Positional effects of tRNA genes: transfer RNA genes as chromatin boundaries in Saccharomyces cerevisiae

Recently, much evidence has been brought forth into the scientific community supporting the idea that RNA Polymerase III transcribed regions of DNA may serve as chromosomal landmarks for silencing. Transfer RNA genes are known to involve themselves in several extra-transcriptional functions within the chromosome, including the pausing of replication forks, Ty element integration, tRNA position effects (repression of neighboring genes), acting as a barrier to the spread of heterochromatin, and over-riding nuclosome positioning sequences. Our results suggest that many tRNA genes may serve these functions as well as exhibiting behavior similar to metazoan insulators. Also, ETC (Extra TFIIIC) sites within Saccharomyces cerevisiae, which bind only TFIIIC may also act as barriers or insulators. Our results support the idea that extra-transcriptional functions of RNA Polymerase III factors may be widespread and important contributors to genome biology

Functional Characterization of the Chlamydomonas reinhardtii ERG3 Ortholog, a Gene Involved in the Biosynthesis of Ergosterol

The predominant sterol in the membranes of the alga Chlamydomonas reinhardtii is ergosterol, which is commonly found in the membranes of fungi, but is rarely found in higher plants. Higher plants and fungi synthesize sterols by different pathways, with plants producing cycloartenol as a precursor to end-product sterols, while non-photosynthesizing organisms like yeast and humans produce lanosterol as a precursor. Analysis of the C. reinhardtii genome sequence reveals that this algae is also likely to synthesize sterols using a pathway resembling the higher plant pathway, indicating that its sterols are synthesized somewhat differently than in fungi. The work presented here seeks to establish experimental evidence to support the annotated molecular function of one of the sterol biosynthetic genes in the Chlamydomonas genome.A gene with homology to the yeast sterol C-5 desaturase, ERG3, is present in the Chlamydomonas genome. To test whether the ERG3 ortholog of C. reinhardtii encodes a sterol C-5 desaturase, Saccharomyces cerevisiae ERG3 knockout strains were created and complemented with a plasmid expressing the Chlamydomonas ERG3. Expression of C. reinhardtii ERG3 cDNA in erg3 null yeast was able to restore ergosterol biosynthesis and reverse phenotypes associated with lack of ERG3 function.Complementation of the yeast erg3 null phenotypes strongly suggests that the gene annotated as ERG3 in C. reinhardtii functions as a sterol C-5 desaturase

Gaseous emissions during concurrent combustion of biomass and non-recyclable municipal solid waste

Background: Biomass and municipal solid waste offer sustainable sources of energy; for example to meet heat and electricity demand in the form of combined cooling, heat and power. Combustion of biomass has a lesser impact than solid fossil fuels (e. g. coal) upon gas pollutant emissions, whilst energy recovery from municipal solid waste is a beneficial component of an integrated, sustainable waste management programme. Concurrent combustion of these fuels using a fluidised bed combustor may be a successful method of overcoming some of the disadvantages of biomass (high fuel supply and distribution costs, combustion characteristics) and characteristics of municipal solid waste (heterogeneous content, conflict with materials recycling). It should be considered that combustion of municipal solid waste may be a financially attractive disposal route if a 'gate fee' value exists for accepting waste for combustion, which will reduce the net cost of utilising relatively more expensive biomass fuels. Results: Emissions of nitrogen monoxide and sulphur dioxide for combustion of biomass are suppressed after substitution of biomass for municipal solid waste materials as the input fuel mixture. Interactions between these and other pollutants such as hydrogen chloride, nitrous oxide and carbon monoxide indicate complex, competing reactions occur between intermediates of these compounds to determine final resultant emissions. Conclusions: Fluidised bed concurrent combustion is an appropriate technique to exploit biomass and municipal solid waste resources, without the use of fossil fuels. The addition of municipal solid waste to biomass combustion has the effect of reducing emissions of some gaseous pollutants

Mitogen Activated Protein Kinase Activated Protein Kinase 2 Regulates Actin Polymerization and Vascular Leak in Ventilator Associated Lung Injury

