Ty1 integrase overexpression leads to integration of non-Ty1 DNA fragments into the genome of Saccharomyces cerevisiae

The integrase of the Saccharomyces cerevisiae retrotransposon Ty1 integrates Ty1 cDNA into genomic DNA likely via a transesterification reaction. Little is known about the mechanisms ensuring that integrase does not integrate non-Ty DNA fragments. In an effort to elucidate the conditions under which Ty1 integrase accepts non-Ty DNA as substrate, PCR fragments encompassing a selectable marker gene were transformed into yeast strains overexpressing Ty1 integrase. These fragments do not exhibit similarity to Ty1 cDNA except for the presence of the conserved terminal dinucleotide 5′-TG-CA-3′. The frequency of fragment insertion events increased upon integrase overexpression. Characterization of insertion events by genomic sequencing revealed that most insertion events exhibited clear hallmarks of integrase-mediated reactions, such as 5 bp target site duplication and target site preferences. Alteration of the terminal dinucleotide abolished the suitability of the PCR fragments to serve as substrates. We hypothesize that substrate specificity under normal conditions is mainly due to compartmentalization of integrase and Ty cDNA, which meet in virus-like particles. In contrast, recombinant integrase, which is not confined to virus-like particles, is able to accept non-Ty DNA, provided that it terminates in the proper dinucleotide sequence

Sudden and gradual responses of phytoplankton to global climate change: case studies from two large, shallow lakes (Balaton, Hungary and the Neusiedlersee Austria/Hungary)

This paper analyses two phytoplankton long-term datasets; both are from large, temperate shallow lakes. The main difference between them is that phytoplankton growth in Lake Balaton remained severely P-limited despite P-driven eutrophication during the last 30 years, whereas extremely high turbidity causes a permanent light limitation in Neusiedlersee and therefore an increase in P-loadings did not result in a similar increase in phytoplankton biomass. Neusiedlersee is a (slightly) saline inland lake. In Lake Balaton, the blue-green alga Cylindrospermopsis raciborskii blooms invariably if the July-august temperature deviates positively from a 30-year average by ca. 2 °C. A supposed global warming is predicted to cause a higher frequency (but not intensity!) of these blooms. Neusiedlersee is very shallow and therefore regulation techniques cannot prevent water levels sinking in successive dry years. Annual averages of phytoplankton seem to follow quite a regular, wave-like cyclicity. Such cycles can be recognised in the population records of the characteristic species. Similar changes were seen in changes of water level, conductivity, inorganic-P, inorganic N-forms and nutrient ratios. How phytoplankton species can follow a climatic cycle that covers 200 to 500 generations has not yet become clear. Because of reasons discussed in the paper, neither of the two cases can be generalised; each is quite individual

Environmental and Genetic Determinants of Colony Morphology in Yeast

Nutrient stresses trigger a variety of developmental switches in the budding yeast Saccharomyces cerevisiae. One of the least understood of such responses is the development of complex colony morphology, characterized by intricate, organized, and strain-specific patterns of colony growth and architecture. The genetic bases of this phenotype and the key environmental signals involved in its induction have heretofore remained poorly understood. By surveying multiple strain backgrounds and a large number of growth conditions, we show that limitation for fermentable carbon sources coupled with a rich nitrogen source is the primary trigger for the colony morphology response in budding yeast. Using knockout mutants and transposon-mediated mutagenesis, we demonstrate that two key signaling networks regulating this response are the filamentous growth MAP kinase cascade and the Ras-cAMP-PKA pathway. We further show synergistic epistasis between Rim15, a kinase involved in integration of nutrient signals, and other genes in these pathways. Ploidy, mating-type, and genotype-by-environment interactions also appear to play a role in the controlling colony morphology. Our study highlights the high degree of network reuse in this model eukaryote; yeast use the same core signaling pathways in multiple contexts to integrate information about environmental and physiological states and generate diverse developmental outputs

Molecular interactions between Hel2 and RNA supporting ribosome-associated quality control

Ribosome-associated quality control (RQC) pathways monitor and respond to stalling of the translating ribosome. Here the authors show that the ribosome associated RQC factor Hel2/ZNF598, an E3 ubiquitin ligase, generally interacts with mRNAs in the vicinity of stop codons

Biochemia magnezu

Magnesium is essential for biochemical functions of cells. Since Mg2+ has a relatively low ionic radius in proportion to the size of the nucleus (0.86 versus 1.14 f A for Ca2+), it shows exceptional biochemical activity. Due to its physicochemical properties, intracellular magnesium can bind to the nucleus, ribosomes, cell membranes or macromolecules occurring in the cell’s cytosol. It is indispensable for the nucleus to function as a whole and for the maintenance of physical stability as well as aggregation of rybosomes into polysomes able to initiate protein synthesis. Mg2+ can also act as a cofactor for ribonucleic acid enzymes (ribozymes) capable of specifically recognizing and cleaving the target mRNA. As an essential cofactor in NER, BER, MMR processes, Mg2+ is required for the removal of DNA damage. An activator of over 300 different enzymes, magnesium participates in many metabolic processes, such as glycolysis, Krebs cycle, β-oxidation or ion transport across cell membranes. Mg2+ plays a key role in the regulation of functions of mitochondria, including the control of their volume, composition of ions and ATP production.Magnez jest składnikiem niezbędnym dla zasadniczych funkcji biochemicznych komórki. Ponieważ Mg2+ ma relatywnie mały promień w stosunku do wymiarów jądra (0.86 i 1.14 A odpowiednio dla Mg2+ i Ca2+), wykazuje dużą aktywność biochemiczną. Dzięki właściwościom fizykochemicznym śródkomórkowy Mg2+ może wiązać się z jądrem komórkowym, rybosomami, błonami komórkowymi oraz makromolekułami cytosolu komórki. Magnez jest niezbędny dla funkcjonowania jądra komórkowego jako całości oraz utrzymania fizycznej stabilności i agregacji rybosomów do polisomów zdolnych do biosyntezy białka. Odgrywa on również rolą kofaktora katalitycznych cząsteczek RNA (rybozymów), odpowiedzialnych za specyficzne rozpoznawanie i fragmentację docelowego mRNA. Jako kofaktor w procesach: NER, BER, MMR, przyczynia się do usuwania uszkodzeń DNA. Magnez, będąc aktywatorem ponad 300 różnych enzymów, uczestniczy w przebiegu wielu szlaków metabolicznych, takich jak glikoliza, cykl Krebsa, β-oksydacja czy transport jonów poprzez błony komórkowe. Odgrywa on ponadto bardzo ważną rolę w regulowaniu funkcji mitochondriów, łącznie z regulacją ich wielkości, kompozycją jonów, a także bioenergetyką i regulacją produkcji ATP