Heavy metal resistance patterns of Frankia strains

The sensitivity of 12 Frankia strains to heavy metals was determined by a growth inhibition assay. In general, all of the strains were sensitive to low concentrations (<0.5 mM) of Ag(1+), AsO(2)(1-), Cd(2+), SbO(2)(1-), and Ni(2+), but most of the strains were less sensitive to Pb(2+) (6 to 8 mM), CrO(4)(2-) (1.0 to 1.75 mM), AsO(4)(3-) (>50 mM), and SeO(2)(2-) (1.5 to 3.5 mM). While most strains were sensitive to 0.1 mM Cu(2+), four strains were resistant to elevated levels of Cu(2+) (2 to 5 mM and concentrations as high as 20 mM). The mechanism of SeO(2)(2-) resistance seems to involve reduction of the selenite oxyanion to insoluble elemental selenium, whereas Pb(2+) resistance and Cu(2+) resistance may involve sequestration or binding mechanisms. Indications of the resistance mechanisms for the other heavy metals were not as clear.     

Heavy metal tolerance in marine strains of Yarrowia lipolytica

Heavy metal tolerance of two marine strains of Yarrowia lipolytica was tested on solid yeast extract peptone dextrose agar plates. Based on minimum inhibitory concentration esteems, it is inferred that the two strains of Y. lipolytica were tolerant to heavy metals such as Pb(II), Cr(III), Zn(II), Cu(II), As(V), and Ni(II) ions. The impact of various heavy metal concentrations on the growth kinetics of Y. lipolytica was likewise assessed. With increased heavy metal concentration, the specific growth rate was reduced with delayed doubling time. Furthermore, biofilm development of both yeasts on the glass surfaces and in microtitre plates was assessed in presence of different heavy metals. In microtitre plates, a short lag phase of biofilm formation was noticed without the addition of heavy metals in yeast nitrogen base liquid media. A lag phase was extended over increasing metal concentrations of media. Heavy metals like Cr(VI), Cd(II), and As(V) are contrastingly influenced on biofilms’ formation of microtitre plates. Other heavy metals did not much influence on biofilms development. Thus, biofilm formation is a strategy of Y. lipolytica under stress of heavy metals has significance in bioremediation process for recovery of heavy metals from contaminated environment.

     

Heavy metal ions are potent inhibitors of protein folding

Environmental and occupational exposure to heavy metals such as cadmium, mercury and lead results in severe health hazards including prenatal and developmental defects. The deleterious effects of heavy metal ions have hitherto been attributed to their interactions with specific, particularly susceptible native proteins. Here, we report an as yet undescribed mode of heavy metal toxicity. Cd²⁺, Hg²⁺ and Pb²⁺ proved to inhibit very efficiently the spontaneous refolding of chemically denatured proteins by forming high-affinity multidentate complexes with thiol and other functional groups (IC₅₀ in the nanomolar range). With similar efficacy, the heavy metal ions inhibited the chaperone-assisted refolding of chemically denatured and heat-denatured proteins. Thus, the toxic effects of heavy metal ions may result as well from their interaction with the more readily accessible functional groups of proteins in nascent and other non-native form. The toxic scope of heavy metals seems to be substantially larger than assumed so far.     

Heavy metal tolerance potential of Aspergillus strains isolated from mining sites

Increased heavy metal pollution generated through anthropogenic activities into the environment has necessitated the need for eco-friendly remediation strategies such as mycoremediation. With a view to prospecting for fungi with heavy metal remediation potentials, the tolerance of five Aspergillus species isolated from soils of three active gold and gemstone mining sites in southwestern Nigeria to varied heavy metal concentrations was investigated. Isolated Aspergillus strains were identified based on the internal transcribed spacer 1 and 2 (ITS 1 and ITS 2) regions. Growth of Aspergillus strains were challenged with a range of varied concentrations of heavy metals: cadmium (Cd) (0–100), copper (Cu) (0–1000), lead (Pb) (0–400), arsenic (As) (0–500), and iron (Fe) (0–800) concentrations (ppm) incorporated into Malt Extract Agar (MEA) in triplicates. Mycelial radial growths were recorded at intervals of 3 days during a 13-day incubation period. Aspergillus strains were identified as A. tubingensis, A. fumigatus, A. terreus, A. nidulans, and A. nomius. A. tubingensis tolerated Cd, Cu, Pb, As, and Fe at all test concentrations (100–1000 ppm), showing no significant (p > .05) difference compared with the control. Similarly, A. nomius tolerated all concentrations of Cu, Pb, As, and Fe and only 50 ppm Cd concentrations. A. nidulans, A. terreus, and A. fumigatus, on the other hand, tolerated all concentrations of Cu, Pb, and Fe with no statistical significance (p > .05) difference from the controls. Overall, the Aspergillus species showed tolerance to heavy metal concentrations above permissible limits for contaminated soils globally. These heavy metal tolerance traits exhibited by the Aspergillus isolates may suggest that they are potential candidates for bioremediation of heavy metal–polluted environments.     