Mechanical ventilation, a fundamental therapy for acute lung injury, worsens pulmonary vascular permeability by exacting mechanical stress on various components of the respiratory system causing ventilator associated lung injury. We postulated that MK2 activation via p38 MAP kinase induced HSP25 phosphorylation, in response to mechanical stress, leading to actin stress fiber formation and endothelial barrier dysfunction. We sought to determine the role of p38 MAP kinase and its downstream effector MK2 on HSP25 phosphorylation and actin stress fiber formation in ventilator associated lung injury. Wild type and MK2−/− mice received mechanical ventilation with high (20 ml/kg) or low (7 ml/kg) tidal volumes up to 4 hrs, after which lungs were harvested for immunohistochemistry, immunoblotting and lung permeability assays. High tidal volume mechanical ventilation resulted in significant phosphorylation of p38 MAP kinase, MK2, HSP25, actin polymerization, and an increase in pulmonary vascular permeability in wild type mice as compared to spontaneous breathing or low tidal volume mechanical ventilation. However, pretreatment of wild type mice with specific p38 MAP kinase or MK2 inhibitors abrogated HSP25 phosphorylation and actin polymerization, and protected against increased lung permeability. Finally, MK2−/− mice were unable to phosphorylate HSP25 or increase actin polymerization from baseline, and were resistant to increases in lung permeability in response to HVT MV. Our results suggest that p38 MAP kinase and its downstream effector MK2 mediate lung permeability in ventilator associated lung injury by regulating HSP25 phosphorylation and actin cytoskeletal remodeling

The Saccharomyces cerevisiae TRT2 tRNA(Thr) gene upstream of STE6 is a barrier to repression in MATα cells and exerts a potential tRNA position effect in MATa cells

A growing body of evidence suggests that genes transcribed by RNA polymerase III exhibit multiple functions within a chromosome. While the predominant function of these genes is the synthesis of RNA molecules, certain RNA polymerase III genes also function as genomic landmarks. Transfer RNA genes are known to exhibit extra-transcriptional activities such as directing Ty element integration, pausing of replication forks, overriding nucleosome positioning sequences, repressing neighboring genes (tRNA position effect), and acting as a barrier to the spread of repressive chromatin. This study was designed to identify other tRNA loci that may act as barriers to chromatin-mediated repression, and focused on TRT2, a tRNA(Thr) adjacent to the STE6 α2 operator. We show that TRT2 acts as a barrier to repression, protecting the upstream CBT1 gene from the influence of the STE6 α2 operator in MATα cells. Interestingly, deletion of TRT2 results in an increase in CBT1 mRNA levels in MATa cells, indicating a potential tRNA position effect. The transcription of TRT2 itself is unaffected by the presence of the α2 operator, suggesting a hierarchy that favors assembly of the RNA polymerase III complex versus assembly of adjacent α2 operator-mediated repressed chromatin structures. This proposed hierarchy could explain how tRNA genes function as barriers to the propagation of repressive chromatin

Modulation of Yeast Genome Expression in Response to Defective RNA Polymerase III-Dependent Transcription

We used genome-wide expression analysis in Saccharomyces cerevisiae to explore whether and how the expression of protein-coding, RNA polymerase (Pol) II-transcribed genes is influenced by a decrease in RNA Pol III-dependent transcription. The Pol II transcriptome was characterized in four thermosensitive, slow-growth mutants affected in different components of the RNA Pol III transcription machinery. Unexpectedly, we found only a modest correlation between altered expression of Pol II-transcribed genes and their proximity to class III genes, a result also confirmed by the analysis of single tRNA gene deletants. Instead, the transcriptome of all of the four mutants was characterized by increased expression of genes known to be under the control of the Gcn4p transcriptional activator. Indeed, GCN4 was found to be translationally induced in the mutants, and deleting the GCN4 gene eliminated the response. The Gcn4p-dependent expression changes did not require the Gcn2 protein kinase and could be specifically counteracted by an increased gene dosage of initiator tRNA(Met). Initiator tRNA(Met) depletion thus triggers a GCN4-dependent reprogramming of genome expression in response to decreased Pol III transcription. Such an effect might represent a key element in the coordinated transcriptional response of yeast cells to environmental changes