. cerevisiae pmt mutants showed functional similarity to the yeast Pmt2 protein.