Hyperosmotic stress yields reprogramming of gene expression in Saccharomyces cerevisiae cells. Most of this response is orchestrated by Hog1, a stress-activated, mitogen-activated protein kinase (MAPK) homologous to human p38. We investigated, on a genomic scale, the contribution of changes in transcription rates and mRNA stabilities to the modulation of mRNA amounts during the response to osmotic stress in wild-type and hog1 mutant cells. Mild osmotic shock induces a broad mRNA destabilization; however, osmo-mRNAs are up-regulated by increasing both transcription rates and mRNA half-lives. In contrast, mild or severe osmotic stress in hog1 mutants, or severe osmotic stress in wild-type cells, yields global mRNA stabilization and sequestration of mRNAs into P-bodies. After adaptation, the absence of Hog1 affects the kinetics of P-bodies disassembly and the return of mRNAs to translation. Our results indicate that regulation of mRNA turnover contributes to coordinate gene expression upon osmotic stress, and that there are both specific and global controls of mRNA stability depending on the strength of the osmotic stress.

As an adaptive response to new conditions, mRNA concentrations in eukaryotes are readjusted after any environmental change. Although mRNA concentrations can be modified by altering synthesis and/or degradation rates, the rapidity of the transition to a new concentration depends on the regulation of mRNA stability. There are several plausible transcriptional strategies following environmental change, reflecting different degrees of compromise between speed of response and cost of synthesis. The recent development of genomic techniques now enables researchers to determine simultaneously (either directly or indirectly) the transcription rates and mRNA half-lifes, together with mRNA concentrations, corresponding to all yeast genes. Such experiments could provide a new picture of the transcriptional response, by enabling us to characterize the kinetic strategies that are used by different genes under given environmental conditions. Gene expression changes in eukaryotesGene expression in eukaryotes is a complex process that involves numerous successive steps, from the binding of transcription factors to their target sequence to the posttranslational modification of proteins. After any environmental change (e.g. a temperature shift), the cell adapts to the new circumstances by, among other responses, altering the expression of certain genes. Each step of gene expression can be quantitatively regulated. However, it is not always recognized that the rate at which gene expression changes is as important as the magnitude of that change. 77Cells need to cope with the 'time factor' throughout the process of modification of gene expression. For example, the transcription and translation processes take place at a limited speed. RNA polymerase II has been calculated to travel at ~18-42 nucleotides per second on chromatin templates [1][2][3][4][5]. This speed might not be constant across all genes and conditions, but if we take it to be a representative average value, then the time required to 'read' a gene is not negligible: 25-50 seconds for 1 kb (the average length of a yeast gene [6]); 2-3 minutes for a typical mammalian gene [7]; and up to 16 hours for certain long intron-containing human genes [3]. Pausing and termination further delay the release of mRNA molecules from the genes (as discussed in Ref. [4]). Moreover, maturation and transport of the mRNA to the cytoplasm [4,8], and translation and transport of the protein to its correct subcellular location are also time-consuming processes. Therefore, the appearance of a 'functional protein' after a 'transcription order' has been received can take from several minutes in unicellular eukaryotes to several hours for long genes in vertebrates. This limits how fast a cell can react to environmental shifts. Furthermore, an optimal response requires an ordered sequence of gene expression changes. Therefore, the cell must control the timing of these changes in a gene-specific manner.Here, we focus on the transcription kinetics of the yeast Saccharomyces cerevisiae, highlighting ...

Acid pretreatment of lignocellulosic biomass releases furan and phenolic compounds, which are toxic to microorganisms used for subsequent fermentation. In this study, we isolated new microorganisms for depletion of inhibitors in lignocellulosic acid hydrolysates. A sequential enrichment strategy was used to isolate microorganisms from soil. Selection was carried out in a defined mineral medium containing a mixture of ferulic acid (5 mM), 5-hydroxymethylfurfural (5-HMF, 15 mM), and furfural (20 mM) as the carbon and energy sources, followed by an additional transfer into a corn stover hydrolysate (CSH) prepared using dilute acid. Subsequently, based on stable growth on these substrates, six isolates--including five bacteria related to Methylobacterium extorquens, Pseudomonas sp, Flavobacterium indologenes, Acinetobacter sp., Arthrobacter aurescens, and one fungus, Coniochaeta ligniaria--were chosen. All six isolates depleted toxic compounds from defined medium, but only C. ligniaria C8 (NRRL 30616) was effective at eliminating furfural and 5-HMF from CSH. C. ligniaria NRRL 30616 may be useful in developing a bioprocess for inhibitor abatement in the conversion of lignocellulosic biomass to fuels and chemicals.

An a-amylase inhibitor that inhibits insect and mammalian a-amylases, but not plant a-amylases, is present in seeds of the common bean (Phaseolus vulgaris). We have purified the a-amylase inhibitor by using a selective heat treatment in acidic medium and affinity chromatography with porcine pancreas a-amylase coupled to agarose. Under sodium dodecyl sulfate gel electrophoresis, the purified inhibitor gave rise to five bands with mobilities corresponding to molecular masses ranging from 14 to 19 kDa. N-terminal sequencing (up to 15 amino acids) of the polypeptides obtained from these bands resulted in only two different sequences matching two stretches of the amino acid sequence deduced from an already described lectin gene [Hoffman, L. M. (1984) J. Mol. Appl. Gen. 2, [447][448][449][450][451][452][453]. This gene is different from but closely related to the genes that code for phytohemagglutinin, the major lectin of bean. Further evidence based on amino acid composition, identification of a precursor, and recognition of the product of the gene (expressed in Escherichia coli) by an anti-a-amylase inhibitor serum confirms that the inhibitor is encoded by this or a closely related lectin gene. This finding assigns a biological function, which has been described at the molecular level, to a plant lectin gene product and supports the defense role postulated for seed lectins. The lack of homology with other families of enzyme inhibitors suggests that this may be the first member of a new family of plant enzyme inhibitors.

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