Thermal Adaptation of the Small Subunit Ribosomal RNA Gene: A Comparative Study

We carried out a comprehensive survey of small subunit ribosomal RNA sequences from archaeal, bacterial, and eukaryotic lineages in order to understand the general patterns of thermal adaptation in the rRNA genes. Within each lineage, we compared sequences from mesophilic, moderately thermophilic, and hyperthermophilic species. We carried out a more detailed study of the archaea, because of the wide range of growth temperatures within this group. Our results confirmed that there is a clear correlation between the GC content of the paired stem regions of the 16S rRNA genes and the optimal growth temperature, and we show that this correlation cannot be explained simply by phylogenetic relatedness among the thermophilic archaeal species. In addition, we found a significant, positive relationship between rRNA stem length and growth temperature. These correlations are found in both bacterial and archaeal rRNA genes. Finally, we compared rRNA sequences from warm-blooded and cold-blooded vertebrates. We found that, while rRNA sequences from the warm-blooded vertebrates have a higher overall GC content than those from the cold-blooded vertebrates, this difference is not concentrated in the paired regions of the molecule, suggesting that thermal adaptation is not the cause of the nucleotide differences between the vertebrate lineages. Electronic Supplementary Material Electronic Supplementary material is available for this article at and accessible for authorised users. [Reviewing Editor: Dr. Nicolas Galtier]     

Nonneutral GC3 and Retroelement Codon Mimicry in Phytophthora

Phytophthora is a genus entirely comprised of destructive plant pathogens. It belongs to the Stramenopila, a unique branch of eukaryotes, phylogenetically distinct from plants, animals, or fungi. Phytophthora genes show a strong preference for usage of codons ending with G or C (high GC3). The presence of high GC3 in genes can be utilized to differentiate coding regions from noncoding regions in the genome. We found that both selective pressure and mutation bias drive codon bias in Phytophthora. Indicative for selection pressure is the higher GC3 value of highly expressed genes in different Phytophthora species. Lineage specific GC increase of noncoding regions is reminiscent of whole-genome mutation bias, whereas the elevated Phytophthora GC3 is primarily a result of translation efficiency-driven selection. Heterogeneous retrotransposons exist in Phytophthora genomes and many of them vary in their GC content. Interestingly, the most widespread groups of retroelements in Phytophthora show high GC3 and a codon bias that is similar to host genes. Apparently, selection pressure has been exerted on the retroelement’s codon usage, and such mimicry of host codon bias might be beneficial for the propagation of retrotransposons. Reviewing Editor: Dr. Yves van de Peer     

Wax esters of the new zealand silver fern,Cyathea dealbata

The New Zealand silver fern epicuticular wax contained wax esters (C₃₈–C₆₀) of which the C₄₀–C₅₂ homologues were shown by capillary column GC/MS to comprise C₂₂–C₃₄ even and odd n-alkanols randomly combined with C₁₆–C₂₄ even n-acids.     

Capillary gas chromatography using electron capture or selected ion monitoring detection for the determination of muramic acid,diaminopimelic acid and the ratio of d/l-alanine in bacteria

Gas chromatographic analyses of muramic acid, diaminopimelic acid and D-alaline, which are specific components of the bacterial cell wall, have been performed using electron capture or selected ion monitoring detection. Intact cells or peptidogylycan preparations were hydrolyzed in HCl and DCl. After purification by cation exchange chromatography, followed by conversion to the N-heptafluobutyrliso-butyl esters, the components were separated on a 25 m fused silica column coated with SE-54 or on a chiral glass capillary column.The detection limits for muramic acid and diaminopimelic acid were about 10 pg using either detection method and the procedure has the potential sensitivity for detecting about 3 × 10⁵ bacterial cells, e.g., Escherichia coli.Mass spectrometric determination of the d/l ratio of alamine in intact cells of Group A streptococci, type M 15 and in peptidogylcan preparations thereof indicated the proportions 10.2% and 10.5% of D-alanine, respectively. The values uncorrected for racemization during acid hydrolysis were 10.3% and 10.7%, respectively.     

A new cytokinin from Populus x robusta

A new cytokinin was isolated from mature leaves of poplar. Its structure was determined by UV and MS and confirmed by synthesis as 6-(o-hydroxybenzylamino)-9-β-d-ribofuranosylpurine. This cytokinin has medium activity in the soybean callus test but shows high activity in the radish leaf senescence test.     