Inferring angiosperm phylogeny from EST data with widespread gene duplication

Background

Most studies inferring species phylogenies use sequences from single copy genes or sets of orthologs culled from gene families. For taxa such as plants, with very high levels of gene duplication in their nuclear genomes, this has limited the exploitation of nuclear sequences for phylogenetic studies, such as those available in large EST libraries. One rarely used method of inference, gene tree parsimony, can infer species trees from gene families undergoing duplication and loss, but its performance has not been evaluated at a phylogenomic scale for EST data in plants.

Results

A gene tree parsimony analysis based on EST data was undertaken for six angiosperm model species and Pinus, an outgroup. Although a large fraction of the tentative consensus sequences obtained from the TIGR database of ESTs was assembled into homologous clusters too small to be phylogenetically informative, some 557 clusters contained promising levels of information. Based on maximum likelihood estimates of the gene trees obtained from these clusters, gene tree parsimony correctly inferred the accepted species tree with strong statistical support. A slight variant of this species tree was obtained when maximum parsimony was used to infer the individual gene trees instead.

Conclusion

Despite the complexity of the EST data and the relatively small fraction eventually used in inferring a species tree, the gene tree parsimony method performed well in the face of very high apparent rates of duplication.

     

N-hydroxyarylamine O-acetyltransferase-deficient Escherichia coli strains are resistant to the mutagenicity of nitro compounds

In Salmonella typhimurium, a single enzyme catalyzes both the acetyl CoA-dependent O-acetylation of hydroxylamines (a key step in the activation of mutagenic nitroaromatic compounds and related aromatic and heterocyclic amines) and the N-acetylation of aromatic amines. S. typhimurium Ames test mutants lacking this activity are highly resistant to the genotoxic effects of nitro compounds. However, such mutants have not yet been obtained in Escherichia coli. We used a PCR-based method to engineer a null mutation (deletion) of the nhoA gene encoding the enzyme in E. coli and we transduced this mutation into a lacZ strain background suitable for use in mutation assays. In E. coli, as in S. typhimurium, nhoA mutants show marked resistance to nitro compound mutagenicity. The new strains provide a clean background for expression of recombinant N-acetyltransferases.     

Isolation and investigation of natural yeast strains resistant to heavy metal salts and radionuclides

The collection of yeasts (more than 2000 strains) from extreme natural environment of Kamchatka peninsular and Kuril Islands was created. 448 strains were selected for their resistance to salts of such heavy metals as Cu, Cd, Co and to high temperature (37-52 degrees C). 72% of strains appeared to be resistant to one or more selective factors. We obtained several strains able to grow on medium with 0.1 M/L nonradioactive strontium and (or) cesium. Four of this strains accumulated radioactive isotope 90Sr with 45-80% efficiency. Thus, we demonstrated that yeast strains from nature could be used for bioremediation of industrial waste solutions, polluted by radionuclides and salts of heavy metals.     

Epoxide hydrolase activity of Streptomyces strains

The discovery of epoxide hydrolases within a Streptomyces sp. strain collection is described. Screening was performed in 96 well microtiter plates using a modified 4-(p-nitrobenzyl)pyridine assay with styrene oxide, 1,2-epoxy-hexane or 3-phenyl ethylglycidate (3-PEG) as substrates. Out of 120 strains investigated, S. antibioticus Tü4, S. arenae Tü495 and S. fradiae Tü27 exhibited epoxide hydrolase activity. These strains were further investigated by performing laboratory-scale biotransformations utilizing styrene oxide, 1,2-epoxy-hexane and 3-PEG followed by subsequent quantitative analysis employing chiral gas chromatography. The highest conversions were achieved with whole cells from S. antibioticus Tü4 in the presence of 10% (v/v) DMSO. However, enantioselectivity was only satisfying (E = 31) in the presence of 5% (v/v) acetone, which allowed isolation of optically pure non-hydrolyzed (R)-styrene oxide (99% enantiomeric excess (ee)) and (S)-phenyl-1,2-ethandiol (72% ee) at 55% conversion after 24 h. The resolution of 3-PEG proceeded with slightly lower enantioselectivity albeit higher reaction rates. With S. fradiae Tü27 and S. arenae Tü495 enantioselectivity towards styrene oxide was only E = 3-4.     

Streptavidin secretion by Streptomyces lividans strains

Recombinant strains of S. lividans capable of secreting streptavidin were isolated. Various constructions containing either streptavidin gene copies integrated within a chromosome or a streptavidin gene within the secretory vector were investigated. S. lividans SA2 containing a gene copy integrated within the chromosome had the maximum productivity amounting to 60-80 per cent of the S. avidinii productivity. New vectors for Streptomyces used in the study are described.     

