Complete genome sequence of the termite hindgut bacterium Spirochaeta coccoides type strain (SPN1(T)), reclassification in the genus Sphaerochaeta as Sphaerochaeta coccoides comb. nov. and emendations of the family Spirochaetaceae and the genus Sphaerochaeta

Spirochaeta coccoides Dröge et al. 2006 is a member of the genus Spirochaeta Ehrenberg 1835, one of the oldest named genera within the Bacteria. S. coccoides is an obligately anaerobic, Gram-negative, non-motile, spherical bacterium that was isolated from the hindgut contents of the termite Neotermes castaneus. The species is of interest because it may play an important role in the digestion of breakdown products from cellulose and hemicellulose in the termite gut. Here we provide a taxonomic re-evaluation for strain SPN1^T, and based on physiological and genomic characteristics, we propose its reclassification as a novel species in the genus Sphaerochaeta, a recently published sister group of the Spirochaeta. The 2,227,296 bp long genome of strain SPN1^T with its 1,866 protein-coding and 58 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.     

Boreal forests of Siberia: Genetic, species and ecosystem diversity

Being of global ecological significance, boreal forests of Siberia located at the high latitudes of Northern Eurasia serve as a unique source of genetic, species, and ecosystem diversity. Previously conducted research revealed a wide range of scientific problems regarding the intraspecific diversity of trees, estimation of the structure and current state of forest ecosystems, as well as their ordination and classification. The use of modern information technologies (databases, species diversity indices, GIS) can promote the knowledge on Siberian boreal forests to a higher level.     

Dissecting meiosis of rye using translational proteomics

BACKGROUND AND AIMS: Much of our understanding of the genetic control of meiosis has come from recent studies of model organisms, which have given us valuable insights into processes such as recombination and the synapsis of chromosomes. The challenge now is to determine to what extent these models are representative of other groups of organisms, and to what extent generalisations can be made as to how meiosis works. Through a comparative proteomic approach with Arabidopsis thaliana, this study describes the spatial and temporal expression of key structural and recombinogenic proteins of cereal rye (Secale cereale). METHODS: Antibodies to two synaptonemal complex-associated proteins (Asy1 and Zyp1) and two recombination-related proteins (Spo11 and Rad51) of A. thaliana were bound to meiocytes throughout meiotic prophase of rye, and visualized using conventional fluorescence microscopy and confocal laser scanning microscopy. Western analysis was performed on proteins extracted from pooled prophase I anthers, as a prelude to more advanced proteomic investigations. KEY RESULTS: The four antibodies of A. thaliana reliably detected their epitopes in rye. The expression profile of Rad51 is consistent with its role in recombination. Asy1 protein is shown for the first time to cap the ends of bivalents. Western analysis reveals structural variants of the transverse filament protein Zyp1. CONCLUSIONS: Asy1 cores are assembled by elongation of early foci. The persistence of foci of Spo11 to late prophase does not fit the current model of molecular recombination. The putative structural variants of Zyp1 may indicate modification of the protein as bivalents are assembled.     

The Activity of Key Enzymes in Xylose-Assimilating Yeasts at Different Rates of Oxygen Transfer to the Fermentation Medium

The activities of xylitol dehydrogenase and xylose reductase in the yeasts Candida shehatae, C. didensiae, C. intermediae, C. tropicalis, Kluyveromyces marxianus, Pichia stipitis, P. guillermondii, Pachysolen tannophilus, and Torulopsis molishiama were studied at different oxygen transfer rates (OTRs) to the fermentation medium (0, 5, and 140 mmol O₂/(l h)). The activities of these enzymes were maximum in the yeasts P. stipitis and C. shehatae. The xylitol dehydrogenase of all the yeasts was NAD⁺-dependent, irrespective of the intensity of aeration. The xylose reductase of the yeasts C. didensiae, C. intermediae, C. tropicalis, Kl. marxianus, P. guillermondii, and T. molishiama was NADPH-dependent, whereas the xylose reductase of P. stipitis, C. shehatae, and Pa. tannophilus was specific for both NADPH and NADH. The effect of OTR on the activities of the different forms of xylitol dehydrogenase and xylose reductase in xylose-assimilating yeasts is discussed.     

Molecular structure of the glibenclamide binding site of the beta-cell K(ATP) channel.

We have investigated the structure of the glibenclamide binding site of pancreatic beta-cell ATP-sensitive potassium (K(ATP)) channels. K(ATP) channels are a complex of four pore-forming Kir6.2 subunits and four sulfonylurea receptor (SUR1) subunits. SUR1 (ABCC8) belongs to the ATP binding cassette family of proteins and has two nucleotide binding domains (NBD1 and NBD2) and 17 putative transmembrane (TM) sequences. Co-expression in a baculovirus expression system of two parts of SUR1 between NBD1 and TM12 leads to restoration of glibenclamide binding activity, whereas expression of either individual N- or C-terminal part alone gave no glibenclamide binding activity, confirming a bivalent structure of the glibenclamide binding site. By using N-terminally truncated recombinant proteins we have shown that CL3 - the cytosolic loop between TM5 and TM6 - plays a key role in formation of the N-terminal component of the glibenclamide binding site. Analysis of deletion variants of the C-terminal part of SUR1 showed that CL8 - the cytosolic loop between TM15 and TM16 - is the only determinant for the C-terminal component of the glibenclamide binding site. We suggest that in SUR1 in the native K(ATP) channel close proximity of CL3 and CL8 leads to formation of the glibenclamide binding site.     

