The ability of Desulfovibrio vulgaris Hildenborough to reduce, and therefore contain, toxic and radioactive metal waste has made all factors that affect the physiology of this organism of great interest. Increased salinity is an important and frequent fluctuation faced by D. vulgaris in its natural habitat. In liquid culture, exposure to excess salt resulted in striking elongation of D. vulgaris cells. Using data from transcriptomics, proteomics, metabolite assays, phospholipid fatty acid profiling, and electron microscopy, we used a systems approach to explore the effects of excess NaCl on D. vulgaris. In this study we demonstrated that import of osmoprotectants, such as glycine betaine and ectoine, is the primary mechanism used by D. vulgaris to counter hyperionic stress. Several efflux systems were also highly up-regulated, as was the ATP synthesis pathway. Increases in the levels of both RNA and DNA helicases suggested that salt stress affected the stability of nucleic acid base pairing. An overall increase in the level of branched fatty acids indicated that there were changes in cell wall fluidity. The immediate response to salt stress included up-regulation of chemotaxis genes, although flagellar biosynthesis was down-regulated. Other down-regulated systems included lactate uptake permeases and ABC transport systems. The results of an extensive NaCl stress analysis were compared with microarray data from a KCl stress analysis, and unlike many other bacteria, D. vulgaris responded similarly to the two stresses. Integration of data from multiple methods allowed us to develop a conceptual model for the salt stress response in D. vulgaris that can be compared to those in other microorganisms.Originally isolated in 1946 from clay soils in Hildenborough, Kent, United Kingdom, Desulfovibrio vulgaris Hildenborough belongs to the sulfate-reducing class of bacteria that are ubiquitous in nature (23, 45). These anaerobes generate energy by reducing sulfate (42) and play important roles in global sulfur cycling and complete mineralization of organic matter. D. vulgaris has been implicated in biocorrosion of oil and gas pipelines both on land and in the ocean (5, 23, 57). Members of this species have also been found to reduce metals in sediments and soils with high concentrations of NaCl and a milieu of toxic metals (6) and to cope with salt stresses that result from environmental hydration-dehydration cycles. An understanding of the ability of D. vulgaris to survive in the presence of high concentrations of NaCl and osmotic stress is critical for determining the biogeochemistry at metal-contaminated sites for bioremediation and natural attenuation and for predicting the potential for biocorrosion of pipelines and tanks in soils, sediments, and off-shore oil production facilities (8,38,62). The availability of an annotated genomic sequence for D. vulgaris makes this organism ideal for studying the complex physiology of sulfate-reducing bacteria (25).The bacterial response to hyperionic stress includes a range of mechan...

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We have developed a proteomics technology featuring on-line three-dimensional liquid chromatography coupled to tandem mass spectrometry (3D LC-MS/MS). Using 3D LC-MS/MS, the yeast-soluble, urea-solubilized peripheral membrane and SDS-solubilized membrane protein samples collectively yielded 3019 unique yeast protein identifications with an average of 5.5 peptides per protein from the 6300-gene Saccharomyces Genome Database searched with SEQUEST. A single run of the urea-solubilized sample yielded 2255 unique protein identifications, suggesting high peak capacity and resolving power of 3D LC-MS/MS. After precipitation of SDS from the digested membrane protein sample, 3D LC-MS/MS allowed the analysis of membrane proteins. Among 1221 proteins containing two or more predicted transmembrane domains, 495 such proteins were identified. The improved yeast proteome data allowed the mapping of many metabolic pathways and functional categories. The 3D LC-MS/MS technology provides a suitable tool for global proteome discovery.

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This paper describes the molecular structure dependent thermoresponsive behaviors of pyrrolidone-based water-soluble polymers. A series of well-defined poly[N-(2-methacryloyloxyethyl)pyrrolidone] (PNMEP), poly[N-(3-acryloyloxypropyl)pyrrolidone] (PNAPP), and poly[N-(3-methacryloyloxypropyl)pyrrolidone] (PNMPP) were synthesized via visible light activating RAFT polymerization at 25 °C. Kinetic studies indicate a rapid and well-controlled behavior of this polymerization. Gel permeation chromatography (GPC) and 1H NMR analysis confirm their intact molecular structure, well-defined molecular weight, and narrow distribution. Laser light scattering and temperature-variable 1H NMR analyses demonstrate that the cloud point of a PNMEP sample at a degree of polymerization (DP) of 96 is 1.5 °C lower than that of PNAPP at a DP = 104. Additional backbone methyl groups in PNMPP lead to a dramatic cloud point lowering, e.g., cloud point of PNMPP at a DP = 100 is 37 °C lower than that of PNAPP at a DP = 104. This is contrary to what was observed in poly(N-isopropylacrylamide) (PNIPA) and its polymethacrylamide analogues. These pyrrolidone-based polymers show a dramatic solvent isotopic effect that is different from that of PNIPA; e.g., the cloud point of PNMEP at a DP = 237 is 8.5 °C lower in D2O than in H2O. Increasing polymer chain length or hydrophobicity may suppress this solvent isotopic effect. This phase transition is correlated to Hofmeister series but more sensitive than PNIPA. Na2CO3 dramatically lowers cloud point, while NaI significantly improves cloud point, up to full dissolution in H2O at 95 °C. The solvent isotopic effect in NaCl or Na2CO3 solution is the same as what observed in solution absent of salt. Upon heating D2O solution of PNMEP, the polymer first forms the hydrated irregular colloidal aggregates near the cloud point, the phase transition occurs at the fully hydrated state at cloud point, and further heating leads to the dehydration and separation from D2O. However, in NaCl solution, the dehydration of PNMEP occurs subsequently from apolar backbones, spacers, and finally pyrrolidone groups.

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Background: The role of the RNA polymerase sigma factor RpoN in regulation of gene expression in Geobacter sulfurreducens was investigated to better understand transcriptional regulatory networks as part of an effort to develop regulatory modules for genome-scale in silico models, which can predict the physiological responses of Geobacter species during groundwater bioremediation or electricity production.