Constituent acids of Pinus radiata stem cutin

Stem cutin from P. radiata seedlings grown under winter and summer environmental conditions comprised n-alkanoic, (C₁₀–C₂₆), α, ω-alkanedioic (C₁₄–C₂₂), ω-hydroxyalkanoic (C₁₂–C₂₄), hydroxy-α, ω-alkanedioic and polyhydroxyalkanoic acids. 9-Hydroxyheptadecane-1, 17-dioic, 9-hydroxyoctadecene-1, 18-dioic, 9-hydroxynonadecane-1, 19-dioic, and 10, 17-dihydroxyheptadecanoic acids are newly-identified constituents of gymnosperm cutin. Cutin grown under winter temperatures and photoperiod contained twice the amount of 9, 16-dihydroxyhexadecanoic acid than that in summer-grown cutin, suggesting that the winter-grown cutin was formed from a highly cross-linked polymer, and that summer-grown cutin contained more linear polyester portions in the polymer.     

Physiological and biochemical contributions to the taxonomy of the genus Prototheca

16 strains of the genus Prototheca do not produce extracellular amylolytic enzymes. The base composition of their DNA shows rather continuous values from 62% to 78% GC (guanine + cytosine). Their assignment to four species and their possible relationship with Chlorella protothecoides are discussed.Abbreviations Used GC guanine + cytosine - SSC saline sodium citrate     

Rapid analysis of membrane lipids using a combination of thin-layer chromatography and scanning of photographic negatives

A simple method is proposed for the analysis of the distribution and changes in membrane lipids subjected to different treatments (lipolytic, aging, etc.). This technique involves only one-thin layer chromatographic step followed by a scanning of the photographic negative of the charred thin layer. This method is time saving, inexpensive and does not require the technical skill usually demanded in lipidology. The precision of this method is compared with that obtained with the classical TLC-GLC method: its variability is roughly twice that of the TLC-GC method.     

Cysteine and methionine-precursors of methyl sulphone metabolites of 2,4',5-trichlorobiphenyl in mice

In order to account for the origin of the sulphur atom in methyl sulphones derived from polychlorinated biphenyls (PCB), groups of mice were treated with 2,4'-5-trichlorobiphenyl and [35S]cysteine or [35S]methionine, respectively. Control animals received the labelled amino acids only. The radioactive substances extracted from lung tissue were characterized by partition between hexane and sulphuric acid, thin-layer radiochromatography (TLRC), gas chromatography (GC) and mass fragmentography (MF). In lung extracts of both experimental groups sulphuric acid soluble metabolites were present: Their Rf-values on TLRC were identifical with that of 4-methylsulphonyl-2,4'-5-trichlorobiphenyl and their identity was confirmed by GC and GC-MF, which also indicated the presence of a minor sulphone isomer. The study shows that both cysteine and methionine could function as donors of the sulphur atom in the methyl sulphone metabolites derived from PCB.     

The diversity ofMalassezia yeasts confirmed by rRNA sequence and nuclear DNA comparisons

One hundred and fourMalassezia strains (52 isolated from humans and 52 from animals) were compared using large subunit (LSU) ribosomal RNA sequence similarity and nuclear DNA complementarity. Eight groups of strains were recognized as genetically distinct species. Each taxon was confirmed by a homogeneous mole % GC and percentages of DNA/DNA reassociations higher than 85%. The non-lipid-dependentMalassezia yeasts were maintained as the unique taxonM. pachydermatis. In contrast, lipid-dependent strains were shown to be distributed among seven species:M. furfur, M. sympodialis andM. species 1–5. These taxa matched remarkably well with morphological and serological differences documented by previous investigators. The LSU rRNA sequences allowed a further intraspecific resolution with most of genomic taxa represented by several closely related sequences:M. pachydermatis counted up to seven sequences,M. furfur four sequences,M. species 1 comprised three sequences andM. species 2 andM. species 5 two sequences. Three species,M. sympodialis, M. species 3 andM. species 4, displayed a unique type of sequence. Thus, the present report demonstrates the usefulness of sequencing for both taxonomic and epidemiological purposes.