Evaluation of Bottlenecks in the Late Stages of Protein Secretion in Bacillus subtilis

Despite a high capacity for secretion of homologous proteins, the secretion of heterologous proteins by Bacillus subtilis is frequently inefficient. In the present studies, we have investigated and compared bottlenecks in the secretion of four heterologous proteins: Bacillus lichenifomis α-amylase (AmyL), Escherichia coli TEM β-lactamase (Bla), human pancreatic α-amylase (HPA), and a lysozyme-specific single-chain antibody. The same expression and secretion signals were used for all four of these proteins. Notably, all identified bottlenecks relate to late stages in secretion, following translocation of the preproteins across the cytoplasmic membrane. These bottlenecks include processing by signal peptidase, passage through the cell wall, and degradation in the wall and growth medium. Strikingly, all translocated HPA was misfolded, its stability depending on the formation of disulfide bonds. This suggests that the disulfide bond oxidoreductases of B. subtilis cannot form the disulfide bonds in HPA correctly. As the secretion bottlenecks differed for each heterologous protein tested, it is anticipated that the efficient secretion of particular groups of heterologous proteins with the same secretion bottlenecks will require the engineering of specifically optimized host strains.     

Geochemistry and microbial ecology in alkaline hot springs of Ambitle Island,Papua New Guinea

The availability of microbiological and geochemical data from island-based and high-arsenic hydrothermal systems is limited. Here, the microbial diversity in island-based hot springs on Ambitle Island (Papua New Guinea) was investigated using culture-dependent and -independent methods. Waramung and Kapkai are alkaline springs high in sulfide and arsenic, related hydrologically to previously described hydrothermal vents in nearby Tutum Bay. Enrichments were carried out at 24 conditions with varying temperature (45, 80 °C), pH (6.5, 8.5), terminal electron acceptors (O₂, SO₄ ^2?, S⁰, NO₃ ^?), and electron donors (organic carbon, H₂, As^III). Growth was observed in 20 of 72 tubes, with media targeting heterotrophic metabolisms the most successful. 16S ribosomal RNA gene surveys of environmental samples revealed representatives in 15 bacterial phyla and 8 archaeal orders. While the Kapkai 4 bacterial clone library is primarily made up of Thermodesulfobacteria (74 %), no bacterial taxon represents a majority in the Kapkai 3 and Waramung samples (40 % Proteobacteria and 39 % Aquificae, respectively). Deinococcus/Thermus and Thermotogae are observed in all samples. The Thermococcales dominate the archaeal clone libraries (65–85 %). Thermoproteales, Desulfurococcales, and uncultured Eury- and Crenarchaeota make up the remaining archaeal taxonomic diversity. The culturing and phylogenetic results are consistent with the geochemistry of the alkaline, saline, and sulfide-rich fluids. When compared to other alkaline, island-based, high-arsenic, or shallow-sea hydrothermal communities, the Ambitle Island archaeal communities are unique in geochemical conditions, and in taxonomic diversity, richness, and evenness.     

Transgenic carnation plants obtained by Agrobacterium tumefaciens-mediated transformation of petal explants

Transgenic carnation plants were obtained after infection of petal explants with the supervirulent Agrobacterium tumefaciens strain AGLO. Southern blot techniques confirmed the transgenic nature of four transformed plants. The expression of the gus gene was verified in these plants by histochemical assays on selected shoots. It was very difficult to transfer the transgenic plants to the greenhouse due to vitrification and premature flowering.Abbreviations BA 6-benzyladenine - GA₃ gibberellic acid - gus- glucuronidase gene - MS Murashige and Skoog (1962) - NAA naphthaleneacetic acid - nptII neomycin phosphotransferase II gene - PCR polymerase chain reaction     