Plasmid pSE21 of Streptomyces erythraeus strains

Crossing of S. erythraeus 4, a laboratory strain (NRRL 2338) containing a family of plasmids with S. erythraeus 1, a plasmid-free strain resulted in formation of strain 6. A multi-copy plasmid pSE21 11.5 kb in length was isolated from S. erythraeus 6. A detailed restriction map of plasmid pSE21 was constructed. Its cloning to E. coli YM83 on vector pUC19 showed that plasmid pSE21 was not stable in E. coli. It was found that the status of plasmid pSE21 changed in relation to the physiological state of S. erythraeus 6. Southern hybridization of the plasmid pSE21 DNA with the total DNA of the cultures of S. erythraeus 1 maintained for various periods at 4 degrees C demonstrated that plasmid pSE21 was present in S. erythraeus 1 in an autonomous state in 0.1 to 0.2 copies per genome. The number of the plasmid pSE21 copies could be decreased. The chromosomal DNA of S. erythraeus 1 contained the DNA sequences highly homologous to those of plasmid pSE21. It was assumed that during the crossing of S. erythraeus 4 with S. erythraeus 1 the genetic element from the donor strain was transferred to the recipient strain which in some way changed the plasmid pSE21 status and imparted the multicopy pattern to it. Further investigation of the plasmid pSE21 properties and construction of a vector for S. erythraeus on the plasmid basis are under way.     

n-Alkane uptake and utilisation by Streptomyces strains

Streptomyces strains isolated from the Kuwait Burgan oil field were defined as S. griseoflavus, S. parvus, and S. plicatus utilised n-hexadecane, n-octadecane (purified fractions of mineral oil), kerosene, and crude oil as sole carbon and energy sources. The strains were incubated with n-alkanes and increase of the fatty acid content with chain length equivalent to the employed n-alkanes was observed. Signal transducing GTP-binding proteins (GBPs) play an important role in n-alkane uptake in streptomycetes. Specific activators of GBPs increased the uptake of hydrocarbons. Using the hydrophobic fluorescent dye diphenylhexatrien (DPH) as a probe, it was found that the microviscosity of the hydrophobic inner region of the cellular membrane is significantly lower in hydrocarbon utilisers than in non-utilisers. This difference probably reflects differences in the fatty acid composition of the strains. When cultures were grown in n-alkane containing media, electron microscopy revealed that the hydrocarbon utilisers showed less-electron dense areas as inclusions in the cytoplasm. Soil samples inoculated with Streptomyces strains eliminated hydrocarbons much faster than those not containing these strains, serving as control. When inorganic medium was supplied with n-hexadecane-1-¹⁴C as sole carbon and energy source, radioactive CO₂ was detected. Since streptomycetes have not been used until now for oil elimination, though they are known as abundant soil bacteria tolerating extreme conditions, their possible use for bioremediation of hydrocarbon contaminated soils is discussed.     

Molecular probes of phylogeny and biogeography in toads of the widespread genus Bufo

Genetic relationships among 25 species of Central and South American Bufo and among representative North, Central, and South American, Asian, and African Bufo were probed, using the quantitative immunological technique of microcomplement fixation (MC'F) which indicated a clear separation of North, Central, and South American lineages of Bufo. The South American lineage likely diverged from the Central and North American lineages in the Eocene; the latter two lineages diverged later, probably in the mid-Oligocene. Some species groups of South American toads, defined on the basis of traditional morphological studies, are genetically quite similar within groups, whereas others are genetically divergent. The amount of albumin evolution does not appear to parallel the amount of karyotypic, morphological, ecological, or behavioral evolution documented. Comparisons suggest that the African lineages separated from the American and Asian lineages in the late Cretaceous, corresponding to the time of the final separation of Gondwanaland, the southern supercontinent including the modern continents of South America, Africa, Australia, Antarctica, and India. The Asian lineages diverged from the lineage giving rise to all of the American species in the early Paleocene.      

Gut microbiome ADP-ribosyltransferases are widespread phage-encoded fitness factors

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Chloroplast phylogeny indicates that bryophytes are monophyletic

Opinions on the basal relationship of land plants vary considerably and no phylogenetic tree with significant statistical support has been obtained. Here, we report phylogenetic analyses using 51 genes from the entire chloroplast genome sequences of 20 representative green plant species. The analyses, using translated amino acid sequences, indicated that extant bryophytes (mosses, liverworts, and hornworts) form a monophyletic group with high statistical confidence and that extant bryophytes are likely sisters to extant vascular plants, although the support for monophyletic vascular plants was not strong. Analyses at the nucleotide level could not resolve the basal relationship with statistical confidence. Bryophyte monophyly inferred using amino acid sequences has a good statistical foundation and is not rejected statistically by other data sets. We propose bryophyte monophyly as the currently best hypothesis.