Specific Features of Fermentation of D-Xylose and D-Glucose by Xylose-Assimilating Yeasts

The ability to assimilate D-glucose and D-xylose was studied in 21 yeast species of the following genera: Candida, Kluyveromyces, Pachysolen, Pichia, and Torulopsis. All the cultures fermented D-glucose with the formation of ethanol. During the assimilation of D-xylose, ethanol was produced by P. stipitis and C. shehatae, whereas xylitol was produced by C. didensiae, C. intermediae, C. parapsilosis, C. silvanorum, C. tropicalis, K. fragilis, K. marxianus, P. guillermondii, and T. molishiama. The yeast P. tannophilus produced comparable amounts of both alcohols. The possible use of xylose-assimilating yeasts for the production of xy-litol and ethanol is discussed.     

Resistance of Penicillium piceum F-648 to Hydrogen Peroxide under Short-Term and Prolonged Oxidative Stress

Resistance of Penicillium piceumF-648 to hydrogen peroxide under short-term and prolonged oxidative stress was studied. An increase in the activity of intracellular catalase in fungal cells after short-term exposure to hydrogen peroxide was shown. Activation of fungal cells induced by H₂O₂ depends on the H₂O₂ concentration, time of exposure, and growth phase of the fungus. Variants of P. piceum F-648 that produced two forms of extracellular catalase with different catalytic properties were obtained due to prolonged adaptation to H₂O₂. Catalase with low affinity for substrate was produced predominantly by the parent culture and variant 3; however, a high substrate affinity of catalase was observed in variant 5. Variant 5 of P. piceum F-648 displayed a high catalytic activity and operational stability of catalase in the presence of phosphate ions and a concentration of substrate less than 30 mM at pH more than 7.     

Genetic Analysis of Mutation sy2 which Causes Nonhomologous Meiotic Synapsis in Chromosomes of Diploid Rye Secale cereale L.

Partially nonhomologous (heterologous) synapsis of meiotic chromosomes in a spontaneous desynaptic mutant form of rye is determined by two recessive genes, sy2a and sy2b, that have independent expression and inheritance. The third gene, dominant inhibitor suppressing the mutant phenotype, has been revealed in hybrid combinations between sy2 mutants and lines segregating other meiotic mutants: sy10 (heterologous synapsis), sy1, and sy9(asynapsis). All three genes determining desynapsis (sy2a, sy2b, and I) were shown to be nonallelic to monogenic mutations sy10, sy1, and sy9, inherited independently of them and expressed at later stages of prophase I than the sy10 gene. The possibility of modifying monogenic segregation of mutation sy2 by gametophyte selection for a locus linked to the gene expressed as sy2 at particular frequencies of recombination between this gene and selected locus is discussed.     

Genetic Control of Chromosome Synapsis at Meiosis in Rye Secale cereale L.: The sy19 Gene Controlling Heterologous Synapsis

Analysis of manifestation and inheritance of a new mutation inducing irregular synapsis in rye showed that abnormal phenotype is determined by a recessive allele of the sy19 gene. In the homozygotes for this mutation, even at the light microscopic level, abnormal formation of bivalents is already observed at pachytene–diakinesis. At metaphase I, the univalent frequency varies from 0 to 14; in a few cells, multivalent associations of chromosomes, which are not clearly oriented in the spindle, are detected. Electron microscopy of synaptonemal complexes revealed both homologous and heterologous synapsis in homozygotes for sy19, namely partial loss of the ability to stringent homology search. Analysis of joint inheritance of sy19 and asynaptic sy1 mutations showed that they are nonallelic, inherited independently, and interact by recessive epistasis. The phenotype of doublesy1sy19 mutants indicates that thesy19 gene conditioning heterologous synapsis operates at meiosis later than the synaptic gene sy1. The epistatic group of mutations, sy9 > sy1 > sy19 and sy3, was determined.     

Biosynthesis of pectinlyases in Penicillium adametzii,P. citrinum and P. janthinellum

Pectinlyase complexes of Penicillium adametzii, P. citrinum and P. janthinellum occur as multiple molecular forms distinguished by their biosynthetic control. AMP is involved in derepression of pectinlyase formation.The authors are with the Institute of Microbiology, Belarus Academy of Sciences, Zhodinskaya 2, 220141, Minsk, Republic of Belarus.