Proteomic insights into adaptive responses of Saccharomyces cerevisiae to the repeated vacuum fermentation

The responses and adaptation mechanisms of the industrial Saccharomyces cerevisiae to vacuum fermentation were explored using proteomic approach. After qualitative and quantitative analyses, a total of 106 spots corresponding to 68 different proteins were identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. The differentially expressed proteins were involved in amino acid and carbohydrate metabolisms, various signal pathways (Ras/MAPK, Ras–cyclic adenosine monophosphate, and HOG pathway), and heat shock and oxidative responses. Among them, alternations in levels of 17 proteins associated with carbohydrate metabolisms, in particular, the upregulations of proteins involved in glycolysis, trehalose biosynthesis, and the pentose phosphate pathway, suggested vacuum-induced redistribution of the metabolic fluxes. The upregulation of 17 heat stress and oxidative response proteins indicated that multifactors contributed to oxidative stresses by affecting cell redox homeostasis. Taken together with upregulation in 14-3-3 proteins levels, 22 proteins were detected in multispots, respectively, indicating that vacuum might have promoted posttranslational modifications of some proteins in S. cerevisiae. Further investigation revealed that the elevations of the differentially expressed proteins were mainly derived from vacuum stress rather than the absence of oxygen. These findings provide new molecular mechanisms for understanding of adaptation and tolerance of yeast to vacuum fermentation. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

A cDNA Microarray for Crassostrea virginica and C. gigas

The eastern oyster, Crassostrea virginica, and the Pacific oyster, C. gigas, are species of global economic significance as well as important components of estuarine ecosystems and models for genetic and environmental studies. To enhance the molecular tools available for oyster research, an international group of collaborators has constructed a 27,496-feature cDNA microarray containing 4460 sequences derived from C. virginica, 2320 from C. gigas, and 16 non-oyster DNAs serving as positive and negative controls. The performance of the array was assessed by gene expression profiling using gill and digestive gland RNA derived from both C. gigas and C. virginica, and digestive gland RNA from C. ariakensis. The utility of the microarray for detection of homologous genes by cross-hybridization between species was also assessed and the correlation between hybridization intensity and sequence homology for selected genes determined. The oyster cDNA microarray is publicly available to the research community on a cost-recovery basis.     

Isolation and expression analysis of low temperature-induced genes in white poplar (Populus alba)

Poplar is an important crop and a model system to understand molecular processes of growth, development and responses to environmental stimuli in trees. In this study, we analyzed gene expression in white poplar (Populus alba) plants subjected to chilling. Two forward suppression-subtractive-hybridization libraries were constructed from P. alba plants exposed to low non-freezing temperature for 6 or 48 h. Hundred and sixty-two cDNAs, 54 from the 6-h library and 108 from the 48-h library, were obtained. Isolated genes belonged to six categories of genes, specifically those that: (i) encode stress and defense proteins; (ii) are involved in signal transduction; (iii) are related to regulation of gene expression; (iv) encode proteins involved in cell cycle and DNA processing; (v) encode proteins involved in metabolism and energetic processes; and (vi) are involved in protein fate.Different expression patterns at 3, 6, 12, 24, 48 h at 4 °C and after a recovery of 24 h at 20 °C were observed for isolated genes, as expected according to the class in which the gene putatively belongs. Forty-four of 162 genes contained DRE/LTRE cis-elements in the 5′ proximal promoter of their orthologs in Populus trichocarpa, suggesting that they putatively belong to the CBF regulon. The results contribute new data to the list of possible candidate genes involved in cold response in poplar.     

Evolutionary Analysis of the Small Heat Shock Proteins in Five Complete Algal Genomes