Differential responses of freshwater wetland soils to sulphate pollution

Sulphate (SO₄ ^2-)reduction rates are generally low in freshwaterwetlands and are regulated by the scarceavailability of the ion. Increasedconcentrations of this electron acceptor due tosulphur (S) pollution of groundwater andsurface water may, however, lead to highSO₄ ^2- reduction rates now regulatedby the availability of appropriate electrondonors. Due to variations in this availability,the response to S pollution (e.g. from surfacewater or groundwater) is expected to differbetween soils. This hypothesis was tested inlaboratory mesocosm experiments by comparingtwo wetland soil types with distinctlydifferent humus profiles: a Hydromoder and aRhizomull type. In the first type, expected tohave a higher availability of degradable soilorganic matter (SOM), SO₄ ^2-availability appeared to be rate limiting forSO₄ ^2- reduction. In the Rhizomullsoils, in contrast, the electron acceptor didnot limit SO₄ ^2- reduction rates athigher concentrations. These differences inresponse could not, however, be attributed todifferences in the various SOM fractions or inSOM densities. Eutrophication and free sulphideaccumulation, two major biogeochemical problemscaused by SO₄ ^2- pollution, occurredin both types. The absolute extent ofphosphorus mobilisation was determined by theconcentration of this element in the soil (C/Pratio), while the level of sulphideaccumulation was governed by the concentrationof dissolved iron in the pore water. It wastherefore concluded that neither the humusprofile nor the concentrations of different SOMfractions in the soils are reliable indicatorsfor the sensitivity of wetland types to Spollution.     

Development of a 16S rRNA gene-based prototype microarray for the detection of selected actinomycetes genera

Actinomycetes are known for their secondary metabolites, which have been successfully used as drugs in human and veterinary medicines. However, information on the distribution of this group of Gram-positive bacteria in diverse ecosystems and a comprehension of their activities in ecosystem processes are still scarce. We have developed a 16S rRNA-based taxonomic microarray that targets key actinomycetes at the genus level. In total, 113 actinomycete 16S rRNA probes, corresponding to 55 of the 202 described genera, were designed. The microarray accuracy was evaluated by comparing signal intensities with probe/target-weighted mismatch values and the Gibbs energy of the probe/target duplex formation by hybridizing 17 non-actinomycete and 29 actinomycete strains/clones with the probe set. The validation proved that the probe set was specific, with only 1.3% of false results. The incomplete coverage of actinomycetes by a genus-specific probe was caused by the limited number of 16S rRNA gene sequences in databases or insufficient 16S rRNA gene polymorphism. The microarray enabled discrimination between actinomycete communities from three forest soil samples collected at one site. Cloning and sequencing of 16S rRNA genes from one of the soil samples confirmed the microarray results. We propose that this newly constructed microarray will be a valuable tool for genus-level comparisons of actinomycete communities in various ecological conditions.     

Recombination: an underappreciated factor in the evolution of plant genomes

Our knowledge of recombination rates and patterns in plants is far from being comprehensive. However, compelling evidence indicates a central role for recombination, through its influences on mutation and selection, in the evolution of plant genomes. Furthermore, recombination seems to be generally higher and more variable in plants than in animals, which could be one of the primary reasons for differences in genome lability between these two kingdoms. Much additional study of recombination in plants is needed to investigate these ideas further.     

Prediction of effective genome size in metagenomic samples

We introduce a novel computational approach to predict effective genome size (EGS; a measure that includes multiple plasmid copies, inserted sequences, and associated phages and viruses) from short sequencing reads of environmental genomics (or metagenomics) projects. We observe considerable EGS differences between environments and link this with ecologic complexity as well as species composition (for instance, the presence of eukaryotes). For example, we estimate EGS in a complex, organism-dense farm soil sample at about 6.3 megabases (Mb) whereas that of the bacteria therein is only 4.7 Mb; for bacteria in a nutrient-poor, organism-sparse ocean surface water sample, EGS is as low as 1.6 Mb. The method also permits evaluation of completion status and assembly bias in single-genome sequencing projects.