Natural transformation in the Ralstonia solanacearum species complex: number and size of DNA that can be transferred

Ralstonia solanacearum is a widely distributed phytopathogenic bacterium that is known to invade more than 200 host species, mainly in tropical areas. Reference strain GMI1000 is naturally transformable at in vitro and also in planta conditions and thus has the ability to acquire free exogenous DNA. We tested the ubiquity and variability of natural transformation in the four phylotypes of this species complex using 55 strains isolated from different hosts and geographical regions. Eighty per cent of strains distributed in all the phylotypes were naturally transformable by plasmids and/or genomic DNA. Transformability can be considered as a ubiquitous physiological trait in the R. solanacearum species complex. Transformation performed with two independent DNA donors showed that multiple integration events occurred simultaneously in two distant genomic regions. We also engineered a fourfold-resistant R. solanacearum GMI1000 mutant RS28 to evaluate the size of DNA exchanged during natural transformation. The results demonstrated that this bacterium was able to exchange large DNA fragments ranging from 30 to 90 kb by DNA replacement. The combination of these findings indicated that the natural transformation mechanism could be the main driving force of genetic diversification of the R. solanacearum species complex.     

Identification and validation of housekeeping genes in brains of the desert locust Schistocerca gregaria under different developmental conditions

Background  

To obtain reliable quantitative RT-PCR data, normalization relative to stable housekeeping genes is required. However, in practice, expression levels of 'typical' housekeeping genes have been found to vary between tissues and under different experimental conditions. To date, validation studies of reference genes in insects are extremely rare and have never been performed in locusts. In this study, putative housekeeping genes were identified in the desert locust, Schistocerca gregaria and two different software programs (geNorm and Normfinder) were applied to assess the stability of thesegenes.     

Effect of phytate on element bioavailability in the second generation of rats

In this paper the relation between long term consumption of a high dose of sodium phytate and the mineral status of the organism is evaluated in rats. For this purpose, element concentrations (Ca, Mg, Fe, Zn, Mn) were determined in liver, heart, testicle, bone and urine of a second generation of Wistar rats, treated with a phytate free diet (AIN-76A) and with the same diet plus 1% phytate as sodium salt. The most significant differences were observed between bone zinc contents of male and female rats. The zinc content of rats fed a 1% phytate as sodium salt diet resulted clearly lower than that found in no-phytate treated rats. Hence, it is concluded that when up to 1% of phytate as sodium salt is consumed together with an equilibrated purified diet (free of phytate), no decrease in mineral bioavailability is observed in second generation rats, except for an indication of lower zinc availability by lower zinc concentrations in some organs, mainly bone. However, using this purified diet, the zinc concentration in bone resulted around 10 times higher than found in rats fed with a common non purified rat chow.     

Excision and integration of a self-transmissible replicon of Streptomyces ambofaciens

When Streptomyces ambofaciens OSF was crossed with the plasmid-free Streptomyces lividans TK24, almost all S. lividans exconjugants contained the free 11.1-kb plasmid pOS1. Southern hybridizations showed that pOS1 was derived from the integrated copy of previously recognized plasmid pSAM2 present in strain OSF. A shorter derivative of pOS1 was constructed carrying the tsr gene in a non-essential region, and this pOS7 plasmid was used in transformation experiments with protoplasts of S. ambofaciens ATCC23877 (containing pSAM2 only as an integrated sequence) and S. ambofaciens DSM40697 (devoid of pSAM2-related forms). In both cases, some clones carrying pOS7 in an integrated state were found. Integration into strain ATCC23877 was into the pre-existing integrated copy of pSAM2. In contrast, plasmid pOS7 integrated through specific plasmidic and chromosomal sites into strain DSM40697. Thus it is probable that pSAM2 integrates by interaction between preferred regions of the plasmid and host genomes.     

Flavonoids from Pinus sylvestris needles and their variation in trees of different origin grown for nearly a century at the same area

Flavonoids in needles of Scots pine planted in 1912–1914 in Poland from seeds originating from different parts of Europe, were isolated, chemically characterised and analysed by HPLC. It was shown that flavonoid profiles were similar in all tested populations and were different from those previously reported for Scots pine seedlings. They included taxifolin, taxifolin 3′-O-glucoside, quercetin as well as quercetin 3-O-glucoside and 3′-O-glucoside. The quercetin 3-O-glucoside could be found only in a trace amount in all samples and quercetin 3′-O-glucoside appeared in all samples regardless their origin. The relative concentration of taxifolin 3′-O-glucoside, quercetin, taxifolin and total flavonoids showed dependence on the origin of seeds; needles from high latitude populations contained smaller amounts of these compounds. Presented data clearly indicate that Scots pine contain glycosidases specific for glycosylation at C-3′ rather than at C-3. Besides, they indicate that long lasting influence of similar environmental factors is not able to change genetic regulatory systems responsible for flavonoid biosynthesis.     

Soil-specific limitations for access and analysis of soil microbial communities by metagenomics

Metagenomics approaches represent an important way to acquire information on the microbial communities present in complex environments like soil. However, to what extent do these approaches provide us with a true picture of soil microbial diversity? Soil is a challenging environment to work with. Its physicochemical properties affect microbial distributions inside the soil matrix, metagenome extraction and its subsequent analyses. To better understand the bias inherent to soil metagenome 'processing', we focus on soil physicochemical properties and their effects on the perceived bacterial distribution. In the light of this information, each step of soil metagenome processing is then discussed, with an emphasis on strategies for optimal soil sampling. Then, the interaction of cells and DNA with the soil matrix and the consequences for microbial DNA extraction are examined. Soil DNA extraction methods are compared and the veracity of the microbial profiles obtained is discussed. Finally, soil metagenomic sequence analysis and exploitation methods are reviewed.     

Recombinant Environmental Libraries Provide Access to Microbial Diversity for Drug Discovery from Natural Products

To further explore possible avenues for accessing microbial biodiversity for drug discovery from natural products, we constructed and screened a 5,000-clone “shotgun” environmental DNA library by using an Escherichia coli-Streptomyces lividans shuttle cosmid vector and DNA inserts from microbes derived directly (without cultivation) from soil. The library was analyzed by several means to assess diversity, genetic content, and expression of heterologous genes in both expression hosts. We found that the phylogenetic content of the DNA library was extremely diverse, representing mostly microorganisms that have not been described previously. The library was screened by PCR for sequences similar to parts of type I polyketide synthase genes and tested for the expression of new molecules by screening of live colonies and cell extracts. The results revealed new polyketide synthase genes in at least eight clones. In addition, at least five additional clones were confirmed by high-pressure liquid chromatography analysis and/or biological activity to produce heterologous molecules. These data reinforce the idea that exploiting previously unknown or uncultivated microorganisms for the discovery of novel natural products has potential value and, most importantly, suggest a strategy for developing this technology into a realistic and effective drug discovery tool.