Small heat shock proteins (sHSPs) are chaperones that are crucial in the heat shock response but also have important nonstress roles within the cell. sHSPs are found in all three domains of life (Bacteria, Archaea, and Eukarya). These proteins are particularly diverse within land plants and the evolutionary origin of the land plant sHSP families is still an open question. Here we describe the identification of 17 small sHSPs from the complete genome sequences of five diverse algae: Chlamydomonas reinhardtii, Cyanidioschyzon merolae, Ostreococcus lucimarinus, Ostreococcus tauri, and Thalassiosira pseudonana. Our analysis indicates that the number and diversity of algal sHSPs are not correlated with adaptation to extreme conditions. While all of the algal sHSPs identified are members of this large and important superfamily, none of these sHSPs are members of the diverse land plant sHSP families. The evolutionary relationships among the algal sHSPs and homologues from bacteria and other eukaryotes are consistent with the hypothesis that the land plant chloroplast and mitochondrion sHSPs did not originate from the endosymbionts of the chloroplast and mitochondria. In addition the evolutionary history of the sHSPs is very different from that of the HSP70s. Finally, our analysis of the algal sHSPs sequences in light of the known sHSP crystal structures and functional data suggests that the sHSPs possess considerable structural and functional diversity. Electronic supplementary material The online version of this article (doi: ) contains supplementary material, which is available to authorized users. Reviewing Editor: Dr. Rüdiger Cerff     

Histopathology in Pacific oyster (Crassostrea gigas) spat caused by the dinoflagellate Prorocentrum rhathymum

The recognition of an apparent association between seasonal oyster spat mortalities (up to 40%) and high Prorocentrum rhathymum density in the Little Swanport Estuary, Tasmania, prompted further experimental investigation into the toxicity by this dinoflagellate. Standard brine shrimp, haemolysis assays and intraperitoneal mouse bioassays revealed fast acting toxins in methanol but not aqueous extracts of P. rhathymum, with mice dying in less than 20 min. Oyster bioassays involved feeding spat (4 mm shell width) for 21 consecutive days on a diet of cultured P. rhathymum at simulated bloom densities (10⁴ cells ml⁻¹). No oyster mortality was observed, however, histopathological signs of thin, dilated gut tubules and sloughing of gut cells resembled those seen in affected field samples. In contrast to field samples, gill pathology was also observed in experimental exposure oysters.     

Effects of environmental stress on intertidal mussels and their sea star predators

Consumer stress models of ecological theory predict that predators are more susceptible to stress than their prey. Intertidal mussels, Mytilus californianus, span a vertical stress gradient from the low zone (lower stress) to the high zone (higher thermal and desiccation stress), while their sea star predators, Pisaster ochraceus, range from the low zone only into the lower edge of the mussel zone. In summer 2003, we tested the responses of sea stars and mussels to environmental stress in an experiment conducted on the Oregon coast. Mussels were transplanted from the middle of the mussel bed to cages in the low and high edges of the mussel bed. Sea star predators were added to half of the mussel cages. Mussels and sea stars were sampled between June and August for indicators of sublethal stress. Mussel growth was measured, and tissues were collected for heat shock protein (Hsp70) analyses and histological analyses of reproduction. Sea stars were weighed, and tissues were sampled for Hsp70 analyses. Mussels in high-edge cages had higher levels of total Hsp70 and exhibited spawning activity earlier in the summer than mussels in the low-edge cages. Sea stars suffered high mortality in the high edge, and low-edge sea stars lost weight but showed no differences in Hsp70 production. These results suggest that stress in the intertidal zone affected the mobile predator more than its sessile prey, which is consistent with predictions of consumer stress models. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Identification of c-type cytochromes involved in anaerobic, bacterial U(IV) oxidation

Anaerobic, bacterial reduction of water-soluble U(VI) complexes to the poorly soluble U(IV) mineral uraninite has been intensively studied as a strategy for in situ remediation of uranium-contaminated groundwater. A novel and potentially counteracting metabolic process, anaerobic, nitrate-dependent U(IV) oxidation, has recently been described in two bacterial species (Geobacter metallireducens and Thiobacillus denitrificans), but the underlying biochemistry and genetics are completely unknown. We report here that two diheme, c-type cytochromes (putatively c ₄ and c ₅ cytochromes) play a major role in nitrate-dependent U(IV) oxidation by T. denitrificans. Insertion mutations in each of the two genes encoding these cytochromes resulted in a greater than 50% decrease in U(IV) oxidation activity, and complementation in trans restored activity to wild-type levels. Sucrose-density-gradient ultracentrifugation confirmed that both cytochromes are membrane-associated. Insertion mutations in genes encoding other membrane-associated, c-type cytochromes did not diminish U(IV) oxidation. This is the first report of proteins involved in anaerobic U(IV) oxidation. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.